Contacts of the helix formed by residues 99 - 116 (chain T) in PDB entry 3LUE
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 MET 99 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T LYS* 1.3 89.0 - - + +
100T ARG* 1.3 67.1 + - - +
101T PHE* 3.3 43.3 - - + -
102T HIS* 3.0 32.3 + - + +
103T LYS* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J MET* 3.8 0.9 - - - -
48J GLY* 2.4 51.0 - - - +
98T LYS 3.9 0.2 + - - -
99T MET* 1.3 72.1 - - - +
101T PHE* 1.3 67.6 + - + +
103T LYS* 3.0 15.0 + - - +
104T ILE* 3.0 28.3 + - + +
127T GLU* 3.9 15.3 + - - +
130T VAL* 4.3 17.3 - - + +
131T ASP* 2.6 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLN* 5.3 9.2 - - + +
99T MET* 3.3 40.6 - - + -
100T ARG* 1.3 80.5 - - + +
102T HIS* 1.3 101.2 + + - +
104T ILE* 3.5 14.1 + - + +
105T ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95T ASP* 4.5 16.6 + - + +
96T LYS 3.4 19.1 + - - +
97T GLY* 3.5 32.0 - - - +
98T LYS 4.6 0.2 - - - -
99T MET* 3.0 47.6 + - + +
101T PHE* 1.3 99.3 - + - +
103T LYS* 1.3 58.1 + - + +
105T ALA* 3.4 6.8 + - - +
106T ASN* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T ARG* 3.7 48.6 - - + +
75T ASN* 3.7 34.0 - - + +
98T LYS* 3.6 25.2 + - - +
99T MET 3.5 9.4 - - - +
100T ARG* 3.0 10.7 + - - +
102T HIS* 1.3 77.5 - - + +
104T ILE* 1.3 60.3 + - - +
106T ASN* 3.8 0.5 - - - +
107T VAL* 2.8 35.0 + - - +
130T VAL* 3.8 19.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J GLY* 2.9 20.0 - - - -
49J GLN* 1.6 83.2 - - + +
50J LYS* 4.1 1.6 - - + +
100T ARG* 3.0 25.3 + - + +
101T PHE* 3.7 11.0 - - - +
103T LYS* 1.3 75.7 - - - +
105T ALA* 1.3 58.6 + - - +
107T VAL 3.8 0.2 - - - -
108T ASN* 2.9 40.9 + - - +
126T ALA* 3.9 10.7 - - + +
127T GLU* 5.1 2.9 - - - -
130T VAL* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95T ASP* 4.2 23.6 - - - +
101T PHE 3.0 18.1 + - - +
102T HIS* 3.6 5.8 - - - +
104T ILE* 1.3 79.5 - - - +
106T ASN* 1.3 62.0 + - - +
108T ASN* 3.3 6.9 + - - +
109T LYS* 3.1 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75T ASN 3.7 17.6 + - - +
76T GLY* 4.6 3.1 - - - -
77T LEU* 4.1 13.5 - - - +
80T MET* 3.5 17.3 - - - +
94T PRO* 3.2 8.7 - - - +
95T ASP* 2.7 48.0 + - - +
97T GLY 5.3 1.2 + - - -
102T HIS* 3.0 22.8 + - - +
103T LYS* 4.0 0.4 - - - +
105T ALA* 1.3 75.3 - - - +
107T VAL* 1.3 65.1 + - - +
109T LYS* 3.0 31.7 + - - +
110T ALA 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T ARG 3.8 15.5 - - - +
76T GLY* 3.7 23.3 - - - +
79T LEU* 4.7 4.5 - - + -
103T LYS 2.8 22.9 + - - +
104T ILE 4.0 2.7 - - - +
106T ASN* 1.3 72.1 - - - +
108T ASN* 1.3 56.3 + - - +
110T ALA* 3.3 6.2 + - - +
111T LEU* 2.9 35.1 + - + +
126T ALA* 3.5 29.6 - - + -
129T ILE* 3.7 28.5 - - + -
130T VAL* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLN* 4.2 11.8 + - - +
51J ASP* 4.4 15.8 + - - +
