Contacts of the strand formed by residues 55 - 71 (chain B) in PDB entry 1WQ9
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 LYS 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B CYS* 3.6 5.8 - - - -
54B MET* 1.3 75.6 - - - +
56B CYS* 1.3 74.3 + - - +
57B THR* 2.8 21.6 + - + +
93B CYS* 3.4 0.2 - - - -
94B ARG 2.8 25.6 + - - -
96B ALA* 3.9 24.0 - - + -
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Residues in contact with CYS 56 (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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14B CYS* 2.0 54.7 - - + -
15B GLN 3.7 2.9 - - - -
45B CYS* 3.8 14.5 - - - +
46B SER* 3.4 27.6 - - - -
47B GLY 3.5 24.5 + - - +
49B CYS* 3.5 6.0 - - - -
55B LYS* 1.3 88.5 - - - +
57B THR* 1.3 57.7 + - - +
58B PRO* 4.4 3.3 - - - +
92B GLU 3.9 0.4 - - - -
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B CYS* 4.2 4.3 - - - -
55B LYS* 2.8 24.9 + - + +
56B CYS* 1.3 73.9 + - - +
58B PRO* 1.3 83.6 - - + +
59B VAL* 3.5 2.1 + - - +
91B CYS* 3.3 2.1 - - - -
92B GLU* 2.8 39.2 + - - +
94B ARG* 3.7 27.7 + - + +
96B ALA* 5.0 3.6 - - - +
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B CYS* 3.6 6.2 - - + -
55B LYS* 6.4 0.9 - - - -
56B CYS 4.4 3.8 - - - +
57B THR* 1.3 98.8 - - + +
59B VAL* 1.3 62.6 + - - +
60B GLY 3.5 5.2 - - - +
61B LYS* 6.0 0.2 - - + -
88B HIS* 3.5 52.9 - - + +
90B ALA 3.4 8.1 - - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR 4.1 6.5 - - - +
58B PRO* 1.3 77.0 - - - +
60B GLY* 1.3 57.8 + - - +
90B ALA* 2.9 32.8 + - + +
91B CYS* 3.9 8.1 - - - +
92B GLU* 4.1 11.2 - - + +
94B ARG* 3.6 37.7 - - - +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 3.5 4.5 - - - +
59B VAL* 1.3 82.6 + - - +
61B LYS* 1.3 63.7 + - - +
88B HIS* 3.6 5.0 - - - +
89B THR* 2.8 30.9 + - - -
90B ALA* 3.6 11.3 + - - +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 6.0 0.2 - - + -
60B GLY* 1.3 75.9 - - - +
62B HIS* 1.3 67.7 + - - +
86B MET* 4.1 27.3 - - + +
87B GLU 3.2 17.0 - - - +
88B HIS* 4.3 5.2 - - + -
89B THR* 3.1 10.0 + - - +
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLU* 5.7 4.5 - - - -
43B LEU* 6.0 0.2 - - - +
61B LYS* 1.3 79.0 - - - +
63B THR* 1.3 85.6 + - - +
64B ALA* 4.2 6.1 - - + -
86B MET* 3.7 5.4 - - - +
87B GLU* 2.6 69.6 + - + +
89B THR* 3.2 29.4 - - + -
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Residues in contact with THR 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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62B HIS* 1.3 87.1 + - - +
64B ALA* 1.3 62.3 + - - +
65B ASP* 4.1 5.2 + - - +
84B LYS* 3.6 46.0 - - + +
85B PHE 3.4 10.1 - - - +
86B MET* 5.4 1.6 - - - +
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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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3A ARG* 5.1 3.8 - - - +
42B VAL* 4.9 0.9 - - + -
62B HIS* 4.0 8.3 + - + -
63B THR* 1.3 73.7 - - - +
65B ASP* 1.3 62.9 + - - +
66B ILE* 3.9 19.0 + - + -
83B MET 3.7 0.5 - - - +
84B LYS* 3.3 4.9 - - - -
85B PHE* 2.8 37.9 + - - +
87B GLU* 4.0 28.2 - - + +
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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
