Contacts of the strand formed by residues 77 - 91 (chain A) in PDB entry 5VZ4
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 CYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A CYS* 3.6 3.6 - - - -
62A LYS* 4.7 7.6 - - - -
75A ALA 4.8 2.9 - - - -
76A PRO* 1.3 76.5 - - - +
78A CYS* 1.3 63.0 + - - +
79A VAL* 3.4 18.7 + - + +
111A CYS* 3.5 1.6 - - - -
112A ILE* 2.9 39.9 + - - +
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Residues in contact with CYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A CYS* 2.0 55.4 - - + -
16A ARG 3.8 1.3 - - - -
44A CYS* 3.5 41.1 - - - +
45A ILE* 3.6 2.9 - - - -
46A GLY 3.4 22.2 + - - +
48A CYS* 3.5 4.3 - - - -
77A CYS* 1.3 71.2 - - - +
79A VAL* 1.3 63.0 + - - +
110A HIS 3.6 0.7 - - - -
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Residues in contact with VAL 79 (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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44A CYS* 3.7 6.7 - - - -
77A CYS* 3.9 18.8 - - + +
78A CYS* 1.3 78.8 - - - +
80A PRO* 1.3 75.2 - - + +
109A CYS* 3.4 3.8 - - - -
110A HIS* 2.9 51.3 + - + +
112A ILE* 3.5 29.2 - - + -
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Residues in contact with PRO 80 (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 MET* 5.9 0.2 - - - -
44A CYS* 3.6 10.3 - - + +
79A VAL* 1.3 92.0 - - + +
81A ALA* 1.3 61.3 + - - +
82A SER 4.0 5.4 - - - +
83A TYR* 3.7 39.3 + - + +
106A ALA* 3.9 26.5 - - + -
108A ASP 3.3 7.9 - - - +
110A HIS* 3.9 7.5 - - - -
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Residues in contact with ALA 81 (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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79A VAL 3.4 2.0 + - - -
80A PRO* 1.3 72.3 - - - +
82A SER* 1.3 63.1 + - - +
83A TYR* 5.6 0.9 - - - -
108A ASP* 2.9 24.1 + - - +
109A CYS 4.1 6.3 - - - +
110A HIS* 3.3 41.1 + - + -
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Residues in contact with SER 82 (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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80A PRO* 3.4 3.4 - - - +
81A ALA* 1.3 79.0 - - - +
83A TYR* 1.3 74.7 + - - +
106A ALA* 3.8 2.9 - - - -
107A LYS* 2.9 28.3 + - - +
108A ASP* 2.7 25.2 + - - +
204A EDO 3.1 42.3 + - - -
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Residues in contact with TYR 83 (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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80A PRO* 3.7 40.4 + - + +
81A ALA 5.6 0.2 - - - -
82A SER* 1.3 81.3 - - - +
84A ASN* 1.3 60.1 + - - +
85A PRO* 3.9 5.9 - - - +
102A ASP 2.9 23.5 - - - +
103A ASP* 3.7 34.1 - - + -
104A LEU 3.7 2.7 - - - -
105A LEU 3.3 21.1 - - - +
106A ALA* 4.0 4.3 - - - -
107A LYS* 3.7 16.4 - - - +
204A EDO 5.7 1.2 + - - -
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Residues in contact with ASN 84 (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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17A LEU* 6.1 0.8 - - - +
42A THR* 5.0 4.2 + - - +
83A TYR* 1.3 73.9 - - - +
85A PRO* 1.3 74.7 - - + +
86A MET 3.6 0.5 + - - -
101A TYR 4.4 1.0 - - - +
102A ASP 4.3 2.8 - - - +
105A LEU* 2.9 40.0 + - + +
106A ALA 4.1 4.9 + - - -
107A LYS* 3.4 42.0 + - - +
146B ALA* 6.2 3.6 - - + -
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Residues in contact with PRO 85 (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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83A TYR 3.9 6.1 - - - +
