Contacts of the helix formed by residues 32 - 43 (chain A) in PDB entry 2QW4
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 ASN 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 1.3 62.5 + - - +
34A LEU* 3.4 32.3 - - - +
35A THR* 3.3 36.3 + - - -
36A SER* 3.6 7.7 + - - -
203A CYS* 5.1 2.4 - - - -
206A GLU* 6.2 2.4 - - - +
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Residues in contact with LEU 33 (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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32A ASN* 1.3 71.1 - - - +
34A LEU* 1.3 60.3 + - - +
35A THR 3.0 2.2 - - - -
36A SER* 2.6 28.1 + - - -
37A LEU* 2.9 30.2 + - + -
93A ILE* 5.8 0.4 - - + -
94A PRO* 3.8 34.8 - - + +
196A LEU* 5.5 3.4 - - + -
199A ARG* 4.0 42.2 - - + +
200A ILE* 4.1 10.5 - - + +
203A CYS* 4.1 10.3 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.4 19.4 - - - +
33A LEU* 1.3 77.6 - - - +
35A THR* 1.3 57.0 + - - +
37A LEU* 3.3 6.8 + - + +
38A VAL* 3.0 29.1 + - + +
170A PRO* 4.1 31.9 - - + +
174A CYS* 3.2 34.1 - - - -
203A CYS* 3.6 21.6 - - - +
206A GLU* 6.3 1.8 - - + -
207A HIS* 4.1 22.7 - - + +
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Residues in contact with THR 35 (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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32A ASN* 3.3 26.7 + - - +
33A LEU 2.9 1.0 + - - -
34A LEU* 1.3 75.0 - - - +
36A SER* 1.3 69.9 + - - +
37A LEU 3.0 1.1 - - - -
38A VAL* 2.7 18.9 + - + +
39A ARG* 2.8 50.0 + - + +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN 3.6 9.4 + - - -
33A LEU* 2.6 16.0 + - - -
35A THR* 1.3 77.3 - - - +
37A LEU* 1.3 60.2 + - - +
39A ARG* 3.9 5.9 - - - +
40A ALA* 2.9 26.4 + - - +
92A LYS 4.2 3.2 - - - +
94A PRO* 3.2 37.0 - - - +
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Residues in contact with LEU 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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33A LEU* 2.9 37.0 + - + +
34A LEU* 3.5 9.2 - - + +
35A THR 3.0 0.2 - - - -
36A SER* 1.3 80.3 - - - +
38A VAL* 1.3 62.9 + - - +
40A ALA* 3.3 3.7 + - - +
41A HIS* 3.0 18.5 + - - +
89A TRP* 5.1 1.4 + - - -
93A ILE* 3.8 37.9 - - + -
94A PRO* 4.6 1.6 - - + -
173A ALA* 3.7 22.6 - - + +
174A CYS* 3.9 25.8 - - - -
177A ALA* 4.2 11.9 - - + -
200A ILE* 4.0 19.7 - - + -
203A CYS* 4.4 5.6 - - - -
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Residues in contact with VAL 38 (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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34A LEU* 3.0 22.5 + - + +
35A THR* 2.7 16.1 + - + +
37A LEU* 1.3 68.5 - - - +
39A ARG* 1.3 69.0 + - + +
41A HIS* 3.2 2.5 + - - +
42A LEU* 2.8 44.6 + - + +
169A VAL* 4.4 10.5 - - + -
170A PRO* 3.8 37.5 - - + -
173A ALA* 4.2 9.0 - - + -
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Residues in contact with ARG 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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35A THR* 2.8 45.1 + - + +
36A SER* 3.9 5.8 - - - +
38A VAL* 1.3 74.1 - - + +
40A ALA* 1.3 55.1 + - - +
42A LEU* 4.5 4.0 - - - -
43A ASP* 2.5 60.9 + - - +
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Residues in contact with ALA 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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36A SER 2.9 19.2 + - - +
37A LEU* 3.6 6.1 - - - +
39A ARG* 1.3 77.3 - - - +
41A HIS* 1.3 63.3 + - - +
43A ASP* 3.4 4.6 + - - +
44A SER* 3.4 14.9 + - - -
89A TRP* 3.3 25.7 - - + +
92A LYS* 3.7 40.7 - - + +
93A ILE* 4.5 4.7 - - + -
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Residues in contact with HIS 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 LEU 3.0 12.9 + - - +
38A VAL 3.6 6.3 - - - +
40A ALA* 1.3 77.9 - - - +
42A LEU* 1.3 76.7 + - + +
44A SER* 3.2 14.1 + - - -
45A GLY* 3.4 9.0 + - - -
89A TRP* 3.7 14.4 + - - +
119A ARG* 4.4 15.1 + - + -
122A TYR* 4.6 12.7 - + - -
169A VAL* 4.1 26.6 - - + +
172A PHE* 3.5 38.3 - + - -
173A ALA* 3.9 17.4 - - + -
176A SER* 4.9 1.6 + - - -
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Residues in contact with LEU 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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38A VAL* 2.8 37.6 + - + +
39A ARG* 3.7 4.3 - - - +
41A HIS* 1.3 92.9 - - + +
43A ASP* 1.3 60.4 + - - +
44A SER 3.0 5.3 + - - -
45A GLY 3.8 12.0 + - - +
47A SER* 5.8 2.8 - - - -
169A VAL* 4.6 11.4 - - + -
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Residues in contact with ASP 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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39A ARG* 2.5 55.6 + - - +
40A ALA* 3.4 4.4 + - - +
41A HIS 3.3 0.2 - - - -
42A LEU* 1.3 75.3 - - - +
44A SER* 1.3 58.2 + - - +
45A GLY 4.8 0.9 - - - -
92A LYS* 4.5 27.0 + - + +
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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