52J SER* 5.4 2.6 + - - +
104T ILE* 2.9 33.3 + - - +
105T ALA* 3.6 8.6 - - - +
106T ASN 3.1 0.2 - - - -
107T VAL* 1.3 75.4 - - - +
109T LYS* 1.3 59.3 + - - +
111T LEU* 3.8 13.2 - - - +
112T ASP* 2.9 44.8 + - - +
126T ALA* 3.0 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T MET* 3.8 19.7 - - + -
91T LEU* 4.4 3.3 - - - +
92T PRO* 4.4 28.1 - - + +
93T ARG 3.4 21.1 + - - +
95T ASP* 3.2 23.5 + - - -
105T ALA* 3.1 16.4 + - - +
106T ASN* 3.0 36.0 + - - +
108T ASN* 1.3 76.8 - - + +
110T ALA* 1.3 58.4 + - - +
112T ASP* 3.9 4.6 - - - +
113T PHE* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79T LEU* 3.7 26.5 - - + -
80T MET* 4.1 14.5 - - + +
83T LEU* 3.6 25.1 - - + +
91T LEU* 4.2 6.3 - - - -
106T ASN 3.3 3.4 + - - +
107T VAL 3.5 7.4 - - - +
108T ASN 3.2 0.2 - - - -
109T LYS* 1.3 77.4 - - - +
111T LEU* 1.3 65.4 + - - +
113T PHE* 3.1 4.3 + - - +
114T ILE* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J SER* 4.2 2.7 - - - +
79T LEU* 5.4 0.2 - - + -
107T VAL* 2.9 25.0 + - + +
108T ASN* 3.8 16.2 - - - +
110T ALA* 1.3 74.0 - - - +
112T ASP* 1.3 59.8 + - - +
114T ILE* 3.4 8.2 + - + +
115T ALA* 2.9 28.4 + - - +
121T LEU* 3.7 22.3 - - + +
124T ILE* 4.1 22.9 - - + +
125T GLY 3.8 4.7 - - - +
126T ALA* 3.4 38.6 - - - +
129T ILE* 4.7 1.3 - - + -
140T MET* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108T ASN* 2.9 35.2 + - - +
109T LYS* 3.9 5.0 - - - +
111T LEU* 1.3 75.2 - - - +
113T PHE* 1.3 61.6 + - - +
115T ALA* 3.2 8.5 + - - +
116T SER* 2.8 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T LEU* 4.1 21.3 - - + -
87T SER* 3.7 22.2 - - - -
89T GLU* 3.8 21.1 - - + -
90T ARG 5.1 3.1 - - - -
91T LEU* 3.6 39.7 - - + -
92T PRO* 5.7 2.7 - - + -
109T LYS 3.0 16.2 + - - +
110T ALA 3.1 8.0 + - - +
112T ASP* 1.3 77.2 - - - +
114T ILE* 1.3 62.4 + - - +
116T SER* 2.5 27.3 + - - -
117T LYS* 3.4 29.3 + - - +
148T PHE* 3.7 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T LEU* 4.0 22.7 - - + -
110T ALA* 3.0 22.9 + - + +
111T LEU* 3.5 13.7 - - + +
113T PHE* 1.3 74.8 - - - +
115T ALA* 1.3 60.4 + - - +
117T LYS* 2.9 24.9 + - - +
119T VAL* 3.2 45.2 - - + +
121T LEU* 4.0 10.5 - - + -
140T MET* 4.5 13.7 - - + +
143T THR* 4.4 6.5 - - + +
144T ILE* 3.4 34.8 - - + -
148T PHE* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J LYS* 5.1 9.4 - - - -
111T LEU 2.9 13.1 + - - +
112T ASP* 3.6 10.3 - - - +
114T ILE* 1.3 76.6 - - - +
116T SER* 1.3 62.6 + - - +
117T LYS 3.0 1.8 + - - -
118T GLY* 3.1 11.4 + - - -
119T VAL 3.2 20.6 + - - +
121T LEU* 3.4 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112T ASP 2.8 13.0 + - - -
113T PHE* 2.5 29.6 + - - -
115T ALA* 1.3 76.6 - - - +
117T LYS* 1.3 62.3 + - - +
118T GLY 3.1 3.8 + - - -
----------------------------------------------------------
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