Contacts of the helix formed by residues 56 - 71 (chain B) in PDB entry 3NTV
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 ASP 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 4.5 12.8 + - - +
44B ARG* 4.1 8.1 + - - +
54B ILE 3.4 5.5 + - - +
55B VAL* 1.3 79.2 - - - +
57B ARG* 1.3 59.9 + - - +
58B LEU 3.5 0.4 - - - -
59B THR* 3.4 4.3 + - - +
60B LEU* 2.9 27.5 + - - +
175B ASP* 4.9 2.7 + - - +
222B ASP* 3.3 40.2 - - + +
223B ASP* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.3 32.8 - - + +
33B HIS* 3.0 24.2 + - + +
34B GLN* 3.7 14.3 - - - +
36B GLN* 3.7 9.1 + - - +
37B ASN* 2.8 37.7 + - - +
38B SER 5.2 0.2 - - - +
41B GLU* 3.5 36.6 + - - +
44B ARG* 3.3 22.2 - - - +
56B ASP* 1.3 73.4 + - - +
58B LEU* 1.3 61.3 + - + +
60B LEU* 3.3 5.6 + - - +
61B ASP* 2.8 57.5 + - - +
84B TYR* 4.2 4.3 - - - -
88B GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 5.0 0.3 + - - -
218A PHE 3.7 20.8 - - - +
219A LEU* 4.2 8.5 - - + +
220A ASN* 3.5 30.3 - - - +
26B LYS* 4.3 17.0 - - + +
29B LEU* 4.0 28.0 - - + -
30B ILE* 4.0 23.3 - - + +
33B HIS* 3.8 26.0 - - + +
56B ASP 3.5 0.4 - - - -
57B ARG* 1.3 72.4 - - + +
59B THR* 1.3 65.3 + - - +
61B ASP* 3.5 3.8 + - - +
62B LEU* 3.1 23.0 + - - +
221B ILE* 4.7 4.3 - - + -
222B ASP* 3.7 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 3.9 11.9 - - + -
56B ASP* 3.6 8.5 - - - -
57B ARG 3.2 0.4 - - - -
58B LEU* 1.3 73.3 - - - +
60B LEU* 1.3 65.9 + - - +
62B LEU* 3.2 4.9 + - - +
63B ILE* 3.0 35.4 + - + +
175B ASP* 4.0 13.5 + - - +
221B ILE* 3.5 20.2 + - - +
222B ASP* 2.7 33.1 + - - +
225B LEU* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 4.7 0.2 - - - +
55B VAL* 4.1 11.9 - - + -
56B ASP 2.9 18.3 + - - +
57B ARG* 3.5 9.0 - - - +
59B THR* 1.3 76.8 - - - +
61B ASP* 1.3 71.2 + - - +
63B ILE* 3.0 8.6 + - - +
64B LYS* 2.9 32.9 + - + +
84B TYR* 3.5 33.2 - - + +
85B SER* 4.4 9.4 - - - -
88B GLN* 3.7 43.7 - - + +
89B PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 4.0 3.5 - - + +
33B HIS* 2.6 41.5 + - + +
36B GLN* 3.6 18.3 + - - +
57B ARG* 2.8 45.8 + - - +
58B LEU 4.1 0.9 - - - +
59B THR 3.3 0.2 - - - -
60B LEU* 1.3 82.1 - - - +
62B LEU* 1.3 60.6 + - - +
64B LYS* 3.6 26.9 + - - +
65B GLN* 3.2 26.3 + - - +
68B ARG* 4.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.2 4.7 - - + -
217A ASN* 3.6 23.9 - - - +
219A LEU* 3.9 11.4 - - + -
227A ILE* 3.9 21.3 - - + -
58B LEU 3.1 14.8 + - - +
59B THR* 3.5 8.3 - - - +
60B LEU 3.2 0.2 - - - -
61B ASP* 1.3 74.6 - - - +
63B ILE* 1.3 65.2 + - - +
65B GLN* 3.0 7.6 + - + +
66B LEU* 2.9 45.1 + - + +
219B LEU* 3.6 30.7 - - + -
221B ILE* 3.9 7.9 - - + -
225B LEU* 3.8 17.9 - - + -
227B ILE* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.6 1.3 - - + -
59B THR* 3.0 30.7 + - + +
60B LEU* 3.0 9.2 + - - +
62B LEU* 1.3 75.0 - - - +
64B LYS* 1.3 56.5 + - - +
66B LEU* 3.0 12.6 + - + +
67B ILE* 2.9 28.8 + - + +
