Contacts of the helix formed by residues 71 - 87 (chain B) in PDB entry 3NSI
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 4.4 15.4 + - - +
98A PRO* 5.0 5.5 - - - +
16B PHE* 4.1 3.4 - - - -
27B TYR 3.8 13.9 - - - +
28B LYS* 4.2 15.9 - - - -
69B GLU 3.0 6.8 + - - +
70B VAL* 1.3 76.3 - - - +
72B PHE* 1.3 66.2 + - - +
73B VAL* 3.8 13.6 - - - +
74B GLU* 2.9 25.9 + - - +
75B TYR* 2.9 21.0 + - - +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.8 19.7 - - + -
83A CYS* 3.5 25.8 - - + -
84A LEU* 4.3 12.8 - - + -
90A PHE* 3.3 36.6 - + + -
12B ILE* 4.3 5.2 - - + -
13B VAL* 3.6 36.6 - - + -
16B PHE* 3.7 22.6 - + + -
27B TYR 4.3 1.4 + - - -
71B ASP* 1.3 74.8 - - - +
73B VAL* 1.3 58.3 + - - +
75B TYR* 3.2 32.9 + + - +
76B VAL* 2.9 48.2 + - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.6 20.1 - - + -
80A ALA* 4.3 21.4 - - + +
81A CYS* 5.2 0.7 - - - -
84A LEU* 3.9 21.5 - - + -
98A PRO* 3.2 39.3 - - + -
99A CYS* 4.7 3.6 - - - -
71B ASP* 3.2 10.8 + - - +
72B PHE* 1.3 76.9 - - + +
74B GLU* 1.3 59.0 + - - +
76B VAL* 3.4 2.6 + - - +
77B ARG* 2.9 29.0 + - + +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.8 19.8 + - - +
34B LEU* 5.5 3.8 - - + +
69B GLU 4.0 6.2 - - - +
70B VAL* 3.8 27.4 + - + +
71B ASP* 2.9 21.2 + - - +
73B VAL* 1.3 75.1 - - - +
75B TYR* 1.3 61.3 + - - +
77B ARG* 3.3 37.7 + - - +
78B SER* 2.9 27.9 + - - -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.8 6.9 - - - +
12B ILE* 2.7 52.8 + - + +
15B THR* 3.6 13.9 - - - -
16B PHE* 3.5 31.0 - + + -
29B LEU* 4.6 1.3 - - + -
34B LEU* 4.0 17.7 - - + -
37B LEU* 3.6 33.2 - - + -
70B VAL* 4.1 11.8 - - + +
71B ASP 2.9 12.8 + - - +
72B PHE* 3.3 21.8 - + - +
74B GLU* 1.3 77.7 - - - +
76B VAL* 1.3 69.8 + - + +
78B SER* 2.5 26.9 + - - -
79B LEU* 3.2 20.5 + - + +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 2.9 42.2 - - + +
77A ARG* 5.3 0.7 - - - -
79A LEU* 5.7 1.3 - - + -
80A ALA* 4.0 11.2 - - + +
12B ILE* 4.1 11.0 - - + -
72B PHE* 2.9 51.7 + - + +
73B VAL 3.8 4.0 - - - +
75B TYR* 1.3 82.9 - - + +
77B ARG* 1.3 66.7 + - - +
79B LEU* 3.0 12.8 + - + +
80B ALA* 2.9 20.4 + - - +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 4.8 18.2 - - + -
76A VAL* 5.4 0.7 - - - -
58B PHE* 6.1 2.1 - - - -
73B VAL* 2.9 17.3 + - + +
74B GLU* 3.4 43.1 + - - +
76B VAL* 1.3 78.2 - - - +
78B SER* 1.3 56.6 + - - +
80B ALA* 3.1 9.1 + - - +
81B CYS* 2.8 30.0 + - - -
98B PRO* 5.7 1.3 - - - -
99B CYS 2.4 52.1 + - - -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.6 29.4 - - - +
38B LEU* 4.1 11.0 - - - +
58B PHE* 3.8 25.4 - - - -
74B GLU* 2.9 13.1 + - - -
75B TYR 2.5 21.4 + - - -
77B ARG* 1.3 77.8 - - - +
79B LEU* 1.3 61.2 + - - +
81B CYS* 3.3 5.6 + - - +
82B LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 19.5 - - + -
9A VAL* 4.2 16.1 - - + +
76A VAL* 5.7 1.3 - - + -
12B ILE* 3.7 43.3 - - + -
38B LEU* 3.6 26.7 - - + -
42B LEU* 4.0 9.3 - - + +
75B TYR* 3.5 28.0 - - + +
76B VAL* 3.0 13.8 + - + +
78B SER* 1.3 82.1 + - - +
80B ALA* 1.3 63.2 + - - +
82B LEU* 3.1 9.3 + - - +
83B CYS* 3.1 25.4 + - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.7 19.8 - - + -
