Contacts of the helix formed by residues 35 - 49 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A MET* 1.3 75.4 - - - +
36A GLN* 1.3 64.8 + - - +
37A ARG* 3.0 5.4 - - - +
38A GLU* 3.0 17.9 + - - +
39A VAL* 3.1 15.6 + - - +
272A DOD 4.4 0.4 - - - -
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 20.1 - - + -
25A ASN* 2.8 17.0 + - - +
28A THR* 3.1 35.8 + - - +
34A MET 5.2 0.2 - - - +
35A LYS* 1.3 71.9 - - - +
37A ARG* 1.3 61.1 + - - +
39A VAL 3.7 0.2 + - - -
40A LYS* 3.2 18.9 + - - +
217A DOD 4.2 3.8 + - - -
227A DOD 1.9 33.1 + - - -
272A DOD 3.8 6.4 + - - -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 4.8 1.6 - - - -
36A GLN* 1.3 78.4 - - - +
38A GLU* 1.3 64.9 + - - +
40A LYS* 3.4 6.2 + - - +
41A LYS* 3.2 43.1 + - - +
286A DOD 3.5 23.5 + - - -
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET* 6.0 0.4 - - - +
35A LYS* 3.0 14.8 + - - +
37A ARG* 1.3 80.8 - - - +
39A VAL* 1.3 59.9 + - - +
41A LYS* 3.3 10.2 + - - +
42A ILE* 3.1 30.1 + - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.1 1.1 - - + -
27A PHE* 4.2 7.4 - - + +
28A THR* 4.0 33.7 - - + +
31A PHE* 4.1 26.2 - - + -
34A MET* 4.7 4.7 - - - -
35A LYS 3.1 16.0 + - - +
36A GLN 4.2 0.4 - - - +
38A GLU* 1.3 73.2 - - - +
40A LYS* 1.3 65.4 + - - +
42A ILE* 3.3 12.7 + - + +
43A LEU* 3.0 40.3 + - + +
272A DOD 3.8 17.7 - - - +
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.5 30.5 - - + -
36A GLN 3.2 19.0 + - - +
37A ARG* 3.8 6.1 - - - +
38A GLU 3.4 0.2 - - - -
39A VAL* 1.3 76.0 - - - +
41A LYS* 1.3 59.5 + - + +
43A LEU* 3.5 1.6 + - - +
44A THR* 2.8 37.6 + - - +
54A TYR* 5.3 0.6 - - - -
61A THR* 3.3 23.6 + - - +
63A TYR* 2.8 28.7 + - - +
228A DOD 3.5 12.9 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.2 29.4 + - + +
38A GLU* 3.5 11.7 - - - +
39A VAL 3.2 0.2 - - - -
40A LYS* 1.3 75.2 - - + +
42A ILE* 1.3 66.0 + - + +
44A THR* 3.4 6.0 + - - -
45A ALA* 3.0 23.9 + - - +
286A DOD 3.2 26.5 + - - -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ALA* 3.7 29.6 - - + +
5A LYS* 3.8 35.7 - - + +
8A VAL* 4.6 11.2 - - + -
31A PHE* 5.2 10.3 - - + -
38A GLU 3.1 18.7 + - - +
39A VAL* 3.3 12.8 + - + +
41A LYS* 1.3 76.9 - - + +
43A LEU* 1.3 63.9 + - + +
45A ALA* 3.3 8.1 + - - +
46A LEU* 3.3 22.4 + - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.9 34.1 - - + -
24A PHE* 3.7 30.7 - - + -
27A PHE* 4.0 31.6 - - + -
39A VAL* 3.0 22.0 + - + +
40A LYS 4.0 2.7 - - - +
42A ILE* 1.3 74.1 - - + +
44A THR* 1.3 66.4 + - - +
46A LEU* 3.2 7.2 + - + +
47A VAL* 3.1 27.7 + - - +
52A LEU* 4.1 11.5 - - + +
63A TYR* 3.6 30.1 - - + +
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 2.8 30.5 + - - +
41A LYS* 3.8 7.0 - - - -
42A ILE 3.3 0.2 - - - -
43A LEU* 1.3 76.9 - - - +
45A ALA* 1.3 56.6 + - - +
47A VAL* 3.2 6.6 + - + +
48A ASN* 2.8 47.1 + - - +
54A TYR* 6.4 0.9 - - + -
228A DOD 2.9 21.1 + - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.0 18.6 - - - +
41A LYS 3.0 16.8 + - - +
42A ILE* 3.6 6.3 - - - +
44A THR* 1.3 76.2 - - - +
46A LEU* 1.3 57.8 + - - +
48A ASN* 3.6 9.4 - - - +
49A ASP* 3.2 31.9 + - - +
260A DOD 3.3 2.2 + - - -
270A DOD 4.2 3.6 - - - +
290A DOD 3.5 18.2 + - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.1 31.2 - - + +
8A VAL* 4.0 19.1 - - + -
9A VAL* 4.5 7.6 - - + -
42A ILE* 3.3 15.2 + - + +
43A LEU* 3.2 9.6 + - - +
44A THR 3.2 0.6 - - - -
45A ALA* 1.3 75.3 - - - +
47A VAL* 1.3 61.5 + - - +
48A ASN 3.3 0.2 - - - -
49A ASP* 3.6 1.4 + - - +
50A GLU 3.1 4.5 + - - -
51A VAL* 2.9 54.6 + - + +
52A LEU* 3.2 33.6 + - + -
260A DOD 3.3 18.4 - - - +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU 3.1 15.6 + - - +
44A THR* 3.2 11.2 + - + +
46A LEU* 1.3 76.2 - - - +
48A ASN* 1.3 66.7 + - - +
50A GLU* 3.1 11.1 + - - +
52A LEU* 3.6 22.0 - - + +
54A TYR* 3.7 29.2 - - + -
63A TYR* 4.2 11.7 - - + -
206A DOD 3.6 22.7 - - - +
229A DOD 3.4 14.7 + - - +
258A DOD 4.5 5.4 - - - +
276A DOD 3.7 12.8 - - - +
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 2.8 37.8 + - - +
45A ALA* 3.6 7.2 - - - +
47A VAL* 1.3 77.7 - - - +
49A ASP* 1.3 63.4 + - - +
50A GLU* 3.1 1.8 + - - +
258A DOD 3.3 22.4 + - - -
270A DOD 3.3 22.5 + - - +
295A DOD 2.9 23.5 + - - -
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 3.2 13.8 + - - +
46A LEU 4.0 3.8 - - - +
47A VAL 3.2 0.2 - - - -
48A ASN* 1.3 79.5 - - - +
50A GLU* 1.3 69.3 + - - +
51A VAL* 3.5 9.8 + - + -
230A DOD 3.0 26.0 + - - +
260A DOD 2.6 23.3 + - - +
290A DOD 3.3 16.7 + - - -
49B ASP* 6.3 0.2 - - + -
51B VAL* 3.8 6.2 - - - +
259B DOD 3.5 20.7 + - - +
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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