Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 2V8W
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 GLY 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY* 1.3 74.7 - - - -
112A ARG* 1.3 59.1 + - - -
166A TRP* 3.3 4.3 - - - -
167A THR 2.9 26.6 + - - +
197A TYR* 3.0 20.9 + - - -
198A GLN 3.1 15.3 - - - -
199A SER* 3.8 0.9 - - - -
200A HIS* 3.4 15.9 + - - -
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Residues in contact with ARG 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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102A TRP* 6.1 1.0 - - - +
111A GLY* 1.3 75.8 - - - +
113A TRP* 1.3 60.9 + - - +
114A LEU* 3.7 31.8 - - + +
153A VAL* 5.9 1.6 - - - +
155A ASN* 4.1 16.0 + - - -
162A LYS* 4.7 9.9 - - - +
164A ALA* 4.1 15.6 - - + +
165A ILE 3.1 5.4 - - - +
166A TRP* 3.7 31.8 - - + +
196A GLY 3.7 0.9 - - - +
197A TYR* 3.2 10.2 - - - -
198A GLN* 2.9 58.2 + - + +
200A HIS* 4.0 9.3 - - + -
203A THR* 4.2 26.3 - - - +
211A THR* 5.5 0.6 - - - +
1218A MGO 4.3 14.3 + - - -
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Residues in contact with TRP 113 (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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112A ARG* 1.3 69.1 - - - +
114A LEU* 1.3 58.8 + - - +
115A ILE* 4.2 1.1 + - - -
163A ILE 3.9 0.2 - - - +
164A ALA* 3.0 25.1 - - - -
165A ILE* 2.9 14.2 + - + +
167A THR* 4.4 6.5 - - + -
176A VAL* 2.7 44.3 + - + +
177A THR* 4.4 5.6 - - - -
179A ILE* 4.1 15.7 - - + -
180A GLY* 3.4 23.8 - - - +
183A TYR* 4.3 20.6 - + + -
195A ILE* 3.5 37.0 - - + -
196A GLY 3.5 16.2 - - - -
197A TYR* 3.5 39.5 - + + -
215A PHE* 3.9 18.2 - - + -
216A VAL 4.0 5.6 - - - -
217A VAL* 3.6 20.4 - - + -
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Residues in contact with LEU 114 (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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112A ARG* 3.7 37.2 + - + +
113A TRP* 1.3 73.2 - - - +
115A ILE* 1.3 64.4 + - - +
116A THR* 3.0 29.9 + - - +
155A ASN* 5.3 0.2 - - - +
162A LYS* 3.8 32.5 - - + -
163A ILE 3.7 6.7 - - - +
164A ALA* 4.1 6.5 - - + -
195A ILE* 3.5 21.7 - - - +
196A GLY 3.1 12.6 + - - +
198A GLN* 3.6 28.3 - - - +
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Residues in contact with ILE 115 (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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114A LEU* 1.3 79.3 - - - +
116A THR* 1.3 69.8 + - - +
117A LEU* 4.4 17.1 - - + +
129A PHE* 4.4 13.9 - - + -
162A LYS* 3.2 8.8 - - - +
163A ILE* 2.8 47.9 + - + +
183A TYR* 3.7 36.3 - - + +
187A LEU* 3.8 13.2 - - + -
189A LEU* 4.5 14.1 - - + -
193A ILE* 6.3 1.1 - - + -
195A ILE* 3.8 30.3 - - + -
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Residues in contact with THR 116 (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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114A LEU* 3.0 24.2 + - - +
115A ILE* 1.3 76.6 - - - +
117A LEU* 1.3 74.1 + - - +
121A GLN* 4.1 7.1 + - - +
160A GLY* 5.6 3.4 - - - -
161A ASP 3.8 5.6 - - - +
162A LYS* 4.4 8.9 - - + +
195A ILE* 5.8 0.2 - - - +
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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