Contacts of the strand formed by residues 158 - 164 (chain A) in PDB entry 1VAV
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 PHE 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A THR* 3.4 1.6 - - - -
87A LEU* 2.7 74.3 + - + +
89A ILE* 3.8 28.7 - - + -
100A ILE* 3.6 23.1 - - + -
121A TYR* 4.1 8.1 - + - -
130A VAL* 3.9 9.9 - - + -
152A ILE* 3.5 34.1 - - + -
156A GLN 3.6 5.2 - - - -
157A PRO* 1.3 74.3 - - - +
159A SER* 1.3 64.4 - - - +
160A TYR* 4.6 2.5 - + - -
174A VAL* 4.0 16.2 - - + -
175A ASN* 3.4 23.8 - - - +
18B ILE* 3.9 7.0 - - - -
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Residues in contact with SER 159 (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 ALA 3.1 12.1 - - - -
86A THR* 4.2 1.1 - - - -
158A PHE* 1.3 77.2 - - - +
160A TYR* 1.3 64.5 + - - +
161A ARG* 6.0 0.2 - - - -
174A VAL* 3.1 10.2 - - - +
175A ASN* 2.9 38.9 + - - +
217A GLU* 5.3 0.4 - - - -
11B ILE* 5.3 0.2 - - - +
13B GLN* 2.8 27.7 + - - +
14B GLY* 4.1 24.7 - - - -
18B ILE* 4.1 4.4 - - - +
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Residues in contact with TYR 160 (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 LEU* 3.8 23.0 - - + +
85A ALA* 2.9 49.9 + - + +
87A LEU* 3.6 31.9 - - + -
100A ILE* 2.8 42.8 + - + -
101A GLY* 3.4 10.7 - - - -
119A LEU* 3.3 28.5 - - + -
158A PHE* 4.6 1.3 - + + -
159A SER* 1.3 77.9 - - - +
161A ARG* 1.3 73.8 + - - +
162A ILE* 4.0 4.9 - - + -
173A SER 3.1 13.0 - - - +
174A VAL* 4.1 7.6 - - + +
196A ALA* 3.7 15.8 - - - +
215A PHE* 3.8 4.7 - + - -
13B GLN* 4.9 0.9 - - - -
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Residues in contact with ARG 161 (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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82A TRP* 3.4 48.7 - - + -
83A LEU 3.3 7.4 - - - +
84A GLU* 4.0 32.0 + - + -
159A SER* 6.0 0.2 - - - -
160A TYR* 1.3 80.1 - - - +
162A ILE* 1.3 65.6 + - - +
171A SER* 3.9 1.8 - - - +
172A VAL* 3.4 3.3 - - - -
173A SER* 2.9 47.7 + - - +
13B GLN* 4.0 31.8 - - + +
32B ASP* 5.1 8.1 + - - -
33B TYR* 5.7 1.3 - - - -
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Residues in contact with ILE 162 (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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82A TRP* 3.6 5.0 - - - -
83A LEU* 2.8 42.0 + - + +
101A GLY 4.2 0.4 - - - -
102A GLN* 4.1 24.5 - - - +
103A ILE* 3.3 31.2 - - + +
117A VAL* 4.8 8.1 - - + -
119A LEU* 3.5 37.9 - - + +
160A TYR* 4.0 12.8 - - + -
161A ARG* 1.3 81.4 - - - +
163A GLY* 1.3 60.2 + - - +
170A LEU* 4.7 0.9 - - + -
171A SER 3.4 2.7 - - - -
172A VAL* 4.0 21.1 - - + -
194A PHE* 3.7 2.7 - - - -
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Residues in contact with GLY 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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81A ASN 3.0 13.7 - - - -
82A TRP* 3.7 13.3 - - - -
103A ILE* 4.4 6.3 - - - -
162A ILE* 1.3 78.2 - - - +
164A VAL* 1.3 61.1 + - - -
165A SER 4.3 0.2 - - - -
169A LEU 4.4 0.4 - - - -
170A LEU* 3.4 9.8 - - - +
171A SER* 2.8 36.6 + - - +
194A PHE* 4.6 0.9 - - - -
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Residues in contact with VAL 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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74A TRP* 3.3 26.7 - - + -
76A TYR* 3.4 20.9 - - + -
81A ASN* 2.9 49.0 + - + +
82A TRP* 5.3 2.2 - - - -
103A ILE* 5.1 3.8 - - + -
116A LEU* 5.7 0.9 - - + -
163A GLY* 1.3 74.8 - - - +
165A SER* 1.3 66.9 + - - +
168A GLY 4.1 4.9 - - - -
169A LEU 3.3 9.6 - - - +
170A LEU* 4.6 4.7 - - + +
183A LEU* 3.7 27.6 - - + -
192A LEU* 4.8 4.5 - - + -
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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