Contacts of the helix formed by residues 63 - 77 (chain B) in PDB entry 1NWW
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 GLY 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU 3.9 8.3 - - - -
50B ASP* 5.2 0.9 - - - -
51B THR* 2.8 24.3 + - - -
61B ALA 4.2 0.2 + - - -
62B TYR* 1.3 73.4 - - - +
64B ARG* 1.3 66.6 + - - -
65B ASP 3.3 2.7 - - - -
66B ALA 3.2 4.1 + - - -
67B VAL* 3.1 20.6 + - - +
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Residues in contact with ARG 64 (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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44B ILE* 3.3 45.6 + - + +
45B GLU* 3.4 33.1 + - - +
47B PHE* 3.2 18.1 + - + -
48B ALA 3.5 20.4 - - - +
49B GLU* 3.1 49.7 + - - +
51B THR* 3.7 8.5 - - - +
63B GLY* 1.3 71.6 - - - -
65B ASP* 1.3 69.7 + - - +
67B VAL* 3.2 3.4 + - - +
68B GLU* 2.9 28.4 + - - +
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 5.5 4.2 - - - +
63B GLY 3.3 0.8 - - - -
64B ARG* 1.3 85.4 + - - +
66B ALA* 1.3 57.8 + - - +
68B GLU* 3.2 13.0 + - - +
69B GLN* 2.9 47.9 + - - +
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Residues in contact with ALA 66 (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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61B ALA* 3.9 15.0 - - + -
62B TYR 3.4 26.2 - - - +
63B GLY 3.2 2.2 + - - +
65B ASP* 1.3 77.1 - - - +
67B VAL* 1.3 61.2 + - - +
69B GLN* 3.4 14.0 + - - +
70B THR* 2.9 29.3 + - - -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.8 15.7 - - + -
47B PHE* 3.9 24.9 - - + -
51B THR* 4.0 16.2 - - + -
52B MET* 4.1 0.9 - - - -
53B TYR* 3.8 35.9 - - + +
61B ALA* 3.9 13.2 - - + +
63B GLY 3.1 15.2 + - - +
64B ARG* 3.5 8.1 - - - +
66B ALA* 1.3 77.8 - - - +
68B GLU* 1.3 63.4 + - - +
70B THR* 3.2 5.3 + - - -
71B LEU* 3.0 30.3 + - + +
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Residues in contact with GLU 68 (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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40B ALA* 4.0 10.6 - - + +
41B ALA* 3.9 22.0 + - - +
44B ILE* 3.8 35.8 - - + +
64B ARG* 2.9 20.7 + - - +
65B ASP* 3.6 15.9 - - - +
67B VAL* 1.3 76.1 - - - +
69B GLN* 1.3 59.5 + - + +
71B LEU* 3.3 6.1 + - - +
72B ALA* 2.9 30.6 + - + +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 2.9 35.7 + - - +
66B ALA* 3.8 11.5 - - - +
67B VAL 3.2 0.2 - - - -
68B GLU* 1.3 77.8 - - + +
70B THR* 1.3 61.3 + - - +
72B ALA* 3.5 7.3 + - - +
73B GLY* 3.1 19.1 + - - -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 4.0 26.0 - - + +
55B ASN* 5.3 4.5 - - - +
61B ALA* 3.7 13.3 - - + +
66B ALA 2.9 14.7 + - - -
67B VAL* 3.2 11.0 + - - -
69B GLN* 1.3 74.5 - - - +
71B LEU* 1.3 60.9 + - - +
73B GLY* 3.2 3.0 + - - -
74B LEU* 2.8 29.4 + - + +
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Residues in contact with LEU 71 (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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31B PHE* 5.6 0.4 - - + -
35B LEU* 5.8 0.9 - - + -
40B ALA* 3.8 15.3 - - + +
43B LEU* 4.4 24.2 - - + -
44B ILE* 4.7 6.3 - - + -
47B PHE* 4.5 13.5 - - + -
53B TYR* 3.7 31.9 - - + +
67B VAL* 3.0 34.1 + - + +
68B GLU* 3.7 4.7 - - - +
70B THR* 1.3 76.2 - - - +
72B ALA* 1.3 63.6 + - - +
74B LEU* 3.1 15.9 + - + +
75B PHE* 3.0 40.6 + - + -
130B TRP* 4.4 10.3 - - + -
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Residues in contact with ALA 72 (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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40B ALA* 3.6 14.7 - - + +
68B GLU* 2.9 18.3 + - + +
69B GLN* 3.8 8.5 - - - +
70B THR 3.2 0.2 - - - -
71B LEU* 1.3 77.9 - - - +
73B GLY* 1.3 58.6 + - - +
75B PHE* 3.6 3.7 + - - +
76B THR* 2.8 27.0 + - - -
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Residues in contact with GLY 73 (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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69B GLN 3.1 14.7 + - - -
70B THR* 3.2 2.9 + - - -
72B ALA* 1.3 74.9 - - - +
74B LEU* 1.4 65.3 + - - +
76B THR* 3.0 22.7 + - - -
77B VAL* 3.5 10.8 + - - +
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Residues in contact with LEU 74 (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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53B TYR* 4.4 7.2 - - + +
55B ASN* 5.5 2.5 - - - +
70B THR* 2.8 17.1 + - + +
71B LEU* 3.4 21.8 - - + +
73B GLY* 1.4 75.1 - - - +
75B PHE* 1.3 86.0 + - + +
77B VAL* 3.1 12.1 + - + +
78B MET* 2.9 68.6 + - + +
80B ILE* 4.7 3.4 - - + -
1900B HPN 3.8 35.4 - - + -
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Residues in contact with PHE 75 (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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35B LEU* 4.1 2.9 - - + -
38B ASN* 3.4 58.6 - - + +
39B ASP 4.0 0.7 - - - -
40B ALA* 4.0 8.7 - - + +
43B LEU* 3.5 33.2 - - + -
71B LEU* 3.0 42.3 + - + +
72B ALA* 3.6 4.5 + - - +
74B LEU* 1.3 88.2 - - + +
76B THR* 1.3 59.9 + - - +
77B VAL 3.3 0.4 - - - -
78B MET 3.4 16.0 - - - +
80B ILE* 3.7 29.6 - - + -
106B LEU* 3.8 10.0 - - - +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 2.8 15.8 + - - -
73B GLY* 3.0 15.0 + - - -
75B PHE* 1.3 79.3 - - - +
77B VAL* 1.3 62.9 + - + +
106B LEU* 3.5 15.4 - - - +
107B PRO* 5.5 0.7 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 4.0 10.3 - - - +
74B LEU* 3.1 15.2 + - + +
76B THR* 1.3 88.4 - - + +
78B MET* 1.3 73.5 + - + +
105B ALA* 3.6 3.3 - - - +
106B LEU* 2.8 28.1 + - - -
107B PRO* 3.4 12.6 - - + +
145B LEU* 4.4 18.6 - - + +
147B LEU* 5.4 3.8 - - + -
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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
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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