Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 3Q1H
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 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A ALA 3.4 5.1 + - - +
1A MET* 1.3 72.7 - - - +
3A ILE* 1.3 58.8 + - - +
4A SER* 3.4 21.8 - - - +
90A GLU* 2.9 36.6 + - + +
91A GLU* 3.2 18.1 - - + +
92A VAL 2.9 26.5 + - - -
109A ASN* 3.5 12.1 - - - +
110A ARG* 3.7 40.4 - - + +
158A GLU* 5.2 0.4 - - - +
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Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.4 20.8 + - + +
2A ILE* 1.3 75.9 - - - +
4A SER* 1.3 61.0 + - - +
83A LEU* 3.9 26.7 - - + -
92A VAL* 3.9 21.5 - - + -
94A VAL* 4.3 7.0 - - + -
104A PHE* 4.2 20.9 - - + -
107A ARG* 3.5 26.0 - - + +
108A ALA* 3.4 19.7 - - + +
109A ASN* 2.9 36.7 + - - +
110A ARG 3.2 5.8 + - - +
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Residues in contact with SER 4 (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* 3.4 15.6 - - - +
3A ILE* 1.3 72.2 - - - +
5A LEU* 1.3 60.3 + - - +
6A ILE* 3.7 0.5 + - - +
91A GLU* 2.7 28.8 + - - -
92A VAL 3.0 12.5 + - - +
93A MET* 3.6 4.4 - - - -
94A VAL* 2.8 33.6 + - - +
110A ARG* 3.2 14.8 - - - +
112A TYR* 3.5 20.9 - - - -
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Residues in contact with LEU 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 SER* 1.3 73.7 - - - +
6A ILE* 1.3 58.5 + - - +
7A ALA 4.2 0.4 - - - -
94A VAL* 3.7 20.9 - - + -
101A TYR* 4.1 26.7 - - + +
104A PHE* 3.9 22.2 - - + -
105A LEU* 4.0 25.6 - - + -
108A ALA* 3.8 25.1 - - + -
110A ARG 2.9 9.5 + - - +
111A MET* 3.2 14.6 - - + +
112A TYR 2.7 27.7 + - - +
113A LEU* 4.7 1.1 - - - +
126A PHE* 4.0 24.5 - - + -
127A PRO* 5.2 0.4 - - + -
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 3.7 0.6 + - - +
5A LEU* 1.3 74.3 - - - +
7A ALA* 1.3 58.6 + - - +
21A MET* 3.5 31.4 - - + -
22A PRO* 3.5 21.4 - - + +
23A TRP* 3.5 39.9 - - + -
93A MET* 4.5 8.1 - - + -
94A VAL 3.0 21.5 + - - +
95A MET* 3.8 16.9 - - + -
101A TYR* 2.6 25.2 + - - -
112A TYR* 3.4 25.1 - - + +
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Residues in contact with ALA 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 LEU 4.2 0.4 - - - -
6A ILE* 1.3 74.8 - - - +
8A ALA* 1.3 61.8 + - - +
9A LEU* 4.1 9.8 + - + +
14A VAL* 5.1 2.2 - - + -
22A PRO* 3.5 11.0 - - - +
101A TYR* 3.3 26.7 - - + +
112A TYR 3.1 7.3 + - - +
113A LEU* 3.4 10.5 - - + +
114A THR 3.0 22.3 + - - -
126A PHE* 3.8 23.8 - - + -
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Residues in contact with ALA 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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7A ALA* 1.3 74.5 - - - +
9A LEU* 1.3 65.0 + - - +
14A VAL* 3.7 3.3 - - - +
15A ILE* 2.8 32.5 + - + +
17A MET* 3.5 43.7 - - + -
22A PRO* 3.5 12.1 + - - +
114A THR* 3.2 12.8 - - - +
116A ILE* 4.3 6.7 - - + -
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Residues in contact with LEU 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 ALA* 4.1 9.2 - - + +
8A ALA* 1.3 85.0 - - - +
10A ALA* 1.3 59.8 + - - +
11A ALA 3.4 19.2 + - - +
12A ASP* 4.6 2.2 - - + +
13A ARG 3.3 11.4 - - - +
14A VAL* 4.0 8.7 - - + -
15A ILE* 3.5 6.4 - - - +
113A LEU* 4.2 23.1 - - + -
114A THR 2.8 11.8 + - - +
115A HIS* 3.5 19.6 - - + +
116A ILE 2.8 30.1 + - - +
117A ASP* 4.4 0.3 + - - -
126A PHE* 3.6 50.5 - - + -
129A TYR* 6.2 0.4 - - + -
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Residues in contact with ALA 10 (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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9A LEU* 1.3 72.0 - - - +
11A ALA* 1.3 69.4 + - - +
13A ARG* 2.9 25.5 + - - +
15A ILE* 3.7 9.5 - - + +
116A ILE 3.7 12.8 - - - +
117A ASP* 4.5 4.9 - - - +
119A GLU 3.6 24.2 - - - +
121A GLY* 3.7 19.3 - - - +
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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