Contacts of the helix formed by residues 2 - 11 (chain A) in PDB entry 2Q9Q
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 ASP 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 75.6 - - - +
3A ALA* 1.3 64.5 + - - +
4A ALA* 3.5 15.7 - - - +
5A GLU* 3.0 42.2 + - - +
6A VAL* 3.3 10.7 + - - +
154A ASN* 3.9 4.5 - - - -
141C LYS* 6.0 1.4 - - - +
142C PRO* 5.0 4.3 - - - +
185D ASP* 3.7 20.3 - - - +
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Residues in contact with ALA 3 (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 ASP* 1.3 72.0 - - - +
4A ALA* 1.3 61.3 + - - +
6A VAL* 3.3 10.8 + - - +
7A GLU* 3.2 21.8 + - - +
151A MET* 3.3 31.1 - - + +
154A ASN* 4.3 1.9 + - - -
155A THR* 5.6 0.9 - - - +
185D ASP* 2.9 24.8 + - - +
186D PHE* 4.2 5.6 - - + -
189D TRP* 3.7 25.4 - - + -
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Residues in contact with ALA 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 ASP* 3.1 18.5 + - - +
3A ALA* 1.3 77.7 - - - +
5A GLU* 1.3 58.6 + - - +
7A GLU 3.5 1.0 + - - -
8A PHE* 3.1 21.0 + - - +
142C PRO* 4.1 13.7 - - + +
144C LYS* 3.2 34.1 + - - +
185D ASP* 5.2 0.6 + - - -
189D TRP* 4.1 15.3 - - + +
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Residues in contact with GLU 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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1A MET* 3.1 23.4 - - + +
2A ASP* 3.0 41.5 + - - +
4A ALA* 1.3 75.1 - - - +
6A VAL* 1.3 65.2 + - - +
8A PHE* 3.2 21.1 - - - +
9A LEU* 3.3 8.7 + - - +
34B TRP* 3.6 12.9 - - + -
38B LYS* 2.9 36.8 + - - -
87B TYR* 2.7 20.3 + - + +
91B SER* 3.7 3.5 + - - -
142C PRO* 3.6 18.8 - - + -
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Residues in contact with VAL 6 (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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1A MET* 4.1 18.6 - - - -
2A ASP 3.6 13.0 - - - +
3A ALA* 3.3 7.6 + - - +
5A GLU* 1.3 77.2 - - - +
7A GLU* 1.3 62.9 + - - +
9A LEU* 3.2 7.5 + - - +
10A ALA* 3.1 18.2 + - - +
91A TYR* 3.8 3.1 - - + -
94A GLU* 2.9 29.6 - - - +
150A LEU* 3.8 21.8 - - + -
151A MET* 3.8 29.8 - - - +
154A ASN* 3.9 22.7 - - + +
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Residues in contact with GLU 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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3A ALA 3.2 4.4 + - - +
4A ALA 3.6 6.1 - - - +
5A GLU 3.2 0.2 - - - -
6A VAL* 1.3 78.6 - - - +
8A PHE* 1.3 59.3 + - - +
10A ALA* 3.0 8.3 + - - +
11A GLU* 2.9 35.7 + - - +
94A GLU* 4.0 6.9 - - + +
97A LYS* 2.8 30.0 + - - -
98A LEU* 3.2 32.0 - - + +
144C LYS* 2.8 30.5 + - - +
189D TRP* 3.0 40.4 + - + +
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Residues in contact with PHE 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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4A ALA 3.1 14.5 + - - +
5A GLU* 3.2 13.9 - - - +
7A GLU* 1.3 78.0 - - - +
9A LEU* 1.3 64.3 + - + +
11A GLU* 3.5 16.1 + - - +
31B GLU* 4.3 11.2 - - - -
34B TRP* 4.0 22.4 - + - -
84B ARG* 3.0 97.8 + - + -
87B TYR* 4.5 5.4 - + - -
88B VAL* 3.5 23.3 - - + -
142C PRO* 4.4 10.3 - - + -
143C PRO* 4.1 22.0 - - + -
144C LYS* 4.8 1.6 - - - +
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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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1A MET* 3.9 22.2 - - + -
5A GLU 3.3 6.5 + - - +
6A VAL 3.2 8.5 + - - +
8A PHE* 1.3 81.4 - - + +
10A ALA* 1.3 66.6 + - - +
12A LYS* 3.2 39.0 + - + +
13A GLU* 4.2 1.4 + - - +
91A TYR* 3.7 21.7 + - + +
150A LEU* 4.3 10.3 - - + -
31B GLU* 4.3 14.6 - - + +
34B TRP* 4.0 18.4 - - + -
35B MET* 4.0 23.6 - - + -
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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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6A VAL 3.1 7.7 + - - +
7A GLU* 3.0 10.4 + - + +
9A LEU* 1.3 73.7 - - - +
11A GLU* 1.3 54.8 + - - +
12A LYS 3.0 5.2 - - - -
13A GLU* 2.9 32.4 + - - +
46A LEU* 4.1 7.9 - - + +
91A TYR* 3.3 38.3 - - + -
94A GLU* 3.5 25.6 - - + -
95A LEU* 4.4 3.3 - - + +
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Residues in contact with GLU 11 (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 GLU* 2.9 34.5 + - - +
8A PHE* 3.5 18.8 - - - +
9A LEU 3.2 0.2 - - - -
10A ALA* 1.3 75.6 - - - +
12A LYS* 1.3 56.9 + - - +
13A GLU 3.3 0.2 - - - -
46A LEU* 3.0 31.8 + - + -
47A TRP* 3.1 34.3 - - + +
50A ILE* 5.9 0.4 - - + -
98A LEU* 4.0 22.2 - - + +
84B ARG* 2.9 25.9 + - - +
143C PRO 4.6 7.1 - - - +
144C LYS* 4.0 12.3 + - - +
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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