Contacts of the helix formed by residues 57 - 71 (chain B) in PDB entry 4WDW
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 ASN 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B THR* 3.0 46.1 + - - -
24B TYR* 4.5 0.6 - - - +
25B ALA 5.0 1.0 - - - +
31B ARG* 4.0 8.2 - - - +
34B ALA* 4.1 13.9 - - + +
51B SER* 2.7 25.3 + - - -
55B TYR* 3.7 17.8 + - - +
56B ASN* 1.3 77.9 - - - +
58B GLU* 1.3 62.9 + - - +
59B GLU 3.2 2.7 - - - -
60B GLN* 3.1 16.8 + - - +
61B VAL* 2.9 33.2 + - - +
272B TYR* 4.2 2.4 + - - -
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Residues in contact with GLU 58 (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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51B SER* 3.5 13.7 - - - +
52B ALA 3.6 11.4 - - - +
53B HIS* 3.4 18.9 + - - +
56B ASN* 3.8 0.8 - - - +
57B ASN* 1.3 79.4 - - - +
59B GLU* 1.3 58.6 + - - +
61B VAL* 4.5 1.3 - - - +
62B GLY* 2.8 28.4 + - - -
81B TYR* 3.3 23.8 + - - +
83B SER* 2.5 28.6 + - - -
102B SER* 3.0 38.6 + - - +
105B LYS* 4.3 22.5 + - + +
106B ALA* 3.6 7.3 - - + +
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Residues in contact with GLU 59 (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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57B ASN 3.2 0.6 - - - -
58B GLU* 1.3 78.8 - - - +
60B GLN* 1.3 68.4 + - + +
62B GLY* 3.7 0.7 - - - -
63B LEU* 2.8 35.7 + - + +
66B ARG* 4.2 7.2 + - - +
105B LYS* 3.3 32.8 + - + +
107B GLN* 5.5 5.1 - - - +
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Residues in contact with GLN 60 (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 ARG* 3.6 45.6 - - + +
32B SER* 4.7 2.0 - - - +
34B ALA* 4.2 3.8 - - + -
35B LEU* 3.6 27.9 - - + +
56B ASN 4.1 3.4 + - - -
57B ASN* 3.1 28.0 + - - +
59B GLU* 1.3 90.4 - - - +
61B VAL* 1.3 62.6 + - - +
62B GLY 3.2 0.9 - - - -
63B LEU* 3.2 7.9 + - + +
64B ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 61 (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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23B THR* 3.9 16.6 - - + +
34B ALA* 4.5 5.6 - - + -
38B THR* 4.1 14.1 - - + +
49B ILE* 3.5 31.6 - - + -
51B SER* 4.5 1.8 - - - +
57B ASN* 2.9 45.6 + - + +
58B GLU* 4.3 3.1 - - - +
60B GLN* 1.3 73.0 - - - +
62B GLY* 1.3 66.3 + - - +
64B ALA* 3.3 6.6 + - - +
65B ILE* 3.1 30.1 + - + +
81B TYR* 3.8 19.7 - - + -
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Residues in contact with GLY 62 (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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58B GLU 2.8 19.5 + - - -
59B GLU 3.7 0.2 - - - -
61B VAL* 1.3 80.2 - - - +
63B LEU* 1.3 60.8 + - - +
65B ILE* 3.4 9.8 + - - +
66B ARG* 3.0 28.1 + - - +
81B TYR* 5.4 1.5 + - - -
106B ALA* 3.6 28.3 - - - -
108B LEU* 4.9 3.0 - - - +
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Residues in contact with LEU 63 (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* 3.9 27.8 - - + -
59B GLU* 2.8 20.3 + - + +
60B GLN* 3.2 8.5 + - + +
62B GLY* 1.3 74.7 - - - +
64B ALA* 1.3 55.3 + - - +
66B ARG* 3.2 33.8 + - + +
67B SER* 2.8 45.0 + - - -
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Residues in contact with ALA 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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35B LEU* 3.6 22.1 - - - +
38B THR* 3.3 37.0 - - + -
