Contacts of the helix formed by residues 24 - 31 (chain B) in PDB entry 1WQ2
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 PHE 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PHE 3.9 0.4 + - - -
23B TYR* 1.3 71.6 - - - +
25B ASN* 1.3 81.4 + - - +
27B PHE* 3.2 21.6 + - - +
28B THR* 3.3 28.0 + - + +
36B GLN* 3.4 36.6 - - + -
39B VAL* 4.1 8.3 - - + -
40B LYS* 3.4 52.9 - - + -
43B LEU* 3.8 13.7 - - + -
60B THR* 4.3 2.5 - - - +
61B THR* 3.2 27.8 + - - +
63B TYR* 4.0 6.2 - + + -
203B DOD 3.5 6.7 + - - +
280B DOD 4.5 6.1 - - - -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.0 3.8 - - + -
24B PHE* 1.3 89.8 - - - +
26B ASP* 1.3 60.2 + - - +
27B PHE 3.1 1.8 - - - -
28B THR* 3.2 11.6 + - - +
29B ASP* 2.9 33.8 + - - +
36B GLN* 3.8 13.8 + - - +
203B DOD 2.9 23.0 + - - +
280B DOD 3.3 14.9 + - - -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 5.7 3.7 - - + -
19B LYS* 4.9 1.9 + - - -
22B PHE* 3.6 28.8 - - + +
23B TYR* 2.9 48.2 + - - +
25B ASN* 1.3 77.3 - - - +
27B PHE* 1.3 59.6 + - + +
29B ASP* 3.4 20.8 - - - +
30B LEU* 3.2 23.4 - - - +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.9 28.5 - - + -
11B PHE* 4.6 9.4 - + - -
12B LEU* 4.1 30.3 - - + -
22B PHE* 4.1 16.8 - - + -
23B TYR 3.3 24.0 - - - -
24B PHE* 3.2 7.8 + - - +
25B ASN 3.1 0.2 - - - -
26B ASP* 1.3 76.0 - - - +
28B THR* 1.3 60.9 + - - +
29B ASP 3.0 1.6 - - - -
30B LEU* 3.0 27.6 + - + +
31B PHE* 3.0 25.3 - + + -
39B VAL* 4.0 7.9 - - + -
43B LEU* 3.7 32.1 - - + -
63B TYR* 3.8 32.3 - + + -
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.3 40.3 + - + +
25B ASN* 3.2 18.7 + - - +
27B PHE* 1.3 76.5 - - - +
29B ASP* 1.3 54.2 + - - +
30B LEU 3.3 0.2 - - - -
31B PHE 3.2 6.3 - - - +
36B GLN* 3.2 34.7 + - - +
39B VAL* 3.8 19.3 - - + -
236B DOD 2.9 19.4 + - - +
244B DOD 2.6 23.6 + - - -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 2.9 25.7 + - - +
26B ASP* 3.4 22.7 - - - +
28B THR* 1.3 81.8 + - - +
30B LEU* 1.3 62.3 + - + +
31B PHE 3.6 0.3 + - - -
32B PRO* 3.9 6.9 - - - +
244B DOD 3.6 11.5 + - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 6.1 0.9 - - - -
11B PHE* 3.7 55.6 - - + -
26B ASP 3.2 17.0 - - - +
27B PHE* 3.0 20.9 + - + +
29B ASP* 1.3 79.9 - - + +
31B PHE* 1.3 72.3 + - + +
32B PRO* 3.1 9.5 - - - +
281B DOD 2.6 27.8 + - - +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 3.9 21.8 - - + -
7B LYS* 4.2 10.1 - - - -
8B VAL* 3.7 40.8 - - + -
27B PHE* 3.0 33.3 + + + +
28B THR 3.3 3.4 - - - -
30B LEU* 1.3 98.8 - - + +
32B PRO* 1.3 58.9 - - - +
33B ASP 3.2 3.6 + - - -
34B MET* 3.3 9.6 + - - +
39B VAL* 4.2 20.0 - - + -
42B ILE* 5.0 6.5 - - + -
210B DOD 3.5 9.9 - - - +
236B DOD 2.4 25.8 + - - -
281B DOD 4.6 7.9 - - - -
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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