Contacts of the helix formed by residues 81 - 104 (chain F) in PDB entry 3TDD
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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PHE* 4.1 19.5 - - + -
19E GLY 5.5 2.2 - - - +
21E LEU* 3.9 28.3 - - + -
30F ALA* 4.5 14.3 + - + +
80F GLY* 1.3 69.7 - - - -
82F ILE* 1.3 66.8 + - - +
83F PRO* 3.4 6.7 - - + -
84F ASP* 3.0 34.9 + - - +
130F ARG* 4.1 1.3 - - - +
133F GLY* 2.9 18.4 + - - +
134F VAL* 3.0 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ASN* 3.9 11.8 + - - +
66F LYS* 3.8 37.5 - - + +
78F TYR* 3.7 30.8 - - + +
80F GLY 3.1 14.4 + - - +
81F LEU* 1.3 70.3 - - - +
83F PRO* 1.3 70.2 - - + +
85F GLY* 2.8 19.4 + - - -
86F ARG* 3.1 19.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E CYS* 4.1 14.8 - - - -
118E ASP* 5.0 0.5 - - - +
121E GLN* 3.4 35.1 - - + +
124E THR* 5.9 0.2 - - - +
154E SER 3.4 23.3 - - - +
155E GLY* 3.6 22.4 - - - +
156E ASN* 3.5 13.0 - - - +
81F LEU* 3.6 7.4 - - + -
82F ILE* 1.3 95.2 - - + +
84F ASP* 1.3 62.8 + - - +
86F ARG* 3.3 4.1 + - + +
87F HIS 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E GLN* 3.1 18.1 - - - +
124E THR* 4.6 0.7 + - - -
125E GLN* 4.7 1.3 - - - -
81F LEU* 3.0 21.7 + - - +
83F PRO* 1.3 79.0 - - - +
85F GLY* 1.3 62.7 + - - +
87F HIS* 3.4 4.9 + - - +
88F LEU* 3.1 22.5 + - - +
130F ARG* 2.7 45.3 + - - -
132F PHE* 3.8 17.4 - - + -
133F GLY* 2.8 19.1 + - - +
134F VAL* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TYR* 3.5 33.7 - - - -
81F LEU 3.3 4.0 + - - -
82F ILE 2.8 9.8 + - - -
84F ASP* 1.3 80.0 - - - +
86F ARG* 1.3 60.5 + - - -
88F LEU* 3.1 6.4 + - - +
89F VAL* 3.0 24.9 + - - +
134F VAL* 3.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E HIS* 3.5 36.1 + - - +
117E CYS* 3.7 23.0 - - - -
118E ASP* 2.9 37.1 + - - +
68F GLN* 2.9 25.6 - - - +
78F TYR* 3.4 16.7 + - - +
82F ILE* 3.1 17.2 + - + +
83F PRO 3.3 6.7 + - - +
85F GLY* 1.3 73.4 - - - +
87F HIS* 1.3 55.4 + - - +
89F VAL* 2.8 4.4 + - - +
90F ASN* 2.8 47.1 + - - +
93F ARG* 5.1 0.2 - - - +
69M ASP* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASP* 4.6 3.2 + - - +
121E GLN* 3.0 31.7 + - - +
122E LYS* 4.8 13.3 - - + +
125E GLN* 4.1 8.7 - - - -
83F PRO 3.1 11.0 + - - +
84F ASP 3.4 8.7 - - - +
85F GLY 3.3 0.2 - - - -
86F ARG* 1.3 77.2 - - - +
88F LEU* 1.3 63.0 + - - +
90F ASN* 3.2 11.7 + - - +
91F ARG* 3.1 19.2 + - + +
119F TYR* 2.7 30.5 + + - -
123F HIS* 4.7 3.0 + - - -
132F PHE* 3.4 27.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TYR* 6.3 0.4 - - + -
84F ASP 3.1 10.4 + - - +
85F GLY* 3.1 9.6 + - - +
87F HIS* 1.3 83.8 - - - +
