Contacts of the helix formed by residues 24 - 35 (chain G) in PDB entry 2QJK
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 PRO 24 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G HIS* 3.9 34.5 - - + +
22G ARG 4.1 1.3 - - - -
23G LEU* 1.3 82.2 - - + +
25G ILE* 1.3 64.2 + - - +
26G VAL* 3.1 3.8 - - + +
27G ALA* 3.0 30.3 + - + +
28G LEU* 3.1 8.0 + - - +
214J TRP* 4.1 16.3 - - + +
218J SER* 3.9 17.5 - - - +
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Residues in contact with ILE 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 4.8 9.2 - - + -
23G LEU* 2.6 38.3 + - + +
24G PRO* 1.3 73.6 - - - +
26G VAL* 1.3 71.5 + - + +
28G LEU* 3.6 5.0 + - + +
29G ALA* 3.2 20.3 + - - +
505G ANJ 5.3 12.5 - - + +
211J ILE* 4.7 18.6 - - + -
214J TRP* 3.4 34.4 - - + -
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G TYR* 3.5 33.9 - - + +
16G GLU* 5.6 6.5 - - + -
19G LEU* 3.7 31.9 - - + -
20G HIS* 6.6 0.2 - - + -
24G PRO* 3.1 1.2 - - + -
25G ILE* 1.3 79.2 - - + +
27G ALA* 1.3 66.4 + - - +
29G ALA* 3.4 7.9 + - + +
30G TYR* 3.0 21.1 + - + +
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G TYR* 3.7 33.8 - - + -
20G HIS* 4.2 8.1 - - + +
24G PRO* 3.0 24.3 + - + +
26G VAL* 1.3 78.8 - - - +
28G LEU* 1.3 64.0 + - - +
30G TYR* 2.8 20.6 + - - +
31G ASP* 2.9 18.1 + - - +
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Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G PRO 3.1 6.7 + - - +
25G ILE* 3.6 11.0 - - + +
27G ALA* 1.3 79.1 - - - +
29G ALA* 1.3 64.9 + - - +
30G TYR 3.0 0.5 + - - -
31G ASP* 3.1 11.3 + - + +
32G THR* 2.9 32.0 + - - +
505G ANJ 5.9 6.3 - - + -
214J TRP* 3.7 33.7 - - + -
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 3.2 10.9 + - + +
26G VAL* 3.5 13.2 - - + +
27G ALA 3.3 0.2 - - - -
28G LEU* 1.3 78.8 - - - +
30G TYR* 1.3 57.6 + - - +
32G THR* 3.3 8.3 + - - +
33G ILE* 2.9 32.3 + - - +
505G ANJ 3.7 31.4 - - + +
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Residues in contact with TYR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G HIS* 5.8 0.2 - - - -
7G ASP* 3.0 31.8 + - - +
8G HIS* 3.5 7.4 + - - -
9G TYR* 3.3 46.4 - + + -
26G VAL* 3.0 12.6 + - + +
27G ALA 2.8 11.1 + - - +
29G ALA* 1.3 76.0 - - - +
31G ASP* 1.3 77.6 + - - +
33G ILE* 2.7 13.7 + - + +
34G MET* 2.7 73.1 + - + +
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Residues in contact with ASP 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G HIS* 4.8 9.6 - - + +
8G HIS* 4.3 9.0 - - - +
9G TYR* 4.2 7.0 + - - +
27G ALA* 2.9 25.1 + - - +
28G LEU* 3.7 10.3 + - + +
30G TYR* 1.3 97.6 - - - +
32G THR* 1.3 60.1 + - - +
34G MET* 4.1 2.7 - - - +
35G ILE* 3.7 20.3 + - - +
217G HIS* 4.3 3.7 + - - -
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Residues in contact with THR 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 2.9 22.1 + - - +
29G ALA* 3.4 12.1 - - - +
31G ASP* 1.3 79.3 - - - +
33G ILE* 1.3 67.4 + - + +
34G MET 3.7 0.5 + - - -
35G ILE* 4.1 6.6 - - - +
213G ILE* 5.7 2.5 - - + -
217G HIS* 3.2 33.5 + - + -
244G PHE* 4.6 4.0 - - - -
505G ANJ 3.9 41.0 - - + +
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Residues in contact with ILE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ALA 2.9 13.4 + - - +
30G TYR* 2.7 22.1 + - + +
32G THR* 1.3 79.9 - - + +
34G MET* 1.3 70.4 + - + +
35G ILE 3.6 0.2 - - - -
244G PHE* 3.4 17.6 - - + +
245G TRP* 3.2 33.1 + - + +
249G ILE* 3.3 33.7 - - + -
505G ANJ 5.0 11.0 - - + +
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Residues in contact with MET 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASP* 5.6 2.9 - - - +
30G TYR* 2.7 67.0 + - + +
31G ASP* 4.9 1.6 - - - -
33G ILE* 1.3 88.9 - - + +
35G ILE* 1.3 71.5 + - - +
36G PRO* 3.3 3.5 - - - +
243G PRO* 3.8 26.4 - - + +
244G PHE* 3.6 7.5 + - - +
245G TRP* 3.6 42.4 - - + +
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Residues in contact with ILE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE* 5.2 7.9 - - + -
31G ASP* 3.7 16.2 + - - +
32G THR 4.1 11.0 - - - +
34G MET* 1.3 80.7 - - - +
36G PRO* 1.3 84.8 - - + +
37G THR* 3.2 12.0 + - - +
217G HIS* 4.2 43.1 - - + +
220G GLY* 4.8 11.2 - - - -
221G ASN* 4.6 17.0 - - - +
244G PHE* 3.0 29.2 + - + -
505G ANJ 6.1 1.1 - - + -
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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