Contacts of the strand formed by residues 96 - 111 (chain A) in PDB entry 5VT2
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 VAL 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.7 27.1 - - + -
89A ILE* 4.2 15.7 - - + -
90A GLN 3.2 7.9 - - - +
91A LYS* 4.8 3.4 - - - +
92A THR* 3.5 7.3 + - - +
95A GLY* 1.3 79.5 - - - +
97A SER* 1.3 63.4 + - - +
98A LEU* 6.4 0.2 - - + -
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Residues in contact with SER 97 (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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88A LEU 3.7 0.2 - - - +
89A ILE* 3.2 9.9 - - - +
90A GLN* 2.8 53.2 + - - +
92A THR* 4.3 13.8 - - - +
96A VAL* 1.3 76.3 - - - +
98A LEU* 1.3 61.2 + - - +
99A GLN* 3.8 27.9 + - - -
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Residues in contact with LEU 98 (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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87A VAL* 3.6 24.9 - - + -
88A LEU 3.6 1.1 - - - -
89A ILE* 3.4 31.2 - - + -
96A VAL* 6.4 0.4 - - + -
97A SER* 1.3 73.3 - - - +
99A GLN* 1.3 67.2 + - - +
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Residues in contact with GLN 99 (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 3.6 1.0 - - - +
87A VAL* 3.3 3.9 - - - -
88A LEU* 2.8 42.2 + - - +
90A GLN* 3.3 28.9 + - - +
97A SER* 3.8 21.0 + - - +
98A LEU* 1.3 82.2 - - - +
100A THR* 1.3 62.5 + - - +
101A TYR* 3.9 12.7 + - + -
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Residues in contact with THR 100 (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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85A PRO* 3.8 28.7 - - + -
86A MET 3.4 7.4 - - - +
87A VAL* 3.5 18.4 - - + +
99A GLN* 1.3 75.0 - - - +
101A TYR* 1.3 65.9 + - - +
102A ASP* 4.2 11.3 + - - +
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Residues in contact with TYR 101 (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* 3.8 9.0 - + - -
84A ASN 4.2 1.4 - - - +
85A PRO* 3.3 3.8 - - - +
86A MET* 2.8 38.6 + - - +
88A LEU* 3.6 23.6 - - + -
90A GLN* 2.7 39.5 + - - -
99A GLN* 3.9 20.2 + - + -
100A THR* 1.3 77.0 - - - +
102A ASP* 1.3 63.3 + - - +
103A ASP* 3.5 17.0 + - - +
104A LEU* 3.8 27.5 - - + +
57B MET* 3.8 25.7 - - + +
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Residues in contact with ASP 102 (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* 3.0 22.2 - - - +
84A ASN 5.0 0.9 - - - -
85A PRO* 3.7 25.6 - - - +
100A THR* 4.2 9.5 + - - +
101A TYR* 1.3 74.1 - - - +
103A ASP* 1.3 61.4 + - + +
104A LEU 3.6 2.7 - - - -
204A EDO 3.0 18.4 + - - +
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Residues in contact with ASP 103 (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 12.6 - - - -
101A TYR* 3.9 17.7 - - - +
102A ASP* 1.3 82.1 + - + +
104A LEU* 1.3 57.2 + - - +
204A EDO 3.5 30.7 - - - +
56B ASN* 3.4 12.2 - - + +
57B MET* 3.2 28.9 + - - +
58B HIS* 2.9 26.0 + - - +
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Residues in contact with LEU 104 (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* 4.0 16.8 - - + -
39A VAL* 4.8 6.5 - - + -
41A VAL* 5.0 2.4 - - + +
42A THR 4.6 0.2 - - - +
83A TYR* 3.8 2.2 - - - -
86A MET* 4.0 20.4 - - + -
88A LEU* 4.1 11.7 - - + -
101A TYR* 3.8 33.6 + - + +
102A ASP 3.6 2.6 - - - -
