Contacts of the strand formed by residues 4 - 9 (chain A) in PDB entry 4IR1
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.6 33.0 - - + +
3A LYS* 1.3 79.5 - - - +
5A ILE* 1.3 64.9 + - - +
106A TYR* 3.9 27.8 - - + -
107A LEU 3.3 10.3 - - - +
108A ASP* 4.5 10.5 - - + +
109A VAL* 5.2 0.4 - - - -
142A VAL* 3.4 6.9 - - - +
143A ALA 2.9 41.3 + - - +
144A PRO 3.4 20.9 - - - +
145A VAL* 3.8 9.6 - - - -
146A LYS* 3.9 8.3 - - + +
149A ALA* 3.5 12.2 - - + +
232A ARG 4.8 4.0 - - - +
234A VAL* 4.5 11.0 - - + +
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Residues in contact with ILE 5 (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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4A ILE* 1.3 78.0 - - - +
6A HIS* 1.3 67.1 + - - +
7A VAL* 3.2 31.0 - - + -
105A ALA 3.6 0.9 - - - +
106A TYR* 3.3 2.9 - - - -
107A LEU* 2.6 68.2 + - + +
109A VAL* 4.3 8.7 - - + -
122A ILE* 3.9 21.5 - - + -
123A ALA* 3.7 34.1 - - + -
126A ILE* 4.8 6.3 - - + -
140A ALA* 4.0 5.6 - - + -
141A GLY 3.1 11.9 - - - +
142A VAL* 4.6 6.3 - - + -
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Residues in contact with HIS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 1.3 76.3 - - - +
7A VAL* 1.3 59.0 - - - +
8A ASP* 3.8 13.7 - - + -
100A LEU* 3.8 9.1 - - + +
104A GLU* 2.8 41.8 + - + +
105A ALA 3.5 12.6 - - - -
106A TYR* 3.7 36.1 - + + -
140A ALA* 3.3 5.4 - - - -
141A GLY 2.8 32.2 + - - -
149A ALA* 3.5 17.8 - - - +
150A LYS* 3.4 22.2 - - + +
153A SER* 2.8 27.4 + - - -
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Residues in contact with VAL 7 (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 ILE* 3.2 31.9 - - + -
6A HIS* 1.3 72.7 - - - +
8A ASP* 1.3 64.5 + - - +
9A MET* 5.1 3.6 - - - -
90A PHE* 3.8 38.3 - - + -
103A ASP 3.6 1.2 - - - +
104A GLU* 3.1 25.8 - - - +
105A ALA 3.0 11.8 + - - +
107A LEU* 4.2 8.5 - - + -
126A ILE* 4.6 9.0 - - + -
127A ARG* 5.8 2.7 - - + -
130A ILE* 4.6 5.8 - - + -
138A ALA* 4.5 16.8 - - + -
139A SER 3.6 8.3 - - - +
140A ALA* 4.5 4.0 - - + -
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Residues in contact with ASP 8 (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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6A HIS* 3.8 13.1 - - + -
7A VAL* 1.3 75.5 - - - +
9A MET* 1.3 63.8 + - - +
103A ASP* 3.1 6.8 - - - +
104A GLU* 3.5 11.7 - - - +
138A ALA* 3.6 1.7 - - - -
139A SER* 2.8 34.6 + - - +
150A LYS* 4.2 7.1 - - - -
153A SER* 4.2 10.8 + - - +
154A ASP* 4.5 7.4 - - - +
157A LYS* 3.7 16.2 + - + +
875A 1FZ 3.9 1.8 + - - -
901A MG 2.2 31.9 - - - -
902A MG 2.8 20.9 - - - -
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Residues in contact with MET 9 (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 VAL* 5.1 2.7 - - - -
8A ASP* 1.3 77.1 + - - +
10A ASP* 1.3 60.7 + - - +
12A PHE* 3.5 35.0 - - + -
86A ILE* 3.7 29.6 - - + -
103A ASP* 2.9 25.5 + - + +
130A ILE* 3.8 23.8 - - + -
136A LEU* 3.9 27.1 - - + -
137A THR 3.2 24.0 - - - +
138A ALA* 3.8 14.8 - - - -
157A LYS* 3.4 0.7 + - - -
875A 1FZ 3.2 4.9 + - - -
901A MG 2.3 30.5 - - - -
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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