89B PHE* 3.6 26.2 - - + -
145B MSE 3.9 26.2 - - + -
147B PHE* 3.7 38.4 - - + -
173B ILE* 3.9 18.8 - - + -
225B LEU* 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 4.8 11.3 + - - +
38B SER* 4.3 8.9 - - - -
60B LEU* 2.9 28.6 + - + +
61B ASP* 3.6 30.9 + - - +
62B LEU 3.2 0.2 - - - -
63B ILE* 1.3 74.8 - - - +
65B GLN* 1.4 60.7 + - - +
67B ILE* 3.3 5.2 + - - +
68B ARG* 3.1 47.3 + - - +
88B GLN* 3.0 42.9 + - - +
89B PHE* 4.6 8.1 - - + -
91B SER* 4.1 6.6 + - - -
92B ILE* 3.7 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 3.0 28.3 + - - +
216A THR 4.5 0.7 - - - -
217A ASN* 3.0 28.4 + - + +
227A ILE* 3.0 31.8 + - + +
229A ILE* 3.4 20.8 - - + +
36B GLN* 5.9 0.7 - - - +
61B ASP 3.2 13.5 + - - +
62B LEU* 3.0 12.8 + - + +
64B LYS* 1.4 75.3 - - - +
66B LEU* 1.4 57.2 + - - +
68B ARG* 2.9 27.5 + - - +
69B MSE 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.8 0.2 - - + -
66A LEU* 4.3 9.6 - - + -
69A MSE 3.8 26.5 - - + -
62B LEU* 2.9 33.7 + - + +
63B ILE* 3.0 16.6 + - + +
65B GLN* 1.4 75.9 - - - +
67B ILE* 1.3 62.5 + - - +
69B MSE 3.7 12.3 - - + +
70B ASN* 3.0 31.6 + - - +
145B MSE 4.3 4.9 - - + -
171B LEU* 4.2 12.3 - - + -
173B ILE* 3.8 28.0 - - + -
225B LEU* 5.4 0.2 - - + -
227B ILE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 2.9 23.0 + - + +
64B LYS 3.5 6.5 - - - +
66B LEU* 1.3 75.9 - - - +
68B ARG* 1.3 58.0 + - - +
71B ASN* 3.0 24.4 + - - -
72B VAL* 3.0 33.8 + - + +
75B ILE* 3.8 14.8 - - + -
89B PHE* 3.6 32.8 - - + -
92B ILE* 3.8 27.1 - - + -
96B ILE* 3.8 21.5 - - + -
145B MSE 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 4.9 6.4 + - - -
215A THR* 3.5 22.7 - - - +
229A ILE* 3.7 12.6 - - + -
36B GLN* 5.0 11.3 - - - +
61B ASP 4.8 0.6 + - - -
64B LYS* 3.1 49.6 + - - +
65B GLN* 2.9 39.9 + - - +
67B ILE* 1.3 77.3 - - - +
69B MSE 1.3 62.1 + - - +
71B ASN* 3.3 21.6 + - - +
92B ILE* 4.1 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.8 21.3 - - + -
69A MSE 3.6 27.8 - - + +
70A ASN* 3.6 32.4 - - - +
171A LEU* 3.7 19.5 - - + -
227A ILE* 3.4 35.4 - - + -
229A ILE* 3.8 16.4 - - + +
65B GLN* 2.9 26.1 + - + +
66B LEU* 3.7 9.0 - - + +
67B ILE 3.4 0.2 - - - -
68B ARG* 1.3 76.4 - - - +
70B ASN* 1.3 62.0 + - - +
71B ASN* 3.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MSE 2.5 61.3 - - - +
66B LEU 3.0 18.3 + - - +
69B MSE 1.3 78.4 - - - +
71B ASN* 1.4 70.9 + - - +
72B VAL* 3.3 15.1 + - + +
144B ASP* 5.9 0.2 - - - +
167B LYS* 4.7 12.9 + - - +
169B GLN 5.0 6.1 - - - +
171B LEU* 3.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 4.2 19.6 + - - +
67B ILE 3.0 7.8 + - - -
68B ARG 3.3 12.9 + - - +
69B MSE 4.2 6.6 - - - +
70B ASN* 1.4 78.4 - - - +
72B VAL* 1.3 63.9 + - - +
73B LYS* 3.5 31.2 + - - +
144B ASP* 4.5 3.1 - - - +
167B LYS* 5.5 1.7 + - - -
----------------------------------------------------------
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