89F VAL* 1.3 58.2 + - + +
91F ARG* 3.4 2.8 + - - +
92F GLY 3.0 21.0 + - - -
116F LEU* 3.6 29.5 - - + +
119F TYR* 3.8 19.7 - - + -
120F VAL* 3.7 34.8 - - + -
132F PHE* 4.3 8.3 - - + -
134F VAL* 4.6 11.4 - - + +
136F THR* 3.8 23.3 - - + +
151F LEU* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLN* 3.1 37.2 - - + +
70F VAL* 3.8 16.1 - - + +
76F CYS* 4.3 14.1 - - + -
78F TYR* 3.7 12.6 - - + -
85F GLY 3.0 15.3 + - - +
86F ARG 2.8 7.6 + - - +
88F LEU* 1.3 74.6 - - + +
90F ASN* 1.3 61.2 + - - +
92F GLY* 3.0 3.6 + - - +
93F ARG* 2.8 59.4 + - - +
112F PHE* 6.3 0.2 - - - -
116F LEU* 5.6 1.1 - - - -
136F THR* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASP* 3.0 32.0 + - - +
68F GLN* 5.2 0.2 - - - +
86F ARG* 2.8 24.4 + - - +
87F HIS* 3.4 12.1 - - - +
89F VAL* 1.3 77.3 - - - +
91F ARG* 1.3 61.4 + - - +
93F ARG* 3.1 31.0 + - - +
94F GLU* 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F HIS* 3.1 9.8 + - + +
88F LEU* 3.5 9.9 - - + +
90F ASN* 1.3 79.6 - - - +
92F GLY* 1.3 52.3 + - - +
94F GLU* 3.3 21.7 + - - +
95F GLU* 2.7 67.3 + - + +
115F ARG 5.8 0.4 - - - +
116F LEU* 5.3 2.5 - - + -
119F TYR* 3.4 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 4.0 2.7 - - - -
88F LEU 3.0 14.5 + - - -
89F VAL* 3.0 4.9 + - - -
91F ARG* 1.3 76.9 - - - +
93F ARG* 1.3 56.6 + - - +
95F GLU* 3.3 6.9 - - - +
96F ALA* 2.7 31.5 + - - +
112F PHE* 3.5 25.9 - - - -
116F LEU* 3.9 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLN* 3.7 11.1 - - - +
69F VAL 2.9 35.1 + - - +
70F VAL* 4.2 14.4 - - + -
89F VAL* 2.8 27.9 + - - +
90F ASN* 3.1 23.9 + - - +
92F GLY* 1.3 74.9 - - - +
94F GLU* 1.3 60.7 + - + +
96F ALA* 3.3 1.9 + - - +
97F ALA* 2.9 30.6 + - - +
65M GLU* 5.6 1.8 - - - +
68M TYR* 3.4 58.5 + - + +
69M ASP* 2.8 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASN* 3.0 17.7 + - + +
91F ARG* 3.7 30.1 + - - +
93F ARG* 1.3 75.3 - - + +
95F GLU* 1.3 64.3 + - - +
97F ALA* 3.3 6.4 + - - +
98F SER* 3.0 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ARG* 2.7 57.8 + - + +
92F GLY* 3.3 11.4 - - - +
94F GLU* 1.3 79.4 - - - +
96F ALA* 1.3 60.6 + - - +
98F SER* 3.6 5.1 + - - -
99F PHE* 3.3 16.5 + - - +
107F ILE* 5.0 1.8 - - - -
112F PHE* 5.1 1.8 - - + -
115F ARG* 3.1 76.2 + - + +
116F LEU* 5.9 0.4 - - + -
119F TYR* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 4.0 16.8 - - + -
71F ASP* 4.4 16.7 - - + +
92F GLY 2.7 19.7 + - - +
93F ARG* 3.8 3.8 - - - +
95F GLU* 1.3 71.8 - - - +
97F ALA* 1.3 66.0 + - - +
99F PHE* 3.3 4.1 + - - +
100F LYS* 3.1 24.4 + - - +
107F ILE* 3.9 32.0 + - + +
112F PHE* 4.7 1.6 - - + -
