Contacts of the helix formed by residues 24 - 33 (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 THR 24 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22Z SER* 2.6 26.2 + - - +
23Z SER* 1.3 79.5 - - - +
25Z TYR* 1.3 68.4 + - - +
26Z CYS 3.6 0.2 - - - -
27Z ASN* 3.6 10.8 + - - +
28Z GLN* 3.2 25.1 + - - +
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Residues in contact with TYR 25 (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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14Z ASP* 2.6 29.1 + - - +
17Z SER* 4.3 7.4 - - - -
18Z SER 5.2 0.4 - - - -
21Z SER* 3.3 22.4 - - - +
22Z SER* 2.6 23.9 + - - +
24Z THR* 1.3 75.6 + - - +
26Z CYS* 1.3 63.8 + - - +
28Z GLN* 3.0 16.0 + - - +
29Z MET* 2.7 56.3 + - + +
46Z PHE* 3.5 28.1 - + - +
48Z HIS* 3.8 15.7 + - - -
82Z THR* 3.7 33.0 - - + -
99Z THR* 4.5 0.9 - - + -
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Residues in contact with CYS 26 (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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24Z THR 3.6 0.2 - - - -
25Z TYR* 1.3 77.6 - - - +
27Z ASN* 1.3 68.6 + - - +
29Z MET* 4.3 1.8 - - - +
30Z MET* 3.0 29.5 + - - +
82Z THR* 4.0 4.7 - - - -
83Z ASP 3.6 4.0 - - - -
84Z CYS* 2.0 56.3 - - + -
97Z TYR* 3.6 18.8 - - + -
99Z THR* 2.9 39.4 + - - +
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Residues in contact with ASN 27 (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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150Y TYR* 6.2 2.4 - - - -
23Z SER 3.6 20.5 + - - -
24Z THR* 3.6 8.2 + - - +
25Z TYR 3.3 0.6 - - - -
26Z CYS* 1.3 76.6 - - - +
28Z GLN* 1.3 63.7 + - - +
30Z MET* 4.8 0.5 - - - +
31Z ARG* 3.7 19.9 + - - +
95Z CYS 4.9 5.9 - - - +
96Z ALA* 3.2 13.2 - - - +
97Z TYR* 2.5 46.2 + - - +
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Residues in contact with GLN 28 (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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24Z THR* 3.2 15.3 + - - +
25Z TYR* 3.0 18.7 + - - +
26Z CYS 3.0 0.4 - - - -
27Z ASN* 1.3 82.7 - - - +
29Z MET* 1.3 77.4 + - + +
31Z ARG* 3.8 2.2 - - - +
32Z ARG* 2.8 69.5 + - - +
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Residues in contact with MET 29 (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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14Z ASP* 3.0 41.5 - - + +
17Z SER* 5.8 0.2 - - - -
25Z TYR* 2.7 49.9 + - + +
26Z CYS* 4.2 1.6 - - - +
28Z GLN* 1.3 83.1 - - - +
30Z MET* 1.3 57.4 + - - +
32Z ARG* 3.3 8.2 + - - +
33Z ARG* 2.9 66.8 + - + +
46Z PHE* 3.7 27.8 - - + -
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Residues in contact with MET 30 (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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26Z CYS 3.0 19.5 + - - +
27Z ASN 4.8 0.4 - - - +
29Z MET* 1.3 77.3 - - - +
31Z ARG* 1.3 59.4 + - - +
33Z ARG 3.8 0.7 + - - -
34Z ASN 3.6 1.7 + - - -
35Z MET* 2.9 43.7 + - + +
36Z THR* 4.2 2.9 - - + -
41Z LYS* 3.3 46.0 - - + +
44Z ASN* 3.6 34.3 - - + -
46Z PHE* 3.8 6.3 - - - -
84Z CYS* 4.0 14.4 - - + -
97Z TYR* 3.6 44.2 - - + +
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Residues in contact with ARG 31 (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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10Y GLN* 2.7 43.5 + - - +
11Y CYS* 3.7 22.7 - - - -
33Y ARG* 3.5 4.7 - - - +
35Y ASP* 2.6 42.5 + - - -
36Y ASP* 4.8 3.0 - - - +
63Y ARG* 5.3 9.4 - - - +
27Z ASN 3.7 16.9 + - - +
28Z GLN* 3.4 3.2 + - - +
29Z MET 3.2 0.6 - - - -
30Z MET* 1.3 79.9 - - - +
32Z ARG* 1.3 62.4 + - + +
34Z ASN* 3.2 18.4 + - - -
36Z THR* 3.7 26.6 + - + +
37Z GLN* 4.2 10.1 + - + +
93Z PRO 5.6 3.4 + - - -
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Residues in contact with ARG 32 (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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1W SER 4.8 1.0 + - - -
11Y CYS* 4.0 13.5 - - + +
36Y ASP* 2.7 43.8 + - - +
64Y SER* 6.2 1.0 - - - -
28Z GLN* 2.8 61.4 + - - +
29Z MET* 3.9 8.6 - - - +
31Z ARG* 1.3 76.1 - - + +
33Z ARG* 1.3 64.6 + - + +
34Z ASN* 3.1 13.3 + - - -
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Residues in contact with ARG 33 (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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9Z GLN 3.5 5.7 + - - -
10Z ARG* 2.9 65.6 + - + +
13Z MET 2.7 30.5 + - - -
14Z ASP* 3.4 23.6 + - - +
29Z MET* 2.9 43.7 + - + +
32Z ARG* 1.3 80.1 - - + +
34Z ASN* 1.3 71.7 + - - +
35Z MET* 3.6 16.0 - - + +
46Z PHE* 3.9 5.6 - - + -
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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