Contacts of the strand formed by residues 162 - 175 (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 VAL 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL* 5.6 0.2 - - + -
70A TYR 3.7 11.0 - - - +
71A HIS* 4.1 0.4 - - - -
122A VAL* 3.3 8.9 - - - +
123A LEU* 2.8 35.0 + - + +
128A ALA* 4.1 26.0 - - + +
131A ALA* 4.1 17.0 - - + -
132A LEU* 3.6 47.8 - - + +
157A LEU* 5.2 2.2 - - + -
160A THR* 3.6 16.0 + - + +
161A SER* 1.3 76.9 - - - +
163A TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 163 (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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68A LEU 4.4 0.2 - - - -
69A VAL* 3.3 10.7 - - - +
70A TYR* 2.9 68.5 + + + +
72A THR* 3.5 31.6 + - + -
74A VAL 5.0 3.8 + - - -
75A VAL* 5.2 4.2 - - - +
79A ARG* 3.1 21.6 + - - -
86A HIS* 3.7 26.9 - + - -
120A ALA* 4.6 2.2 - - + -
121A ARG 3.3 17.0 - - - +
122A VAL* 3.9 20.3 - - + +
123A LEU* 4.3 5.2 - - - +
161A SER* 3.7 28.6 + - - -
162A VAL* 1.3 72.7 - - - +
164A SER* 1.3 60.5 + - - +
165A LEU 4.1 0.2 - - - -
1196A ACT 4.1 5.3 + - - -
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Residues in contact with SER 164 (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 ARG* 4.8 0.2 - - - -
67A ASP* 2.6 31.4 + - - +
68A LEU 3.5 4.7 - - - -
69A VAL* 4.4 2.5 - - - -
119A THR 3.6 2.9 - - - +
120A ALA* 3.2 2.8 - - - -
121A ARG* 2.8 66.0 + - - -
123A LEU* 3.9 16.7 - - - +
163A TYR* 1.3 73.1 - - - +
165A LEU* 1.3 57.9 + - - +
166A SER 3.7 0.2 + - - -
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Residues in contact with LEU 165 (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* 5.0 0.9 - - + -
67A ASP* 3.1 6.0 - - - -
68A LEU* 2.8 41.4 + - + +
70A TYR* 4.1 17.0 - - + +
88A ALA* 3.8 32.3 - - + +
89A THR 4.8 0.2 - - - -
90A LEU* 3.7 35.9 - - + +
116A VAL* 4.3 15.9 - - + +
118A GLY* 3.7 29.8 - - - +
119A THR 3.5 6.7 - - - +
120A ALA* 4.0 3.4 - - + +
163A TYR 4.1 0.4 - - - -
164A SER* 1.3 68.0 - - - +
166A SER* 1.3 64.9 + - - +
167A ILE* 3.5 1.7 + - - +
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Residues in contact with SER 166 (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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65A GLN 5.4 1.7 + - - -
66A GLY 3.6 8.8 + - - -
67A ASP* 4.0 4.0 - - - -
118A GLY* 3.3 2.4 - - - -
119A THR* 2.9 38.8 + - - -
121A ARG* 4.4 16.2 - - - -
164A SER 3.7 1.4 + - - -
165A LEU* 1.3 72.4 - - - +
167A ILE* 1.3 65.6 + - - +
168A ASP* 3.5 4.7 + - - +
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Residues in contact with ILE 167 (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* 5.3 0.7 - - + -
61A TYR* 3.6 32.5 - - + +
66A GLY* 3.0 23.9 + - - +
68A LEU* 3.8 20.0 - - + -
116A VAL* 3.7 20.0 - - + -
117A PHE 4.0 2.9 - - - -
165A LEU* 4.1 3.4 - - - +
166A SER* 1.3 74.5 + - - +
168A ASP* 1.3 69.9 + - - +
169A ARG* 3.9 23.6 - - - +
170A TRP* 4.3 22.2 - - + -
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Residues in contact with ASP 168 (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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117A PHE 2.9 15.3 + - - +
118A GLY* 3.6 18.9 - - - -
119A THR* 4.3 7.5 + - - -
166A SER* 3.5 4.6 + - - +
167A ILE* 1.3 80.6 - - - +
169A ARG* 1.3 81.8 + - + +
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Residues in contact with ARG 169 (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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116A VAL* 3.7 0.7 - - - -
117A PHE* 2.9 66.1 + - + +
167A ILE* 3.9 6.3 - - - +
168A ASP* 1.3 99.4 + - + +
170A TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 170 (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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21A ARG* 4.8 6.4 + - - -
24A ASP* 2.8 47.8 + - + -
27A ILE* 3.4 35.3 - - + +
28A ARG* 4.1 12.6 - - + -
31A LEU* 3.6 26.5 - - + -
61A TYR* 3.6 26.7 - + - -
114A VAL* 4.6 0.2 - - + -
115A MET 3.2 12.3 - - - +
116A VAL* 4.2 8.7 - - + -
117A PHE* 4.7 4.0 - - - -
167A ILE* 4.3 22.4 - - + -
169A ARG* 1.3 79.5 - - - +
171A SER* 1.3 63.7 + - - +
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Residues in contact with SER 171 (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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21A ARG* 3.7 27.1 + - - +
27A ILE* 4.0 4.3 - - - -
113A SER 3.9 0.9 - - - +
114A VAL* 3.3 3.4 - - - -
115A MET* 2.9 42.0 + - - +
117A PHE* 4.6 13.7 - - - -
170A TRP* 1.3 76.1 - - - +
172A GLY* 1.3 59.5 + - - +
173A LYS* 5.2 4.8 - - - +
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Residues in contact with GLY 172 (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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21A ARG* 3.3 15.9 - - - +
22A GLN* 3.0 27.4 + - - -
26A TRP* 4.1 2.0 - - - -
27A ILE* 3.5 26.8 - - - +
113A SER 3.5 6.1 - - - -
114A VAL* 4.1 4.5 - - - -
171A SER* 1.3 73.5 + - - +
173A LYS* 1.3 63.7 + - - -
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Residues in contact with LYS 173 (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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19A GLN* 3.7 24.2 + - - +
20A ASN* 3.3 11.4 - - - +
21A ARG* 4.3 9.4 - - - -
22A GLN* 4.0 3.1 - - - -
26A TRP* 3.5 4.4 - - - -
111A TYR* 3.7 29.1 + - + +
112A ARG* 3.4 2.8 - - - -
113A SER* 2.9 38.1 + - - +
115A MET* 6.3 2.9 - - + -
171A SER* 5.2 3.8 - - - +
172A GLY* 1.3 80.0 - - - +
174A GLU* 1.3 60.9 + - - +
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Residues in contact with GLU 174 (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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20A ASN* 3.0 27.1 + - - +
22A GLN* 3.6 22.0 + - - +
26A TRP* 3.4 27.5 + - + -
111A TYR* 3.4 16.8 - - - +
112A ARG* 2.9 32.4 + - + -
173A LYS* 1.3 75.6 - - - +
175A ASN* 1.3 64.1 + - - +
176A TRP* 3.9 17.7 - - + +
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Residues in contact with ASN 175 (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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20A ASN* 3.6 18.4 + - - +
99A LEU* 5.8 1.4 - - - +
108A SER* 6.1 0.9 - - - -
109A VAL 4.0 1.5 - - - +
110A GLN* 3.3 7.1 - - - -
111A TYR* 2.9 58.0 + - + +
174A GLU* 1.3 73.7 - - - +
176A TRP* 1.3 61.3 + - - +
177A ALA* 3.7 17.1 + - - +
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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