Contacts of the helix formed by residues 254 - 263 (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 PRO 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 5.9 1.1 - - - +
76A TYR* 3.3 39.7 - - + +
77A ASP* 5.2 3.1 - - - +
80A SER* 3.3 27.8 - - - +
252A PRO 3.8 2.0 - - - +
253A PRO* 1.3 83.0 - - + +
255A PRO* 1.3 65.6 - - + +
256A ILE* 3.8 11.4 - - + -
257A ILE* 2.8 30.6 + - + +
258A ASP* 3.0 10.6 + - - +
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Residues in contact with PRO 255 (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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253A PRO 3.5 4.6 - - - +
254A PRO* 1.3 84.4 - - + +
256A ILE* 1.3 68.2 + - + +
258A ASP* 3.3 7.9 + - + +
259A LYS* 2.9 27.0 + - - +
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Residues in contact with ILE 256 (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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80A SER* 3.3 32.3 - - - +
83A LEU* 4.2 24.9 - - + -
87A ARG* 5.0 10.1 - - - +
254A PRO* 3.8 13.0 - - + -
255A PRO* 1.3 83.8 - - + +
257A ILE* 1.3 62.4 + - + +
259A LYS* 3.6 9.5 - - - +
260A ILE* 3.4 30.5 + - - +
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Residues in contact with ILE 257 (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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76A TYR* 4.6 20.4 - - + -
79A LEU* 4.2 23.1 - - + -
80A SER* 4.3 10.3 - - - +
83A LEU* 3.8 29.2 - - + -
112A PHE* 3.8 25.8 - - + -
242A ILE* 4.6 20.1 - - + +
253A PRO* 5.1 0.9 - - + -
254A PRO* 2.8 13.7 + - + +
256A ILE* 1.3 85.5 - - + +
258A ASP* 1.3 60.5 + - - +
259A LYS 3.3 1.1 - - - -
260A ILE* 3.6 10.9 + - + +
261A PHE* 2.9 26.2 + - - +
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Residues in contact with ASP 258 (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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242A ILE* 6.1 1.0 - - - +
246A LYS* 2.7 44.9 + - - +
253A PRO* 3.9 19.7 - - + +
254A PRO 3.0 10.8 + - - +
255A PRO* 3.7 11.2 - - + +
257A ILE* 1.3 77.9 - - - +
259A LYS* 1.3 53.1 + - - +
261A PHE* 3.1 8.4 + - - +
262A MET* 2.8 49.8 + - - +
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Residues in contact with LYS 259 (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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109A GLU* 3.2 34.3 - - - +
255A PRO 2.9 17.6 + - - +
256A ILE* 3.6 8.5 - - - +
258A ASP* 1.3 75.6 - - - +
260A ILE* 1.3 56.8 + - - +
262A MET* 2.9 25.2 + - + +
263A ASP* 3.1 19.2 + - - +
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Residues in contact with ILE 260 (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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83A LEU* 4.0 24.5 - - + -
109A GLU* 3.5 56.3 - - + +
112A PHE* 4.3 24.7 - - + -
113A LEU* 5.4 11.0 - - + -
239A LEU* 5.4 3.8 - - + +
242A ILE* 6.2 2.7 - - + -
256A ILE 3.4 16.8 + - - +
257A ILE* 3.7 14.1 - - + +
258A ASP 3.4 0.2 - - - -
259A LYS* 1.3 77.6 - - - +
261A PHE* 1.3 68.1 + - - +
262A MET 3.2 0.3 + - - -
263A ASP* 3.2 25.3 + - - +
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Residues in contact with PHE 261 (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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239A LEU* 4.0 32.0 - - + +
242A ILE* 3.6 29.8 - - + -
243A PHE* 3.8 47.1 - + + -
246A LYS* 4.2 21.5 - - + -
257A ILE 2.9 16.2 + - - +
258A ASP* 3.1 11.4 + - - +
260A ILE* 1.3 79.5 - - - +
262A MET* 1.3 84.8 + - - +
263A ASP 3.4 2.6 + - - +
264A THR* 3.6 24.7 + - - -
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Residues in contact with MET 262 (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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246A LYS* 3.1 30.3 - - - +
258A ASP* 2.8 34.3 + - - +
259A LYS* 2.9 12.3 + - + +
261A PHE* 1.3 88.6 - - - +
263A ASP* 1.3 61.5 + - - +
264A THR* 2.8 21.4 + - - +
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Residues in contact with ASP 263 (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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106A LEU* 5.6 5.5 - - - +
109A GLU* 4.7 18.4 - - - +
110A SER* 5.7 2.3 + - - -
239A LEU* 5.9 3.3 - - - +
259A LYS* 3.1 18.4 + - - +
260A ILE* 3.2 15.5 + - - +
261A PHE 3.8 2.3 - - - +
262A MET* 1.3 72.3 - - - +
264A THR* 1.3 59.3 + - - +
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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