Contacts of the helix formed by residues 81 - 104 (chain T) in PDB entry 3SDI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 81 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S PHE* 4.2 10.8 - - + -
19S GLY 5.2 3.8 - - - +
21S LEU* 4.0 27.8 - - + -
30T ALA* 4.5 15.3 - - + +
80T GLY* 1.3 70.5 - - - +
82T ILE* 1.3 67.2 + - - +
83T PRO* 3.3 6.1 - - + -
84T ASP* 2.9 39.4 + - - +
130T ARG* 4.3 0.7 - - - +
133T GLY* 2.8 25.1 + - - +
134T VAL* 3.1 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155S GLY 6.0 0.7 - - - +
156S ASN* 3.7 15.2 + - - +
35T THR* 6.2 0.7 - - - -
66T LYS* 3.9 37.9 - - + +
78T TYR* 3.8 36.7 - - + +
79T SER* 5.4 0.2 - - - -
80T GLY 3.4 14.6 + - - +
81T LEU* 1.3 69.0 - - - +
83T PRO* 1.4 75.9 - - + +
85T GLY* 2.9 12.6 + - - -
86T ARG* 3.0 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117S CYS* 4.2 12.1 - - - -
118S ASP* 5.3 0.2 - - - +
121S GLN* 3.4 31.6 - - + +
124S THR* 5.7 1.1 - - - +
154S SER 3.3 23.8 - - - +
155S GLY 3.3 28.0 - - - +
156S ASN* 3.6 15.7 - - - +
81T LEU* 3.6 7.4 - - + -
82T ILE* 1.4 92.6 - - + +
84T ASP* 1.3 61.9 + - - +
86T ARG* 3.2 4.6 + - - +
87T HIS 3.0 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S GLN* 3.2 17.8 - - - +
124S THR* 4.4 0.9 + - - -
81T LEU* 2.9 24.8 + - + +
83T PRO* 1.3 73.3 - - - +
85T GLY* 1.3 60.9 + - - +
87T HIS* 3.5 4.1 + - - +
88T LEU* 3.2 21.3 + - - +
130T ARG* 2.6 47.7 + - - -
132T PHE* 3.6 20.7 - - + -
133T GLY* 2.8 22.1 + - - +
134T VAL* 4.0 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T TYR* 3.6 33.3 - - - -
81T LEU 3.2 6.5 + - - -
82T ILE 2.9 7.7 + - - -
84T ASP* 1.3 74.9 - - - +
86T ARG* 1.3 64.2 + - - +
88T LEU* 3.1 6.9 + - - +
89T VAL* 3.1 24.3 + - - +
134T VAL* 3.6 11.5 - - - +
136T THR* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 ASP* 3.1 18.9 + - - -
114S HIS* 3.1 47.6 + - - +
117S CYS* 3.7 20.4 - - - -
118S ASP* 3.0 38.0 + - - +
68T GLN* 3.1 31.3 + - - +
78T TYR* 3.4 16.7 + - - +
82T ILE* 3.0 19.5 + - + +
83T PRO* 3.2 8.5 + - + +
85T GLY* 1.3 72.4 - - - +
87T HIS* 1.3 65.8 + - - +
89T VAL* 3.0 3.3 + - - +
90T ASN* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S ASP* 4.9 3.5 + - - -
121S GLN* 3.1 39.3 + - + +
122S LYS* 4.7 20.8 - - + +
125S GLN* 4.3 6.9 + - - -
83T PRO 3.0 5.6 + - - +
84T ASP 3.6 8.3 - - - +
85T GLY 3.3 0.2 - - - -
86T ARG* 1.3 74.6 - - - +
88T LEU* 1.3 60.8 + - - +
90T ASN* 3.6 10.5 + - - +
91T ARG* 3.2 18.0 + - - +
119T TYR* 2.6 31.6 + + - -
123T HIS* 4.8 2.7 + - - -
132T PHE* 3.4 29.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T TYR* 6.3 0.2 - - + -
84T ASP 3.2 7.9 + - - +
85T GLY* 3.1 11.1 + - - +
86T ARG 3.1 0.6 - - - -