68M TYR* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ASP* 5.5 1.8 - - - -
93F ARG 2.9 17.4 + - - +
94F GLU* 3.7 7.9 - - - +
96F ALA* 1.3 75.6 - - - +
98F SER* 1.3 58.6 + - - +
100F LYS* 3.4 6.2 + - - +
101F LYS* 2.9 31.0 + - - +
61M ASP* 5.3 8.1 - - - +
65M GLU* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU 3.0 17.4 + - - -
95F GLU* 3.7 8.3 + - - -
97F ALA* 1.3 78.2 - - - +
99F PHE* 1.3 64.1 + - - +
101F LYS* 3.3 10.2 + - - +
102F LEU* 3.2 23.7 + - - +
115F ARG* 4.4 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F GLU 3.3 11.5 + - - +
96F ALA 3.6 7.9 - - - +
97F ALA 3.3 0.2 - - - -
98F SER* 1.3 82.1 + - - +
100F LYS* 1.3 56.8 + - - +
102F LEU* 3.4 0.9 + - - -
103F TYR* 2.9 62.1 + + + +
105F THR* 3.4 26.2 - - + -
107F ILE* 3.6 27.1 - - + -
108F PRO* 3.6 28.7 - - + -
115F ARG* 3.6 22.9 - - - +
66N TYR* 4.0 16.4 - + - -
70N TYR* 3.5 28.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ASP* 3.3 33.7 + - - +
72F ARG* 4.8 5.3 - - - +
96F ALA 3.1 16.9 + - - +
97F ALA* 3.9 5.2 - - - +
99F PHE* 1.3 78.4 - - + +
101F LYS* 1.3 59.9 + - - +
104F LYS* 2.6 48.7 + - + +
105F THR 3.8 13.0 - - - +
106F PRO* 3.9 24.1 - - + +
57M ARG* 6.0 0.2 - - - -
60M LYS* 6.4 0.4 - - + +
61M ASP* 5.5 6.7 - - - +
64M THR* 4.6 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ALA 2.9 19.2 + - - +
98F SER* 3.5 10.1 - - - +
100F LYS* 1.3 79.3 - - - +
102F LEU* 1.3 59.8 + - + +
104F LYS* 5.2 0.2 - - - -
57M ARG* 3.4 52.1 - - - +
81N SER* 4.2 5.4 + - - -
85N GLU* 2.6 41.3 + - - +
89N GLU* 3.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F SER 3.2 13.9 + - - +
99F PHE* 4.1 2.5 - - - +
101F LYS* 1.3 79.9 - - + +
103F TYR* 1.3 95.5 + - + +
104F LYS 3.6 0.2 - - - -
62N HIS* 4.1 24.0 - - + +
81N SER* 2.9 19.9 + - - +
82N VAL* 3.8 23.4 + - + +
85N GLU* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 2.9 68.5 + + + +
102F LEU* 1.3 112.2 - - + +
104F LYS* 1.3 59.5 + - - +
105F THR* 2.7 18.9 + - + +
115F ARG* 4.8 4.8 + - - -
62N HIS* 4.5 12.9 + - + -
63N LEU* 5.8 0.7 - - + -
66N TYR* 3.6 31.5 + + + +
69N GLN* 5.6 2.1 + - - -
70N TYR* 4.2 7.6 + + - -
78N THR* 2.9 45.7 + - + +
81N SER* 3.8 2.5 - - - -
82N VAL* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LYS* 2.6 39.0 + - + +
101F LYS 5.2 0.4 - - - -
102F LEU 3.6 2.0 - - - -
103F TYR* 1.3 72.7 - - - +
105F THR* 1.3 61.7 + - - +
106F PRO* 3.7 3.6 - - - +
57M ARG* 6.5 1.3 - - - -
60M LYS* 5.0 12.5 - - - +
77N GLU* 3.4 36.8 + - + +
81N SER* 3.6 19.8 + - - +
----------------------------------------------------------
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