----------------------------------------------------------
1A GLU 4.0 12.2 + - - +
2A VAL* 3.4 17.4 - - + -
3A ARG* 2.9 24.3 + - - +
63B THR 4.6 4.8 - - - +
64B ALA* 1.3 73.0 - - - +
66B ILE* 1.3 62.8 + - - +
82B VAL* 3.8 19.4 - - + +
83B MET 3.7 3.1 - - - -
84B LYS* 2.8 41.2 + - - +
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Residues in contact with ILE 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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2A VAL* 4.3 0.9 - - - -
3A ARG* 3.3 38.1 - - + +
8A VAL* 3.2 40.8 - - + -
40B VAL* 4.4 13.7 - - + -
41B ALA 4.5 0.7 - - - +
42B VAL* 5.1 2.7 - - + -
64B ALA* 4.3 12.6 - - + -
65B ASP* 1.3 80.5 - - - +
67B GLN* 1.3 63.6 + - - +
68B ILE* 3.6 7.8 + - + +
82B VAL* 4.1 2.8 - - - +
83B MET* 2.7 44.4 + - - +
85B PHE* 3.7 32.1 - - + -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.9 12.8 - - + +
3A ARG 3.0 19.6 + - - +
4A PRO* 3.7 7.2 - - - +
5A PHE* 2.9 37.9 + - - +
6A LEU* 5.0 1.7 - - - +
8A VAL* 3.5 19.4 - - - +
66B ILE* 1.3 71.8 - - - +
68B ILE* 1.3 67.0 + - - +
80B MET* 3.8 33.5 - - + +
81B GLU 3.3 12.3 - - - +
82B VAL* 4.3 6.7 - - + +
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Residues in contact with ILE 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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5A PHE* 4.1 3.6 - - - -
8A VAL* 4.4 4.9 - - + -
23B ILE* 3.8 16.4 - - + -
35B PHE* 3.5 29.4 - - + -
36B ARG 4.0 7.0 - - - +
37B PRO* 4.7 3.6 - - + -
40B VAL* 4.1 26.0 - - + -
66B ILE* 4.3 8.5 - - + +
67B GLN* 1.3 80.8 - - - +
69B MET* 1.3 63.1 + - - +
70B ARG 4.0 0.2 + - - -
80B MET* 3.3 8.7 - - - +
81B GLU* 2.8 42.4 + - + +
83B MET* 3.7 37.2 - - + -
85B PHE* 4.7 2.9 - - + -
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Residues in contact with MET 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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5A PHE* 4.1 12.1 - - + -
35B PHE* 3.2 10.6 - - - -
36B ARG* 2.8 68.0 + - + +
68B ILE* 1.3 74.4 - - - +
70B ARG* 1.3 60.8 + - - +
71B MET* 3.7 2.3 + - + -
78B SER* 4.0 30.7 - - - +
79B LYS* 3.8 11.9 - - - +
80B MET* 3.3 27.6 - - + +
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Residues in contact with ARG 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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30B GLU* 2.4 44.9 + - - -
32B SER* 5.8 1.2 - - - -
33B ASP* 2.9 34.5 + - + +
34B ILE 3.7 2.7 - - - -
35B PHE* 3.6 23.0 - - + -
68B ILE 4.0 1.0 + - - -
69B MET* 1.3 71.0 - - - +
71B MET* 1.3 60.0 + - - +
72B ASN 3.9 0.6 + - - +
77B SER 3.5 2.6 - - - +
78B SER* 3.0 21.0 - - - -
79B LYS* 3.1 16.1 + - + +
81B GLU* 2.7 52.9 + - - +
83B MET* 4.0 0.4 - - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 3.6 2.9 - - - +
34B ILE* 2.7 83.7 + - + +
36B ARG* 5.1 12.6 - - + -
69B MET* 3.7 3.5 + - + +
70B ARG* 1.3 72.1 - - - +
72B ASN* 1.3 61.4 + - - +
73B PRO* 3.1 10.5 - - + +
76B HIS* 3.7 43.7 - - + +
77B SER 3.5 1.6 - - - -
78B SER* 3.6 19.1 - - - +
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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