Contacts of the helix formed by residues 35 - 49 (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 LYS 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP 3.9 0.8 + - - -
34B MET* 1.3 74.9 - - - +
36B GLN* 1.3 66.4 + - - +
37B ARG* 3.1 3.8 - - - +
38B GLU 3.1 3.8 + - - +
39B VAL* 3.0 22.5 + - - +
200B SO4 3.8 14.6 - - - -
211B DOD 2.6 22.1 + - - -
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Residues in contact with GLN 36 (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* 3.4 21.5 - - + -
25B ASN* 3.8 15.4 + - - +
28B THR* 3.2 40.0 + - - +
34B MET 3.9 0.8 + - - -
35B LYS* 1.3 71.3 - - - +
37B ARG* 1.3 58.0 + - + +
39B VAL* 3.4 5.2 + - - +
40B LYS* 3.0 25.1 + - - +
200B SO4 3.0 26.2 + - - +
236B DOD 3.9 5.5 - - - -
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.1 0.8 - - - +
36B GLN* 1.3 79.1 - - + +
38B GLU* 1.3 56.6 + - - +
40B LYS* 3.5 6.5 + - - +
41B LYS* 2.9 24.1 + - - -
200B SO4 2.8 39.4 + - - +
237B DOD 4.5 9.6 - - - +
268B DOD 4.1 6.3 + - - -
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 5.7 0.2 - - - +
34B MET* 5.1 2.7 - - - -
35B LYS* 3.1 7.5 + - - +
37B ARG* 1.3 76.2 - - - +
39B VAL* 1.3 64.6 - - + +
41B LYS* 4.3 3.9 - - - +
42B ILE* 3.1 40.5 + - + +
211B DOD 3.5 25.6 - - - +
237B DOD 3.6 20.3 + - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 4.1 1.6 - - + -
27B PHE* 4.0 14.1 - - + +
28B THR* 3.8 29.4 - - + +
31B PHE* 4.2 27.4 - - + -
34B MET* 4.6 5.8 - - - -
35B LYS 3.0 21.0 + - - +
36B GLN 3.8 4.5 - - - +
38B GLU* 1.3 73.9 - - - +
40B LYS* 1.3 65.7 + - - +
42B ILE* 3.2 15.7 - - + +
43B LEU* 3.2 40.7 + - + +
236B DOD 4.4 5.2 - - - +
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 29.0 - - + -
36B GLN 3.0 17.0 + - - +
37B ARG* 3.7 7.2 - - - +
39B VAL* 1.3 76.5 - - - +
41B LYS* 1.3 58.1 + - - +
43B LEU* 3.5 1.0 + - - +
44B THR* 2.9 45.0 + - - +
54B TYR* 4.9 2.2 + - - -
61B THR* 3.2 26.9 + - - +
63B TYR* 3.0 27.2 + - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG 2.9 15.5 + - - -
38B GLU* 3.4 8.3 + - - +
39B VAL 3.2 0.2 - - - -
40B LYS* 1.3 78.2 - - - +
42B ILE* 1.3 61.0 + - - +
44B THR* 3.4 3.6 + - - -
45B ALA* 3.1 20.1 + - - +
254B DOD 3.4 11.4 + - - -
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Residues in contact with ILE 42 (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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2B GLU* 4.6 6.7 - - - +
4B ALA* 3.8 37.7 - - + +
5B LYS* 4.2 22.8 - - + +
8B VAL* 4.0 16.6 - - + -
31B PHE* 5.0 7.4 - - + -
38B GLU* 3.1 28.0 + - + +
39B VAL* 3.2 26.5 - - + +
41B LYS* 1.3 75.0 - - - +
43B LEU* 1.3 63.0 + - + +
45B ALA* 3.3 8.2 + - - +
46B LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.0 22.2 - - + -
24B PHE* 3.8 23.1 - - + -
27B PHE* 3.7 37.7 - - + -
39B VAL* 3.2 24.8 + - + +
40B LYS 3.9 3.1 - - - +
42B ILE* 1.3 80.3 - - + +
44B THR* 1.3 64.4 + - - +
46B LEU* 3.4 5.5 + - + +
47B VAL* 3.1 29.0 + - - +
52B LEU* 3.7 24.5 - - + +
63B TYR* 3.8 23.4 - - + +
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Residues in contact with THR 44 (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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40B LYS* 2.9 37.9 + - - +
41B LYS* 3.8 5.4 - - - -
43B LEU* 1.3 75.6 - - - +
45B ALA* 1.3 58.6 + - - +
47B VAL* 3.3 9.5 + - + +
48B ASN* 2.9 40.5 + - - +
63B TYR* 4.6 4.0 + - - -
254B DOD 4.2 6.5 - - - +
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Residues in contact with ALA 45 (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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5B LYS* 4.0 24.7 - - - +
41B LYS 3.1 14.2 + - - +
42B ILE* 3.5 8.7 - - - +
43B LEU 3.3 0.2 - - - -
44B THR* 1.3 76.0 - - - +
46B LEU* 1.3 58.8 + - - +
48B ASN* 3.1 9.3 + - - +
49B ASP* 3.0 34.8 + - - +
238B DOD 3.8 2.7 - - - +
254B DOD 3.7 12.5 + - - +
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Residues in contact with LEU 46 (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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5B LYS* 4.0 30.7 - - + +
8B VAL* 3.8 37.7 - - + -
9B VAL* 4.7 6.3 - - + -
42B ILE* 2.9 22.3 + - + +
43B LEU* 3.8 2.0 - - + +
44B THR 3.3 0.2 - - - -
45B ALA* 1.3 77.1 - - - +
47B VAL* 1.3 58.9 + - - +
49B ASP* 3.5 2.2 + - - +
50B GLU 3.3 2.9 + - - -
51B VAL* 3.0 51.1 + - + +
52B LEU* 3.3 26.0 + - + -
238B DOD 3.7 15.5 - - - +
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Residues in contact with VAL 47 (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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43B LEU 3.1 19.1 + - - +
44B THR* 3.5 11.4 - - + +
45B ALA 3.1 0.2 - - - -
46B LEU* 1.3 75.6 - - - +
48B ASN* 1.3 67.2 + - - +
50B GLU* 3.1 9.4 + - - -
52B LEU* 3.6 20.2 - - + +
54B TYR* 3.9 26.9 - - + -
63B TYR* 3.8 27.1 - - + -
212B DOD 4.2 3.8 - - - +
239B DOD 3.6 6.1 + - - -
240B DOD 3.4 20.4 + - - +
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Residues in contact with ASN 48 (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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44B THR* 2.9 33.7 + - - +
45B ALA* 3.1 12.9 + - - +
47B VAL* 1.3 81.9 - - - +
49B ASP* 1.3 59.3 + - - +
50B GLU* 3.1 9.6 + - - +
254B DOD 4.3 6.5 + - - -
297B DOD 3.4 12.1 + - - -
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Residues in contact with ASP 49 (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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49A ASP* 6.3 0.2 - - + -
51A VAL* 3.6 17.7 - - - +
230A DOD 3.9 15.7 + - - +
5B LYS* 4.9 0.5 + - - -
45B ALA* 3.0 14.2 + - - +
46B LEU 3.5 4.2 + - - +
47B VAL 3.2 0.2 - - - -
48B ASN* 1.3 77.7 - - - +
50B GLU* 1.3 69.2 + - - +
51B VAL* 3.3 4.0 + - + -
238B DOD 2.7 24.8 + - - +
259B DOD 3.0 24.9 + - - +
297B DOD 3.6 16.3 + - - -
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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