Contacts of the helix formed by residues 3 - 13 (chain Z) in PDB entry 2Q4G
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 SER 3 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z GLU* 1.3 77.3 - - - +
4Z ARG* 1.3 64.4 + - - +
5Z ALA* 3.6 7.7 + - - +
6Z LYS* 2.8 41.8 + - - +
7Z LYS* 3.0 20.4 + - - +
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Residues in contact with ARG 4 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436Y ILE 5.8 0.6 + - - -
437Y TYR* 4.0 17.8 - - - +
438Y TRP* 2.9 40.5 + - - +
439Y SER* 3.4 17.1 - - - +
440Y GLU* 3.5 5.1 - - - +
443Y GLU* 4.2 32.0 + - + +
2Z GLU 3.7 1.1 + - - +
3Z SER* 1.3 73.5 - - - +
5Z ALA* 1.3 61.0 + - - +
7Z LYS* 3.5 10.6 + - - +
8Z PHE* 3.2 21.8 + - - +
111Z GLU* 2.9 31.2 + - - +
118Z VAL* 3.8 33.3 + - + +
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Residues in contact with ALA 5 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z SER* 3.1 8.4 + - - +
4Z ARG* 1.3 79.6 - - - +
6Z LYS* 1.3 68.8 + - + +
8Z PHE* 3.3 6.4 + - - +
9Z GLN* 3.2 25.4 + - - +
116Z VAL* 4.0 24.5 - - + -
117Z PRO 4.0 11.1 - - - +
118Z VAL* 4.3 3.6 - - + +
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Residues in contact with LYS 6 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z GLU* 4.0 14.5 - - + +
3Z SER* 2.8 30.7 + - - +
5Z ALA* 1.3 77.9 - - + +
7Z LYS* 1.3 67.8 + - - +
9Z GLN* 3.0 26.5 + - - +
10Z ARG* 3.0 24.3 + - - +
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Residues in contact with LYS 7 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438Y TRP* 6.2 1.0 - - - -
443Y GLU* 5.8 2.7 + - - +
460Y SER* 3.0 38.4 + - - -
2Z GLU* 3.3 21.4 + - - +
3Z SER 3.0 12.3 + - - +
4Z ARG* 3.6 13.7 - - - +
6Z LYS* 1.3 76.2 - - - +
8Z PHE* 1.3 54.8 + - - +
10Z ARG* 3.3 14.9 + - - +
11Z GLN* 2.8 74.3 + - - +
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Residues in contact with PHE 8 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z ARG 3.2 8.1 + - - +
5Z ALA 3.4 10.8 - - - +
6Z LYS 3.2 0.2 - - - -
7Z LYS* 1.3 80.1 - - - +
9Z GLN* 1.3 60.0 + - + +
11Z GLN* 5.1 0.7 - - - -
12Z HIS* 2.8 59.2 + + + +
13Z MET* 3.5 21.7 + - + -
47Z VAL* 5.6 2.2 - - + -
51Z LEU* 5.5 3.8 - - + -
54Z VAL* 3.8 28.7 - - + -
108Z VAL* 4.1 10.5 - - + -
117Z PRO* 3.6 38.1 - - + +
118Z VAL* 4.2 4.7 - - - -
119Z HIS* 3.6 35.0 - - - -
120Z PHE* 4.0 8.5 - + + -
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Residues in contact with GLN 9 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Z ALA* 3.2 16.7 + - + +
6Z LYS* 3.0 31.0 + - - +
8Z PHE* 1.3 77.7 - - + +
10Z ARG* 1.3 61.9 + - - +
13Z MET* 2.6 54.1 + - + +
33Z ARG* 4.2 0.9 - - - -
51Z LEU* 2.9 40.1 - - + +
55Z GLN* 5.4 0.4 - - - +
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Residues in contact with ARG 10 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z GLU* 2.6 45.3 + - - +
6Z LYS 3.0 11.1 + - - +
7Z LYS* 3.7 16.7 - - - +
9Z GLN* 1.3 78.0 - - - +
11Z GLN* 1.3 79.1 + - - +
33Z ARG* 2.9 76.0 + - + +
34Z ASN* 3.8 28.0 + - - +
46Z PHE* 3.9 0.2 - - - -
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Residues in contact with GLN 11 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434Y TYR* 5.2 0.4 - - - -
460Y SER* 3.4 26.9 + - - -
7Z LYS* 2.8 52.7 + - - +
8Z PHE* 4.8 0.7 + - - -
10Z ARG* 1.3 92.6 - - - +
12Z HIS* 1.3 77.5 + - + +
35Z MET* 3.6 26.7 - - - +
41Z LYS* 3.8 14.1 - - - +
44Z ASN* 2.8 28.4 + - - -
46Z PHE* 3.1 8.7 - - - -
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Residues in contact with HIS 12 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435Y ASP* 4.7 12.2 + - - -
8Z PHE* 2.8 47.6 + + + +
11Z GLN* 1.3 91.5 + - + +
13Z MET* 1.3 59.4 + - - +
41Z LYS* 5.2 1.3 - - - -
44Z ASN* 2.9 26.2 + - - -
45Z THR 2.7 27.9 + - - +
46Z PHE* 3.3 4.2 - - - -
47Z VAL* 2.8 32.3 + - + +
119Z HIS* 5.4 1.5 + - - -
120Z PHE* 3.6 41.2 + + + +
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Residues in contact with MET 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z PHE* 3.8 25.1 - - + -
9Z GLN* 2.6 38.1 + - + +
12Z HIS* 1.3 76.2 - - - +
14Z ASP* 1.3 57.4 + - - +
15Z SER* 3.0 29.8 - - - +
33Z ARG* 2.7 34.0 + - - -
46Z PHE* 4.5 0.4 - - - -
47Z VAL* 4.4 8.1 - - - +
49Z GLU 3.3 13.9 - - - +
51Z LEU* 3.7 29.4 - - + -
54Z VAL* 3.6 25.8 - - + -
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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