Contacts of the strand formed by residues 54 - 71 (chain A) 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 MET 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A CYS* 3.6 20.1 + - + +
51A ASP* 2.8 41.9 + - + +
52A GLU* 3.9 6.1 - - - +
53A SER* 1.3 99.1 - - - +
55A LYS* 1.3 62.3 + - - +
93A CYS* 3.8 19.1 - - + +
94A ARG* 3.4 12.1 - - - +
95A PRO* 3.3 50.3 - - + -
96A ALA 4.9 1.1 - - - -
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS* 3.8 3.4 - - - -
53A SER 4.3 0.2 + - - -
54A MET* 1.3 76.3 - - - +
56A CYS* 1.3 64.4 + - - +
57A THR* 3.1 26.5 + - - +
94A ARG 2.7 35.3 + - - +
96A ALA* 3.2 40.8 + - + +
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Residues in contact with CYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A CYS* 2.0 59.2 - - + -
15A GLN 3.7 3.1 - - - -
45A CYS* 3.8 17.2 - - - +
46A SER* 3.5 26.2 - - - -
47A GLY 3.7 20.4 + - - +
49A CYS* 3.7 5.8 - - - -
55A LYS* 1.3 75.8 - - - +
57A THR* 1.3 59.8 + - - +
58A PRO* 4.4 1.6 - - - +
92A GLU 3.8 0.9 - - - -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A CYS* 4.0 4.3 - - - -
55A LYS* 3.1 29.8 + - - +
56A CYS* 1.3 74.6 - - - +
58A PRO* 1.3 88.3 - - + +
59A VAL* 3.8 1.6 - - - +
91A CYS* 3.0 2.6 - - - -
92A GLU 2.9 41.6 + - - +
94A ARG* 4.3 24.8 - - - +
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A CYS* 3.5 6.9 - - + -
56A CYS 4.4 1.8 - - - +
57A THR* 1.3 103.2 - - + +
59A VAL* 1.3 61.4 - - - +
60A GLY 3.5 5.4 - - - +
61A LYS* 4.9 7.0 - - + -
88A HIS* 3.5 52.0 - - + +
90A ALA 3.3 8.5 - - - +
94A ARG* 4.5 4.9 + - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR 3.8 3.8 - - - +
58A PRO* 1.3 77.4 - - - +
60A GLY* 1.3 59.3 + - - +
90A ALA* 2.8 38.8 + - + +
91A CYS 3.8 4.0 - - - +
92A GLU* 3.4 33.9 - - + +
94A ARG* 3.4 25.8 - - - +
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.5 1.7 - - - +
59A VAL* 1.3 85.6 + - - +
61A LYS* 1.3 62.1 + - - +
88A HIS* 3.6 5.9 - - - +
89A THR* 2.7 38.2 + - - -
90A ALA* 3.8 3.9 + - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 4.9 6.3 - - + -
60A GLY* 1.3 78.2 - - - +
62A HIS* 1.3 62.5 + - - +
86A MET* 3.9 30.8 - - + +
87A GLU 3.3 8.3 - - - +
88A HIS* 4.0 16.8 - - + +
89A THR* 3.2 8.1 + - - -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 5.4 5.8 - - + +
61A LYS* 1.3 75.0 - - - +
63A THR* 1.3 81.2 + - - +
86A MET* 3.6 6.6 - - - +
87A GLU* 2.9 65.9 + - + +
88A HIS 3.7 14.1 - - - -
89A THR* 2.9 29.8 + - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 1.3 96.5 - - - +
64A ALA* 1.3 64.4 + - - +
65A ASP* 5.2 2.1 + - - -
84A LYS* 3.6 30.0 + - - +
85A PHE 3.2 11.9 - - - +
86A MET* 4.5 8.3 - - + -
87A GLU* 4.9 0.4 - - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 5.5 0.2 - - + -
63A THR* 1.3 75.1 - - - +