84A ASN* 1.3 93.9 - - + +
86A MET* 1.3 59.8 + - - +
100A THR* 4.1 6.3 - - + -
101A TYR 3.3 13.0 - - - +
102A ASP* 3.9 17.0 - - - +
105A LEU* 4.6 2.9 - - - +
145B ASN* 4.4 1.9 - - - +
146B ALA* 4.5 12.3 - - - +
149B ALA* 3.8 27.8 - - + +
150B SER* 5.3 7.0 - - - +
153B LYS* 4.1 18.8 - - + +
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Residues in contact with MET 86 (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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36A PRO* 3.3 35.4 - - + -
39A VAL* 4.0 20.4 - - + -
84A ASN 3.6 0.6 + - - +
85A PRO* 1.3 76.9 - - - +
87A VAL* 1.3 66.2 + - - +
88A LEU* 3.4 21.8 - - + -
99A GLN 3.7 0.7 - - - +
100A THR* 3.4 1.7 - - - -
101A TYR* 2.8 42.6 + - - +
104A LEU* 3.8 31.4 - - + -
105A LEU* 3.9 26.9 - - + -
145B ASN* 3.4 17.0 - - - +
149B ALA* 4.5 1.1 - - - -
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Residues in contact with VAL 87 (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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86A MET* 1.3 75.6 - - - +
88A LEU* 1.3 79.7 + - - +
98A LEU* 4.3 6.7 - - + -
99A GLN 3.3 13.7 - - - +
100A THR* 3.9 8.1 - - - +
139B VAL* 3.5 24.9 - - + +
145B ASN* 2.8 38.9 + - - +
148B LEU* 4.2 7.2 - - + -
149B ALA* 3.7 35.4 - - + +
152B LEU* 4.1 21.5 - - + -
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Residues in contact with LEU 88 (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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29A TRP* 3.9 30.7 - - + -
33A VAL* 4.4 18.2 - - + -
35A SER 3.6 4.5 - - - +
36A PRO* 4.1 3.8 - - + -
86A MET* 3.4 28.7 - - + -
87A VAL* 1.3 86.5 - - - +
89A ILE* 1.3 63.1 + - - +
90A GLN* 3.7 10.0 + - + +
97A SER 3.6 0.9 - - - +
98A LEU* 3.5 2.6 - - - -
99A GLN* 2.9 29.2 + - - +
101A TYR* 3.5 37.2 - - + +
104A LEU* 4.2 10.5 - - + -
139B VAL* 4.6 0.2 - - - -
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Residues in contact with ILE 89 (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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33A VAL* 3.6 4.4 - - - +
34A LEU* 2.8 41.3 + - + -
35A SER* 2.8 31.4 + - - +
88A LEU* 1.3 71.0 - - - +
90A GLN* 1.3 56.5 + - - +
96A VAL* 3.6 38.6 - - + -
97A SER 3.6 3.1 - - - +
98A LEU* 3.9 15.9 - - + -
132B LEU* 4.8 3.4 - - + +
135B ALA* 3.7 40.2 - - + -
136B GLU* 3.8 10.3 - - + +
139B VAL* 3.8 18.1 - - + +
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Residues in contact with GLN 90 (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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32A TRP 3.5 11.9 - - - +
33A VAL* 4.4 7.2 - - + +
88A LEU* 4.6 12.3 - - + +
89A ILE* 1.3 72.6 - - - +
91A LYS* 1.3 63.8 + - - +
92A THR* 4.1 5.9 - - + +
96A VAL* 3.3 8.2 - - - +
97A SER* 2.8 45.3 + - - +
99A GLN* 3.3 27.9 - - - +
101A TYR* 2.5 31.0 + - - -
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Residues in contact with LYS 91 (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 ALA 2.9 24.6 + - - -
31A ASP* 3.5 20.4 + - - +
32A TRP* 3.0 25.2 + - - +
33A VAL 3.7 17.2 + - - -
34A LEU* 4.0 28.5 - - + +
90A GLN* 1.3 73.7 - - - +
92A THR* 1.3 62.0 + - - +
95A GLY 3.8 7.9 - - - +
96A VAL* 4.5 3.4 - - + -
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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