Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 3Q37
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A SER* 2.9 9.3 + - - -
91A TRP* 3.2 57.2 + + + +
92A VAL 3.0 23.9 + - - -
121A GLY 4.7 2.8 + - - -
122A PHE* 1.3 73.4 - - - +
124A VAL* 1.3 60.5 + - - +
161A SER 4.0 12.5 + - - -
162A ARG* 3.3 37.8 - - + +
164A VAL* 5.3 2.5 - - + -
208A ARG* 4.4 11.7 + - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 5.5 0.2 - - - -
92A VAL* 3.3 13.0 - - + +
94A LEU* 3.7 22.0 - - + -
114A VAL* 4.2 4.9 - - + +
117A ALA* 3.4 31.6 - - + -
118A VAL* 3.6 23.6 - - + -
122A PHE* 4.0 2.5 - - + +
123A HIS* 1.3 78.3 - - - +
125A ILE* 1.3 68.6 + - - +
126A VAL* 3.6 24.1 + - + +
162A ARG 2.9 7.9 + - - +
163A VAL* 3.8 1.2 - - - -
164A VAL* 2.9 30.4 + - - +
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Residues in contact with ILE 125 (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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8A ILE* 4.9 1.6 - - + -
10A ALA* 4.1 26.2 - - + -
41A VAL* 4.9 5.8 - - + -
91A TRP* 4.1 30.7 - - + -
92A VAL 2.9 12.3 + - - +
93A VAL* 3.4 19.7 - - + +
94A LEU 2.9 27.7 + - - +
124A VAL* 1.3 75.0 - - - +
126A VAL* 1.3 57.5 + - - +
127A CYS* 3.7 1.6 + - - -
164A VAL* 3.4 18.8 - - + +
166A ALA* 3.7 28.3 - - + -
210A LEU* 4.4 10.3 - - + -
233A LEU* 4.4 14.4 - - + -
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Residues in contact with VAL 126 (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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94A LEU 3.5 6.1 - - - +
100A ARG* 5.1 0.2 - - - +
110A VAL* 4.4 4.3 - - + -
114A VAL* 3.9 24.9 - - + -
124A VAL* 3.6 24.0 - - + +
125A ILE* 1.3 69.7 - - - +
127A CYS* 1.3 70.0 + - - +
128A VAL* 4.6 5.1 - - + +
148A LEU* 6.2 0.7 - - + -
151A VAL* 3.9 31.2 - - + -
163A VAL* 4.4 13.0 - - + -
164A VAL 2.8 18.1 + - - +
165A ILE* 3.4 18.1 - - + +
166A ALA 2.8 23.8 + - - +
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Residues in contact with CYS 127 (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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93A VAL* 3.9 13.0 - - - -
94A LEU 2.9 13.3 + - - -
95A GLY 3.4 16.8 - - - +
96A HIS* 3.7 14.4 - - - -
100A ARG* 2.9 26.0 + - - -
125A ILE 4.2 2.2 - - - -
126A VAL* 1.3 76.4 - - - +
128A VAL* 1.3 62.1 + - - +
166A ALA* 3.3 11.9 - - - +
168A GLU* 3.3 23.3 - - - +
233A LEU* 3.8 29.4 - - - -
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Residues in contact with VAL 128 (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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100A ARG* 4.5 4.0 - - - +
126A VAL* 4.6 12.8 - - + +
127A CYS* 1.3 80.6 - - - +
129A GLY* 1.3 58.5 + - - +
144A VAL* 4.6 6.5 - - + +
147A GLN* 3.2 33.0 - - + +
148A LEU* 4.5 15.0 - - + +
151A VAL* 6.0 0.7 - - + -
165A ILE* 4.1 18.4 - - + -
166A ALA 2.9 14.1 + - - +
167A TYR* 3.5 10.3 - - + -
168A GLU* 2.8 30.5 + - - +
191A LEU* 4.3 19.7 - - + -
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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