65A ASP* 1.3 64.6 - - - +
66A ILE* 3.8 8.3 + - + +
83A MET 3.8 0.5 - - - +
84A LYS* 3.3 2.8 - - - -
85A PHE* 2.8 34.5 + - + +
87A GLU* 3.7 29.6 - - + +
1B PCA 5.9 0.2 - - - -
3B ARG* 4.5 13.7 - - + +
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 5.2 2.1 + - - -
64A ALA* 1.3 74.0 - - - +
66A ILE* 1.3 63.5 + - - +
82A VAL* 3.6 20.6 - - + -
83A MET 3.6 3.6 - - - -
84A LYS* 3.0 36.0 - - - +
1B PCA 3.8 11.9 + - - +
2B VAL* 3.5 18.9 - - + +
3B ARG* 2.8 24.7 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.0 9.6 - - + -
42A VAL* 4.0 15.7 - - + -
64A ALA* 4.2 7.2 - - + +
65A ASP* 1.3 81.2 - - - +
67A GLN* 1.3 65.9 + - - +
68A ILE* 3.6 9.5 + - + +
82A VAL* 3.5 0.2 - - - -
83A MET* 2.8 43.3 + - - +
85A PHE* 3.5 26.5 - - + -
2B VAL* 4.1 4.3 - - - -
3B ARG* 3.5 40.6 - - - +
8B VAL* 3.4 35.9 - - + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 1.3 71.8 - - - +
68A ILE* 1.3 62.2 + - - +
80A MET* 3.9 32.9 - - + +
81A GLU 3.5 12.2 - - - +
82A VAL* 5.3 6.0 - - + +
2B VAL* 3.9 12.6 - - + +
3B ARG 2.9 19.6 + - - +
4B PRO* 3.8 7.2 - - + +
5B PHE* 3.1 33.8 + - - +
8B VAL* 3.3 21.0 - - - +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.1 4.7 - - + -
35A PHE* 4.1 14.6 - - + -
36A ARG 3.4 19.5 - - - +
37A PRO* 4.0 8.5 - - - +
40A VAL* 4.0 14.1 - - + -
66A ILE* 4.0 10.5 - - + +
67A GLN* 1.3 80.5 - - - +
69A MET* 1.3 81.0 + - - +
70A ARG 3.8 0.7 + - - -
80A MET* 3.4 7.8 - - - -
81A GLU* 2.8 40.1 + - + +
83A MET* 3.9 17.9 - - + -
85A PHE* 3.6 38.6 - - + -
5B PHE* 4.2 1.8 - - - -
8B VAL* 4.9 3.1 - - + -
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE 3.7 0.3 - - - +
35A PHE* 3.3 6.9 - - - -
36A ARG* 3.0 59.8 + - + +
68A ILE* 1.3 83.4 - - - +
70A ARG* 1.3 62.1 + - - +
71A MET* 4.9 2.5 - - + +
78A SER* 3.5 44.0 - - - +
79A LYS* 3.7 6.1 - - - +
80A MET* 3.0 35.6 - - + +
5B PHE* 3.8 8.5 - - + -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 2.9 42.4 + - - -
33A ASP* 2.8 38.3 + - + +
34A ILE 3.6 2.2 - - - -
35A PHE* 3.4 24.7 - - + -
68A ILE 3.8 1.2 + - - -
69A MET* 1.3 73.0 - - - +
71A MET* 1.3 62.1 + - - +
72A ASN* 4.0 2.8 + - + +
77A SER 3.9 0.9 - - - +
78A SER* 3.1 21.8 - - - -
79A LYS* 3.0 32.0 + - - +
81A GLU* 2.6 44.0 + - - +
83A MET* 4.1 3.0 - - - +
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 3.3 4.7 - - - +
34A ILE* 2.6 71.7 + - + +
36A ARG* 5.9 10.5 - - + +
69A MET* 3.9 3.8 + - + +
70A ARG* 1.3 73.9 - - - +
72A ASN* 1.3 75.4 + - - +
73A PRO* 3.3 35.3 - - + +
76A HIS* 4.1 17.3 - - - +
77A SER 3.4 8.7 - - - +
78A SER* 3.7 15.7 - - - -
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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
------------------------------------------------------------
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