39B LYS* 3.9 11.7 - - + +
42B ILE* 4.6 1.1 - - - -
60B GLN 2.9 16.3 + - - +
61B VAL 3.5 0.9 - - - +
63B LEU* 1.3 76.6 - - - +
65B ILE* 1.3 62.2 + - - +
67B SER* 3.1 2.5 + - - -
68B LYS* 3.1 28.1 + - - +
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Residues in contact with ILE 65 (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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38B THR* 4.6 0.7 - - + -
42B ILE* 4.2 8.5 - - + -
49B ILE* 3.7 27.6 - - + -
61B VAL* 3.1 19.9 + - + +
62B GLY* 3.7 4.5 - - - +
63B LEU 3.3 0.2 - - - -
64B ALA* 1.3 73.7 - - - +
66B ARG* 1.3 62.9 + - - +
68B LYS* 3.2 3.6 + - - +
69B ILE* 3.0 43.2 + - + +
74B VAL* 4.8 0.5 - - - +
76B ARG* 4.8 2.9 - - - +
79B ILE* 4.2 22.7 - - + -
81B TYR* 3.6 40.8 - - + -
108B LEU* 4.4 20.4 - - + -
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Residues in contact with ARG 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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59B GLU* 4.2 7.3 + - - +
62B GLY 3.0 13.1 + - - +
63B LEU* 3.5 50.2 - - + +
65B ILE* 1.3 75.0 - - - +
67B SER* 1.3 58.0 + - - +
69B ILE* 3.2 12.9 + - + +
70B ALA* 2.9 31.1 + - - +
105B LYS 4.9 0.8 + - - -
106B ALA 2.9 17.7 + - - +
107B GLN* 3.2 53.1 + - - +
108B LEU* 4.6 9.2 - - + -
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Residues in contact with SER 67 (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* 5.8 0.7 - - - -
39B LYS* 3.7 23.2 + - - +
63B LEU* 2.8 25.9 + - - -
64B ALA 3.6 4.3 - - - -
65B ILE 3.1 0.2 - - - -
66B ARG* 1.3 78.9 - - - +
68B LYS* 1.3 57.4 + - - +
70B ALA* 3.8 5.1 - - - +
71B ASP* 2.9 35.3 + - - +
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Residues in contact with LYS 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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39B LYS* 3.8 33.7 - - + +
42B ILE* 3.8 37.7 - - + -
43B GLU* 3.4 34.9 + - - +
64B ALA 3.1 15.9 + - - +
65B ILE 3.2 3.5 + - - +
67B SER* 1.3 73.6 - - - +
69B ILE* 1.3 60.5 + - - +
71B ASP* 3.1 34.3 + - - +
73B SER* 3.2 25.5 + - - -
74B VAL* 3.2 26.4 + - + -
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Residues in contact with ILE 69 (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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65B ILE* 3.0 39.2 + - + +
66B ARG* 3.2 14.1 + - + +
68B LYS* 1.3 77.7 - - - +
70B ALA* 1.3 60.4 + - - +
71B ASP 3.4 0.2 - - - -
72B GLY* 3.0 20.4 + - - -
74B VAL* 3.4 27.5 - - + +
75B LYS* 4.7 2.2 - - + -
76B ARG* 4.0 41.1 - - + +
79B ILE* 5.3 0.2 - - + -
108B LEU* 5.5 0.7 - - + -
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Residues in contact with ALA 70 (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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66B ARG 2.9 17.3 + - - +
67B SER* 3.3 5.6 + - - +
69B ILE* 1.3 80.1 - - - +
71B ASP* 1.3 57.3 + - - +
72B GLY* 3.2 4.7 + - - -
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Residues in contact with ASP 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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67B SER* 2.9 20.9 + - - +
68B LYS* 3.1 35.5 + - - +
70B ALA* 1.3 75.2 - - - +
72B GLY* 1.3 56.8 + - - -
73B SER* 2.7 27.8 + - - -
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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