87T HIS* 1.3 78.2 - - - +
89T VAL* 1.3 60.2 + - + +
91T ARG* 3.4 4.5 + - - +
92T GLY* 2.8 24.4 + - - -
116T LEU* 3.7 19.9 - - + +
119T TYR* 3.8 22.0 - - + -
120T VAL* 3.5 33.7 - - + -
132T PHE* 3.8 18.2 - - + -
134T VAL* 4.7 8.5 - - + -
136T THR* 3.6 27.1 - - + +
151T LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T GLN* 3.2 35.2 - - + +
70T VAL* 4.1 9.5 - - + +
76T CYS* 3.8 31.6 - - + -
78T TYR* 3.9 6.7 - - + -
85T GLY 3.1 11.6 + - - +
86T ARG 3.0 5.9 + - - +
88T LEU* 1.3 75.9 - - + +
90T ASN* 1.3 60.5 + - - +
92T GLY* 3.0 3.5 + - - +
93T ARG* 2.8 63.2 + - - +
112T PHE* 6.2 0.2 - - - -
116T LEU* 5.7 0.4 - - - -
136T THR* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S ASP* 2.7 32.8 + - - +
68T GLN* 5.6 0.4 - - - +
86T ARG* 2.9 26.7 + - - +
87T HIS* 3.6 8.8 - - - +
89T VAL* 1.3 76.5 - - - +
91T ARG* 1.3 61.4 + - - +
93T ARG* 3.3 29.1 + - - +
94T GLU* 3.1 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87T HIS* 3.2 14.2 + - + +
88T LEU 3.7 4.5 - - - +
89T VAL 3.2 0.4 - - - -
90T ASN* 1.3 76.4 - - - +
92T GLY* 1.3 60.7 + - - +
94T GLU* 3.3 22.0 + - - +
95T GLU* 2.7 63.5 + - - +
116T LEU* 5.5 3.1 - - + -
119T TYR* 3.5 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70T VAL* 4.3 2.0 - - - -
88T LEU 2.8 16.4 + - - -
89T VAL* 3.0 5.3 + - - -
91T ARG* 1.3 76.3 - - - +
93T ARG* 1.3 55.8 + - - +
95T GLU* 3.3 5.1 + - - +
96T ALA* 2.9 24.8 + - - +
112T PHE* 3.4 34.2 - - - -
116T LEU* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641 GLU* 6.0 0.4 - - - +
671 TYR* 3.5 56.0 + - + +
681 ASP* 2.6 53.9 + - - +
68T GLN* 4.0 6.3 - - - +
69T VAL 2.9 26.8 + - - +
70T VAL* 4.1 11.9 - - + -
89T VAL* 2.8 39.8 + - - +
90T ASN* 3.6 24.3 - - - +
91T ARG 3.2 0.2 - - - -
92T GLY* 1.3 69.6 - - - +
94T GLU* 1.3 60.0 + - + +
95T GLU 3.1 1.1 - - - -
96T ALA* 3.8 4.6 - - - +
97T ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90T ASN* 3.1 24.5 + - - +
91T ARG* 3.3 23.1 + - - +
93T ARG* 1.3 75.8 - - + +
95T GLU* 1.3 63.0 + - - +
97T ALA* 3.8 5.9 - - - +
98T SER* 3.1 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91T ARG* 2.7 60.7 + - + +
92T GLY* 3.5 8.1 - - - +
94T GLU* 1.3 79.4 - - - +
96T ALA* 1.3 58.6 + - - +
98T SER* 3.7 4.3 + - - -
99T PHE* 3.5 16.8 + - - +
107T ILE* 4.4 3.5 - - - +
112T PHE* 5.4 2.0 - - + -
115T ARG* 3.4 77.1 + - + +
116T LEU* 6.1 0.2 - - + -
119T TYR* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671 TYR* 5.4 0.7 - - - +
70T VAL* 4.2 15.7 - - + -
71T ASP* 4.4 18.5 - - + +
92T GLY 2.9 16.8 + - - +
93T ARG* 3.2 4.5 + - - +
95T GLU* 1.3 76.3 - - - +
97T ALA* 1.3 65.7 + - - +
99T PHE* 3.3 4.8 + - - +
100T LYS* 3.1 23.8 + - - +
107T ILE* 3.9 29.9 + - + +