73A VAL* 4.3 16.4 - - + +
76A VAL* 4.0 29.1 - - + +
76B VAL 2.9 11.6 + - - +
77B ARG* 3.4 12.6 - - - +
79B LEU* 1.3 76.5 - - - +
81B CYS* 1.3 61.9 + - - +
83B CYS* 3.0 15.2 + - - +
84B LEU* 3.1 14.7 + - - +
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 5.3 1.1 - - - -
58B PHE* 4.2 13.2 - - + -
77B ARG* 2.8 22.1 + - - +
78B SER* 3.5 9.2 - - - +
79B LEU 3.3 0.2 - - - -
80B ALA* 1.3 76.5 - - - +
82B LEU* 1.3 62.2 + - - +
84B LEU* 3.2 6.6 + - - +
85B TYR* 3.1 38.6 + - + -
98B PRO* 5.2 0.4 - - - -
99B CYS* 2.0 67.1 - - - -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 6.4 0.2 - - + -
38B LEU* 3.6 26.7 - - + +
42B LEU* 3.4 35.2 - - + -
45B TRP* 4.2 10.2 - - + -
55B TYR* 4.7 16.8 - - + +
58B PHE* 3.2 39.5 - - + -
59B MET* 4.9 3.4 - - - -
78B SER 3.0 12.2 + - - +
79B LEU* 3.5 9.9 - - - +
81B CYS* 1.3 77.6 - - - +
83B CYS* 1.3 57.2 + - - +
85B TYR* 3.4 8.4 + - + -
86B CYS* 2.8 37.5 + - - +
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.1 35.9 - - - -
13A VAL* 3.6 24.0 - - + -
72A PHE* 3.4 22.9 - - + -
45B TRP* 3.9 11.7 - - - -
79B LEU 3.1 12.9 + - - -
80B ALA* 3.0 10.6 + - - +
82B LEU* 1.3 74.7 - - - +
84B LEU* 1.3 60.7 + - - +
87B HIS* 2.8 32.8 + - + +
90B PHE* 3.7 6.9 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 4.4 12.8 - - + -
73A VAL* 3.8 14.8 - - + -
48B THR* 4.7 1.0 + - - -
51B ARG* 2.6 36.0 + - - +
80B ALA 3.1 11.3 + - - +
81B CYS 3.2 6.5 + - - +
83B CYS* 1.3 79.7 - - - +
85B TYR* 1.3 65.6 + - + +
87B HIS 4.7 0.9 - - - +
90B PHE* 3.5 44.6 - - + +
93B CYS* 4.7 10.3 - - - -
95B SER* 4.8 7.9 - - - +
97B PRO* 4.2 6.5 - - + -
98B PRO* 3.6 31.0 - - + -
99B CYS* 4.1 8.1 - - - -
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 3.2 2.1 - - - +
48B THR* 2.7 38.8 + - - -
51B ARG* 3.6 13.8 - - + +
54B ASP* 3.5 29.3 + - + +
55B TYR* 4.0 36.3 - + + -
58B PHE* 3.7 32.1 - + + +
81B CYS* 3.1 28.4 + - + +
82B LEU* 3.8 8.7 - - + +
84B LEU* 1.3 81.8 - - + +
86B CYS* 1.3 53.0 + - - +
87B HIS 3.8 0.4 - - - -
97B PRO* 2.9 46.0 - - + +
99B CYS* 3.8 11.5 - - - +
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Residues in contact with CYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.0 24.8 - - + -
46B THR* 3.1 47.9 + - - +
47B PRO* 3.4 6.1 - - - -
48B THR* 3.9 7.8 - - - +
55B TYR* 3.8 23.6 - - - -
82B LEU* 2.8 21.3 + - - +
85B TYR* 1.3 79.0 - - - +
87B HIS* 1.3 62.0 + - - +
88B GLU* 3.8 2.3 + - - +
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 4.8 10.8 + - + +
13A VAL* 3.6 38.7 - - + +
14A CYS* 6.0 1.8 - - - -
17A GLN* 5.5 3.6 - - - -
45B TRP* 4.4 19.3 - + + -
48B THR* 4.2 4.8 - - - +
83B CYS* 2.8 28.6 + - + +
84B LEU 4.7 1.7 - - - +
86B CYS* 1.3 78.3 - - - +
88B GLU* 1.3 68.9 + - + +
89B TYR* 3.1 33.8 + - + +
90B PHE* 3.1 19.7 + - + +
91B LYS 3.8 4.3 + - - -
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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
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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) + - + + + + + -
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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