Contacts of the helix formed by residues 21 - 28 (chain H) 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 SER 21 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8H VAL* 3.9 10.8 + - - +
9H GLU 3.5 17.4 + - - -
10H SER* 3.5 12.6 + - - -
18H ASN* 3.1 19.1 + - - +
19H PHE 3.3 0.2 - - - -
20H LEU* 1.3 75.4 - - - +
22H LEU* 1.3 63.4 + - - +
23H ASP* 3.5 5.2 + - - +
24H ASP* 3.1 33.3 + - - +
25H ILE* 3.1 25.8 + - - +
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 3.7 42.4 - - + +
13G LEU* 4.1 17.7 - - + -
14G HIS* 4.5 15.0 - - - +
78G ALA* 4.4 19.5 - - + +
79G TYR* 4.8 1.8 - - - +
82G ASP* 3.8 30.5 - - + +
86G ARG* 4.4 4.7 - - - +
7H ARG* 3.1 32.1 - - - +
8H VAL 4.7 1.6 + - - -
20H LEU 3.4 4.8 + - - +
21H SER* 1.3 72.1 + - - +
23H ASP* 1.3 55.3 + - - +
25H ILE* 3.2 5.1 + - - +
26H LEU* 2.9 34.5 + - + +
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Residues in contact with ASP 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G HIS* 3.5 25.8 - - - -
7H ARG* 2.6 26.9 + - - -
8H VAL 4.8 0.5 - - - +
9H GLU* 5.1 2.6 - - - +
10H SER* 4.5 19.8 + - - -
21H SER* 3.5 7.8 + - - +
22H LEU* 1.3 76.4 - - - +
24H ASP* 1.3 58.6 + - - +
26H LEU* 3.0 11.3 + - - +
27H MET* 3.0 27.0 + - - +
115H HIS* 4.0 15.5 - - + +
170H GLU* 5.0 6.2 - - - +
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Residues in contact with ASP 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ARG* 3.7 6.3 - - - +
10H SER* 2.7 24.1 + - - -
11H GLY 3.0 13.6 + - - -
12H ALA* 3.3 13.0 - - + +
17H GLU* 3.2 27.1 - - + +
18H ASN 2.8 26.3 + - - -
21H SER* 3.1 15.8 + - - +
23H ASP* 1.3 77.6 - - - +
25H ILE* 1.3 53.7 + - - +
27H MET* 3.2 8.7 + - + +
28H SER* 2.6 37.6 + - - -
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Residues in contact with ILE 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G MET* 4.0 5.3 - - - +
10G ILE* 3.9 22.0 - - + -
71G ARG* 2.9 39.3 + - - +
74G ARG* 3.3 39.5 - - + +
75G CYS* 3.7 19.3 - - - -
78G ALA* 3.4 33.9 - - + -
19H PHE 3.8 2.2 - - - +
21H SER 3.1 14.8 + - - +
22H LEU* 3.2 8.0 + - - +
24H ASP* 1.3 76.7 - - - +
26H LEU* 1.3 63.1 + - - +
28H SER* 3.5 7.8 + - - -
29H HIS* 3.5 2.6 + - - +
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Residues in contact with LEU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G MET* 3.9 21.5 - - + +
10G ILE* 4.1 13.2 - - + -
11G ARG* 4.3 22.7 - - + +
14G HIS* 3.5 47.8 - - + +
22H LEU 2.9 19.1 + - - +
23H ASP* 3.0 11.6 + - - +
25H ILE* 1.3 78.7 - - - +
27H MET* 1.3 62.5 + - - +
29H HIS* 3.4 17.0 + - - +
30H GLU* 4.0 7.3 + - - +
115H HIS* 4.2 15.2 - - + +
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Residues in contact with MET 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ALA* 4.4 7.6 - - + -
17H GLU* 3.6 22.4 - - - +
23H ASP 3.0 8.0 + - - +
24H ASP* 3.7 13.7 - - - +
26H LEU* 1.3 72.1 - - - +
28H SER* 1.3 71.5 + - - +
29H HIS 3.0 7.4 + - - -
30H GLU* 3.1 23.3 + - - +
70H LEU* 4.5 4.9 - - + -
115H HIS* 3.3 43.0 + - + +
118H GLY* 4.1 4.5 - - - +
119H PHE* 3.7 35.0 - - - +
122H GLN* 3.5 32.1 - - + -
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Residues in contact with SER 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ARG* 3.4 22.9 - - - -
74G ARG* 3.7 0.6 + - - -
17H GLU* 2.6 40.3 + - - -
24H ASP 2.6 11.6 + - - -
25H ILE 3.8 0.7 - - - -
26H LEU 3.3 0.4 - - - -
27H MET* 1.3 82.2 - - - +
29H HIS* 1.3 56.7 + - - +
30H GLU 3.4 0.4 - - - -
70H LEU* 3.2 15.6 + - - -
71H TRP* 3.1 37.4 + - - -
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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