Contacts of the strand formed by residues 86 - 99 (chain A) in PDB entry 2VPA
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 HIS 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 3.6 19.1 - - + -
79A ARG* 3.2 49.7 + - - +
81A ASN* 3.2 18.6 - - - +
84A GLN 5.6 0.2 + - - -
85A GLY* 1.3 76.0 - - - +
87A PRO* 1.3 74.5 - - + +
119A THR* 3.9 5.7 - - - +
120A ALA* 2.8 52.5 + - + +
121A ARG* 5.1 1.1 - - - -
122A VAL 5.5 0.2 - - - -
163A TYR* 3.7 16.4 - + - -
1196A ACT 2.7 26.4 + - - -
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Residues in contact with PRO 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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41A THR* 4.0 11.3 - - - +
42A LEU* 4.8 9.4 + - + +
80A ALA 5.3 0.9 - - - +
81A ASN* 3.5 27.6 - - + +
86A HIS* 1.3 94.2 - - + +
88A ALA* 1.3 60.3 + - - +
118A GLY 3.4 10.8 - - - +
119A THR* 4.3 6.0 - - + +
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Residues in contact with ALA 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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39A VAL* 4.3 6.5 - - + -
40A ALA 3.5 6.3 - - - +
41A THR* 3.9 16.8 - - + -
86A HIS 3.4 0.2 + - - -
87A PRO* 1.3 76.4 - - - +
89A THR* 1.3 61.8 + - - +
116A VAL 3.8 1.6 - - - +
117A PHE* 3.8 1.6 - - - +
118A GLY 2.9 32.3 + - - +
120A ALA* 4.1 17.7 - - + -
165A LEU* 3.8 23.4 - - + +
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Residues in contact with THR 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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38A ARG 3.9 0.5 - - - +
39A VAL* 3.4 4.4 - - - +
40A ALA* 2.8 46.4 + - + +
88A ALA* 1.3 75.0 - - - +
90A LEU* 1.3 65.5 + - - +
91A GLU* 5.7 1.8 - - + -
115A MET* 4.4 18.2 - - + -
116A VAL 3.3 6.7 - - - +
117A PHE* 3.5 36.6 - - + -
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Residues in contact with LEU 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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31A LEU* 4.6 0.4 - - + -
37A ALA* 3.8 15.3 - - + -
38A ARG 3.3 3.6 - - - -
39A VAL* 3.9 20.0 - - + +
59A TYR* 4.8 4.5 - - + -
68A LEU* 4.1 38.6 - - + -
70A TYR* 4.3 9.6 - - + -
88A ALA 4.2 0.2 - - - -
89A THR* 1.3 75.5 - - - +
91A GLU* 1.3 61.6 + - - +
92A VAL* 3.6 29.6 - - + +
114A VAL 3.6 0.9 - - - +
115A MET* 3.4 1.7 - - - -
116A VAL* 2.8 50.7 + - + +
165A LEU* 3.7 20.4 - - + -
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Residues in contact with GLU 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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37A ALA* 3.3 6.1 - - - -
38A ARG* 2.8 53.3 + - + +
89A THR* 4.3 2.7 - - + -
90A LEU* 1.3 76.6 - - - +
92A VAL* 1.3 62.5 + - - +
93A SER* 2.6 31.0 + - - -
113A SER* 2.6 25.2 + - - +
114A VAL 3.2 12.6 - - - +
115A MET* 4.6 11.2 - - + -
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Residues in contact with VAL 92 (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 LEU* 3.6 26.2 - - + +
31A LEU* 3.7 10.8 - - + -
34A GLY* 4.5 9.4 - - - -
36A ILE 3.9 12.6 - - - +
37A ALA* 3.8 3.6 - - + -
59A TYR* 3.6 37.9 - - + +
90A LEU* 3.6 21.3 + - + -
91A GLU* 1.3 79.8 - - - +
93A SER* 1.3 69.0 + - - +
94A GLU* 6.1 1.3 - - + -
113A SER* 3.4 1.4 - - - -
114A VAL* 2.9 32.2 + - + +
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Residues in contact with SER 93 (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 LEU* 5.0 1.8 - - - -
36A ILE 5.0 2.9 + - - +
38A ARG* 5.3 5.2 + - - -
91A GLU* 2.6 31.3 + - - -
92A VAL* 1.3 79.7 - - - +
94A GLU* 1.3 63.9 + - - +
95A ILE* 4.0 24.2 + - - +
112A ARG 3.0 16.8 - - - -
113A SER* 4.0 4.5 - - - -
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Residues in contact with GLU 94 (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 LEU* 4.6 9.7 - - + +
33A ARG* 2.8 49.6 + - - +
34A GLY* 5.2 2.4 + - - -
92A VAL* 6.1 0.9 - - + -
93A SER* 1.3 77.8 - - - +
95A ILE* 1.3 61.5 + - - +
111A TYR* 3.3 4.9 - - - -
112A ARG* 2.8 64.9 + - + +
176A TRP* 3.5 10.9 - - + -
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Residues in contact with ILE 95 (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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93A SER* 4.0 23.1 + - - +
94A GLU* 1.3 79.4 - - - +
96A GLY* 1.3 66.2 + - - +
98A PHE* 6.1 1.3 - - + -
109A VAL* 3.7 28.0 - - + -
110A GLN 3.6 1.6 - - - +
111A TYR* 4.3 14.8 - - + -
113A SER* 6.2 0.4 - - - -
176A TRP* 4.1 3.1 - - - -
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Residues in contact with GLY 96 (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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95A ILE* 1.3 84.7 - - - +
97A GLN* 1.3 75.3 + - - -
98A PHE* 5.5 1.0 - - - -
109A VAL* 4.0 1.2 - - - +
110A GLN* 2.9 20.8 + - - -
176A TRP* 3.5 23.4 - - - -
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Residues in contact with GLN 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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96A GLY* 1.3 82.5 + - - +
98A PHE* 1.3 72.0 + - - +
99A LEU* 3.5 6.1 + - + +
109A VAL* 3.8 3.6 - - - -
110A GLN* 2.8 46.0 + - - +
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Residues in contact with PHE 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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95A ILE* 6.1 1.3 - - + -
96A GLY 5.5 1.1 - - - -
97A GLN* 1.3 81.1 + - - +
99A LEU* 1.3 60.2 + - - +
100A PRO* 3.5 10.7 - - - +
108A SER 3.4 14.6 - - - -
109A VAL* 3.9 25.6 - - + +
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Residues in contact with LEU 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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97A GLN* 3.8 14.8 - - + +
98A PHE* 1.3 74.7 - - - +
100A PRO* 1.3 70.3 - - + +
107A LEU* 3.8 6.6 - - - +
108A SER* 2.8 42.2 + - - +
109A VAL 5.0 0.2 - - - -
110A GLN* 3.9 28.9 - - + +
175A ASN* 5.8 1.1 - - - +
177A ALA* 3.6 28.7 - - + +
178A GLU 3.9 20.0 - - - +
179A GLN* 4.6 1.3 - - - +
180A ALA* 3.8 27.9 - - + +
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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