112T PHE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 ASP* 6.0 4.0 - - - +
641 GLU* 5.9 2.9 - - - +
71T ASP* 5.3 1.5 + - - -
93T ARG 2.9 17.7 + - - +
94T GLU* 3.8 6.7 - - - +
96T ALA* 1.3 76.5 - - - +
98T SER* 1.3 56.9 + - - +
100T LYS* 3.2 6.7 + - - +
101T LYS* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94T GLU 3.1 16.9 + - - -
95T GLU* 4.2 6.8 + - - -
96T ALA 3.3 0.2 - - - -
97T ALA* 1.3 77.3 - - - +
99T PHE* 1.3 60.3 + - - +
101T LYS* 4.1 10.7 - - - +
102T LEU* 3.4 23.2 + - - +
103T TYR* 5.3 0.3 - - - -
115T ARG* 4.3 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662 TYR* 4.0 17.9 - + - -
702 TYR* 3.7 29.8 - + - -
95T GLU 3.5 11.5 + - - +
96T ALA 3.3 7.6 + - - +
97T ALA 3.2 0.6 - - - -
98T SER* 1.3 78.0 + - - +
100T LYS* 1.3 62.0 + - - +
103T TYR* 2.8 61.8 + + - +
105T THR* 3.6 28.3 - - + -
107T ILE* 3.6 32.3 - - + -
108T PRO* 3.5 29.4 - - + -
115T ARG* 3.7 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 ARG* 5.8 0.2 - - - -
601 ASP* 5.3 8.7 - - - +
631 THR* 4.8 5.1 + - - -
71T ASP* 3.0 40.2 + - - +
72T ARG* 4.7 11.7 - - - +
96T ALA 3.1 15.6 + - - +
97T ALA* 3.6 6.1 - - - +
99T PHE* 1.3 75.7 - - - +
101T LYS* 1.3 64.1 + - - +
104T LYS* 2.6 49.4 + - + +
105T THR 3.9 11.4 - - - +
106T PRO* 4.3 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 HIS* 6.1 0.4 - - - -
561 ARG* 3.7 51.6 - - - +
812 SER* 4.0 4.3 + - - -
852 GLU* 3.5 42.4 + - + +
892 GLU* 4.1 12.3 + - - -
97T ALA 2.9 21.1 + - - +
98T SER* 4.1 10.1 - - - +
100T LYS* 1.3 73.7 - - - +
102T LEU* 1.3 64.0 + - + +
104T LYS* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 HIS* 4.1 23.3 - - + +
812 SER* 3.0 22.5 + - - +
822 VAL* 3.9 20.8 - - + +
852 GLU* 4.2 25.1 - - + -
98T SER 3.4 16.4 + - - +
99T PHE 4.3 1.1 - - - +
100T LYS 3.2 0.6 - - - -
101T LYS* 1.3 83.5 - - + +
103T TYR* 1.3 91.6 + - + +
104T LYS 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 HIS* 4.5 16.4 + - - -
632 LEU* 5.6 1.1 - - + -
652 LEU* 5.2 8.3 - - - +
662 TYR* 3.6 32.1 - + + +
692 GLN* 5.7 1.0 + - - -
702 TYR* 4.6 8.0 - + - -
782 THR* 2.7 43.4 + - + +
812 SER* 3.9 4.0 - - - -
822 VAL* 4.0 12.6 - - + -
98T SER 5.3 0.2 - - - -
99T PHE* 2.8 70.9 + + + +
102T LEU* 1.3 106.6 - - + +
104T LYS* 1.3 59.3 + - - +
105T THR* 2.8 15.6 + - + -
115T ARG* 4.8 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 ARG* 6.2 5.6 - - + -
591 LYS* 5.2 10.1 - - - +
772 GLU* 3.6 35.0 + - + +
812 SER* 3.7 19.7 + - - +
842 LYS* 5.3 10.8 - - - +
100T LYS* 2.6 38.3 + - + +
101T LYS 5.2 0.2 - - - -
102T LEU 3.7 1.0 - - - -
103T TYR* 1.3 71.4 - - - +
105T THR* 1.3 62.5 + - - +
106T PRO* 3.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il