103A ASP* 1.3 80.2 - - - +
105A LEU* 1.3 85.0 + - + +
57B MET* 3.9 17.0 - - + -
58B HIS* 2.8 29.6 - - - +
61B ILE* 3.9 24.6 - - + +
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Residues in contact with LEU 105 (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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39A VAL* 4.1 12.8 - - + -
40A GLN 3.9 18.8 - - - +
41A VAL* 4.2 9.4 - - + -
42A THR* 3.8 13.2 - - + +
83A TYR* 3.1 8.4 - - - -
84A ASN* 2.7 50.3 + - + +
85A PRO 4.2 9.6 - - - +
86A MET* 3.6 30.7 - - + -
104A LEU* 1.3 101.3 - - + +
106A ALA* 1.3 57.9 + - - +
202A EDO 4.0 16.2 - - - +
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Residues in contact with ALA 106 (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* 3.4 19.6 - - + +
42A THR* 2.7 48.3 + - - +
43A MET* 3.9 4.0 - - - -
44A CYS* 4.1 4.5 - - - -
80A PRO* 3.9 26.9 - - + -
82A SER 3.8 5.4 - - - -
83A TYR* 4.0 5.7 - - - -
84A ASN* 4.4 4.6 - - - +
104A LEU 3.9 2.6 + - - -
105A LEU* 1.3 71.0 - - - +
107A LYS* 1.3 59.5 + - - +
108A ASP 4.8 0.2 - - - +
58B HIS* 3.9 5.3 - - - +
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Residues in contact with LYS 107 (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* 3.7 20.6 - - - +
82A SER* 2.8 40.9 + - - +
83A TYR 3.7 15.3 - - - +
84A ASN* 3.6 31.2 - - - +
105A LEU 3.5 0.8 + - - -
106A ALA* 1.3 73.7 - - - +
108A ASP* 1.3 64.5 + - + +
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Residues in contact with ASP 108 (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* 4.4 1.8 - - - -
44A CYS* 3.8 0.7 - - - -
53A ARG* 4.7 12.8 + - - +
80A PRO* 3.3 8.0 - - - +
81A ALA* 2.8 31.0 + - - +
82A SER* 2.7 36.5 + - - +
107A LYS* 1.3 83.8 + - + +
109A CYS* 1.3 68.9 + - - +
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Residues in contact with CYS 109 (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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15A CYS* 3.8 21.0 - - - +
16A ARG* 3.7 20.4 - - - -
17A LEU* 3.7 15.7 - - - -
44A CYS* 2.1 50.9 - - + -
53A ARG* 3.1 31.2 + - - +
78A CYS* 4.1 0.2 - - - -
79A VAL 3.4 3.6 - - - -
81A ALA* 4.2 1.6 - - - +
108A ASP* 1.3 81.5 - - - +
110A HIS* 1.3 61.1 + - - +
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Residues in contact with HIS 110 (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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15A CYS* 4.0 2.9 - - - -
53A ARG* 3.5 24.9 - - + +
55A ALA* 3.5 23.1 - - + +
77A CYS 3.7 0.5 - - - +
78A CYS* 3.7 2.3 - - - -
79A VAL* 2.9 40.9 + - + +
80A PRO 3.8 8.1 - - - -
81A ALA* 3.6 34.3 + - + +
109A CYS* 1.3 75.4 - - - +
111A CYS* 1.3 65.2 + - - +
112A ILE* 3.6 26.4 + - + +
201A EDO 4.1 15.2 + - - -
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Residues in contact with CYS 111 (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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15A CYS* 3.8 16.8 - - - -
48A CYS* 2.1 52.9 - - + -
52A PHE* 3.3 30.1 - - - +
53A ARG* 2.9 12.1 + - - +
54A ALA* 4.4 2.5 - - + -
55A ALA* 3.0 27.2 + - - +
59A ALA* 3.5 6.4 - - - +
76A PRO* 4.2 7.6 - - + -
77A CYS 3.5 3.1 - - - -
110A HIS* 1.3 70.4 - - - +
112A ILE* 1.3 62.4 + - - +
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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