Contacts of the helix formed by residues 5 - 13 (chain F) in PDB entry 2I2X
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 THR 5 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411E LYS* 4.0 4.5 - - - +
3F ASP 4.1 0.8 + - - +
4F PHE* 1.3 88.2 - - - +
6F GLU* 1.3 65.3 + - - +
7F ALA* 3.4 8.3 + - - +
8F SER* 3.0 32.7 + - - +
9F LEU* 3.5 7.3 + - - +
345G GLU 5.9 1.1 - - - +
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Residues in contact with GLU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E GLY 5.5 1.0 - - - +
411E LYS* 3.8 27.0 - - + +
5F THR* 1.3 76.4 - - - +
7F ALA* 1.3 62.7 + - - +
9F LEU* 3.4 4.8 + - - +
10F LYS* 3.4 20.3 + - - +
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Residues in contact with ALA 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F THR* 3.4 6.4 + - - +
6F GLU* 1.3 76.1 - - - +
8F SER* 1.3 64.8 + - - +
10F LYS* 3.4 8.4 + - - +
11F LYS* 3.2 25.9 + - + +
345G GLU* 5.1 0.4 - - - -
8M SER* 6.2 4.0 - - - -
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Residues in contact with SER 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F PHE* 3.6 23.3 - - - -
5F THR* 3.0 28.2 + - - +
7F ALA* 1.3 76.4 - - - +
9F LEU* 1.3 56.1 + - - +
11F LYS* 3.2 4.9 + - - +
12F VAL* 3.0 33.2 + - - +
345G GLU* 3.1 43.1 + - - +
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E TYR* 3.7 39.3 - - + -
411E LYS* 3.8 35.4 - - + +
413E GLU* 6.2 1.3 - - + -
4F PHE* 4.1 17.7 - - + +
5F THR 3.5 8.6 + - - +
6F GLU* 3.4 9.8 + - - +
7F ALA 3.3 0.8 - - - -
8F SER* 1.3 75.7 - - - +
10F LYS* 1.3 66.8 + - - +
12F VAL* 3.0 11.3 + - - +
13F LEU* 3.1 37.0 + - + +
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Residues in contact with LYS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLU 3.4 9.9 + - - +
7F ALA* 3.7 11.2 - - - +
8F SER 3.4 0.2 - - - -
9F LEU* 1.3 77.9 - - - +
11F LYS* 1.3 61.7 + - - +
13F LEU 3.4 14.8 - - - +
14F THR* 4.6 5.0 + - - -
79G PRO* 5.5 1.6 - - - +
7M THR* 4.0 29.5 + - - -
8M SER* 4.6 10.1 + - - -
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Residues in contact with LYS 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA* 3.2 13.1 + - + +
8F SER 3.2 10.2 + - - +
9F LEU 3.1 0.6 - - - -
10F LYS* 1.3 78.1 - - - +
12F VAL* 1.3 61.7 + - + +
36G ALA 4.8 3.9 + - - -
37G GLY* 3.8 21.0 + - - -
38G TYR* 4.4 26.0 - - + +
79G PRO* 3.7 15.0 - - - +
341G ASN* 5.4 4.2 + - - +
345G GLU* 3.0 37.3 + - - +
8M SER* 6.1 4.9 - - - +
9M MET 5.9 3.6 - - - +
10M ALA 5.7 1.6 + - - -
12M ALA* 6.1 2.2 - - - +
23M LYS* 5.2 6.2 - - - +
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E SER 4.4 10.8 - - - +
363E ARG* 4.9 3.2 + - - +
4F PHE* 3.8 26.5 - - + -
8F SER 3.0 15.5 + - - +
9F LEU 3.0 5.3 + - - +
11F LYS* 1.3 79.7 - - + +
13F LEU* 1.3 64.7 + - + +
78G PHE* 5.9 0.9 - - - -
79G PRO* 3.5 16.3 - - - +
338G ALA* 4.6 18.0 - - + +
341G ASN* 4.2 22.7 + - + +
342G THR* 4.0 16.2 - - - +
345G GLU* 3.7 22.2 - - + -
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358E LEU 5.8 0.2 - - - +
359E SER 3.6 24.2 - - - +
362E TYR* 3.9 18.4 - - + +
363E ARG* 3.7 46.9 - - + +
4F PHE* 5.8 1.3 - - + -
9F LEU* 3.1 39.6 + - + +
10F LYS* 3.4 11.6 - - - +
11F LYS 3.6 0.4 - - - -
12F VAL* 1.3 81.2 - - + +
14F THR* 1.3 68.6 + - - +
15F ARG* 4.2 14.4 - - + +
77G GLY 3.5 15.0 - - - +
79G PRO* 4.3 3.4 - - - -
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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