Contacts of the helix formed by residues 252 - 261 (chain A) in PDB entry 1GWX
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 ILE 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASP* 1.3 76.8 - - - +
253A GLU* 1.3 58.9 + - - +
255A LEU* 3.2 9.3 - - - +
256A TRP* 2.9 28.5 + - + +
271A LEU* 5.9 6.7 - - + -
277A ILE* 4.5 35.2 - - + -
352A PHE* 4.8 6.1 - - + -
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Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASP* 3.2 7.5 - - + +
252A ILE* 1.3 76.1 - - - +
254A THR* 1.3 52.5 + - + +
255A LEU 3.0 4.7 - - - -
256A TRP* 2.9 20.3 + - + +
257A GLN* 2.7 58.7 + - + +
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A VAL 3.6 17.5 - - - +
249A ILE* 3.9 5.7 - - - +
250A HIS* 2.9 34.0 + - + +
251A ASP* 2.9 30.5 + - - +
253A GLU* 1.3 77.8 - - + +
255A LEU* 1.3 51.8 + - - +
257A GLN* 3.7 19.6 - - - +
258A ALA* 2.7 32.4 + - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 433 5.9 5.6 - - + -
249A ILE* 3.7 17.9 - - + -
251A ASP 3.4 8.2 + - - +
252A ILE 3.2 9.8 + - - +
254A THR* 1.3 79.2 + - - +
256A TRP* 1.3 61.8 + - - +
258A ALA* 3.1 4.1 + - + +
259A GLU* 2.9 50.7 + - + +
264A TRP* 5.2 2.0 - - + -
277A ILE* 3.0 36.6 - - + -
280A HIS* 3.9 18.6 - - + -
281A VAL* 4.5 5.6 - - + -
352A PHE* 3.5 18.6 - - + -
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Residues in contact with TRP 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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252A ILE* 2.9 14.4 + - + +
253A GLU* 2.9 22.3 + - - +
255A LEU* 1.3 72.7 - - - +
257A GLN* 1.3 87.5 + - + +
259A GLU* 3.3 16.5 + - + +
260A LYS* 3.0 56.3 + - + +
268A VAL* 6.5 0.2 - - + -
269A ASN 5.7 4.5 - - - -
271A LEU* 6.6 0.2 - - + -
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Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLU* 2.7 45.7 + - - +
254A THR* 3.7 19.2 - - - +
256A TRP* 1.3 86.0 - - + +
258A ALA* 1.3 53.1 + - - +
260A LYS* 2.6 33.1 + - - +
261A GLY* 2.9 12.8 + - - -
262A LEU* 5.0 0.4 - - - -
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Residues in contact with ALA 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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249A ILE* 3.8 25.6 - - + -
254A THR 2.7 23.3 + - - +
255A LEU* 3.1 8.1 - - - +
257A GLN* 1.3 72.3 - - - +
259A GLU* 1.3 61.1 + - - +
260A LYS 2.8 0.2 + - - -
262A LEU* 2.7 54.5 + - + +
263A VAL 3.2 2.6 + - - -
264A TRP* 4.0 10.3 - - + -
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Residues in contact with GLU 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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255A LEU* 2.9 34.5 + - + +
256A TRP* 3.5 14.6 - - + +
257A GLN 3.1 0.2 + - - -
258A ALA* 1.3 71.7 - - - +
260A LYS* 1.3 61.1 + - + +
263A VAL* 2.9 28.9 - - - +
264A TRP* 2.9 18.9 - - - +
268A VAL* 3.2 31.4 - - + +
280A HIS* 3.3 11.2 + - + +
284A ARG* 2.3 49.2 + - - -
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TRP* 3.0 62.0 - - + +
257A GLN* 2.6 14.2 + - - +
259A GLU* 1.3 75.3 - - + +
261A GLY* 1.3 66.8 + - - +
263A VAL* 3.2 18.8 + - - +
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Residues in contact with GLY 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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247A PHE* 5.0 6.7 - - - -
257A GLN 2.9 15.5 + - - -
258A ALA 3.8 0.4 - - - -
260A LYS* 1.3 75.4 - - - +
262A LEU* 1.3 64.3 + - - +
263A VAL* 4.5 3.8 - - - +
212B LYS* 5.6 3.0 + - - -
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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