Contacts of the strand formed by residues 107 - 112 (chain A) in PDB entry 2VSH
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 ILE 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A HIS* 3.8 26.5 - - + -
1A MET 2.9 10.8 + - - +
2A ILE* 3.5 18.4 - - + -
3A TYR* 2.9 30.8 + - - -
105A GLU* 3.6 11.0 - - - +
106A ASP* 1.3 73.2 - - - +
108A VAL* 1.3 65.3 + - - +
109A VAL* 4.5 0.7 - - + +
127A ILE* 5.1 6.7 - - + +
130A ALA* 4.0 28.3 - - + +
131A GLN* 5.4 3.1 - - + -
172A THR* 3.6 28.7 - - + -
173A PHE 3.5 8.3 - - - +
174A ARG* 4.0 18.8 - - + +
175A CYS* 4.0 3.1 - - - -
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Residues in contact with VAL 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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3A TYR 3.4 4.9 - - - +
4A ALA 4.2 0.2 - - - -
5A GLY* 3.7 28.9 - - - +
92A ILE* 4.4 5.4 - - + -
93A ILE* 4.5 9.9 - - + -
96A ILE* 4.1 17.0 - - + -
107A ILE* 1.3 75.7 - - - +
109A VAL* 1.3 63.6 + - - +
110A THR* 3.6 11.9 + - + -
171A GLN 3.9 0.5 - - - +
172A THR* 3.4 4.2 - - - +
173A PHE* 2.9 60.2 + - + +
175A CYS* 3.8 19.7 - - - -
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Residues in contact with VAL 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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2A ILE* 4.0 8.7 - - + -
3A TYR 2.7 17.5 + - - +
4A ALA* 3.5 4.0 - - - +
5A GLY 2.8 26.2 + - - +
40A PHE* 3.9 21.8 - - + -
46A ILE* 4.7 2.5 - - + -
108A VAL* 1.3 70.5 - - - +
110A THR* 1.3 54.5 + - - +
111A HIS* 3.9 0.7 + - - +
123A ILE* 5.0 5.4 - - + -
126A ASN* 4.6 5.2 - - + -
127A ILE* 3.8 31.4 - - + -
170A PRO* 3.6 25.4 - - + -
172A THR* 3.6 28.9 - - + +
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Residues in contact with THR 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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5A GLY* 3.2 11.0 - - - +
7A LEU* 4.2 13.8 - - + +
85A ARG* 5.5 0.5 + - - -
89A ILE* 4.2 19.5 - - + +
92A ILE* 6.0 1.8 - - + -
108A VAL* 3.8 22.4 - - + -
109A VAL* 1.3 70.9 - - - +
111A HIS* 1.3 62.6 + - - +
169A THR* 4.0 1.5 - - - -
170A PRO* 3.0 8.0 - - - +
171A GLN* 2.6 63.1 + - - +
173A PHE* 3.7 26.3 - - + -
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Residues in contact with HIS 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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5A GLY 2.9 6.5 + - - -
6A ILE* 3.4 9.5 - - + +
7A LEU* 2.9 29.6 + - - +
36A THR* 3.7 17.7 - - + -
40A PHE* 3.9 27.1 - + + -
110A THR* 1.3 76.7 - - - +
112A ASP* 1.3 78.4 + - - +
115A ARG* 2.8 36.6 + - + +
118A ILE* 3.5 25.4 - - + +
169A THR* 2.7 47.1 + - - -
170A PRO* 3.4 4.9 - - + +
216A ASN* 4.0 1.3 - - - -
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Residues in contact with ASP 112 (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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7A LEU* 3.9 9.5 - - - +
36A THR* 3.8 1.1 - - - +
85A ARG* 3.0 33.8 + - - -
111A HIS* 1.3 90.1 - - - +
113A SER* 1.3 64.9 + - - +
114A VAL* 4.1 11.2 - - + +
115A ARG* 2.9 44.4 + - + +
169A THR* 3.0 19.6 + - - +
218A LYS* 3.3 21.7 + - - -
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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