Contacts of the helix formed by residues 235 - 239 (chain S) in PDB entry 2GLJ
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 ASP 235 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151S ILE* 3.8 18.9 - - + +
152S VAL 4.6 3.4 - - - +
153S LYS* 4.4 9.0 - - - +
154S LYS* 4.1 8.3 + - - +
230S ASP 4.4 1.2 - - - +
231S ILE* 3.1 17.0 - - + +
232S SER* 2.8 32.4 + - - +
234S GLU* 1.3 88.2 - - - +
236S PHE* 1.3 58.4 + - - +
237S VAL 2.9 2.1 - - - +
238S SER* 2.8 30.3 + - - +
239S ALA* 3.0 3.5 + - - +
393T ARG* 2.8 34.8 + - - +
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Residues in contact with PHE 236 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S LEU* 4.7 15.7 - - + -
114S LYS 4.5 6.5 - - - +
115S GLN* 3.6 18.4 - - - +
116S ASN* 5.1 0.7 - - - -
117S PRO* 3.9 28.0 - - + -
118S LEU* 4.4 17.9 - - + -
127S LEU* 5.5 5.2 - - + -
151S ILE* 4.7 15.5 - - + -
222S MET* 4.2 22.0 - - + -
225S LEU* 3.7 26.0 - - + -
231S ILE* 4.3 5.2 - - + -
232S SER 4.3 4.0 - - - -
233S GLU* 3.0 26.0 - - + +
234S GLU 2.5 12.4 + - - -
235S ASP* 1.3 72.3 - - + +
237S VAL* 1.3 63.6 + - - +
239S ALA* 2.9 29.8 + - + +
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Residues in contact with VAL 237 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115S GLN* 2.9 47.4 + - - +
116S ASN* 4.0 2.7 - - - +
234S GLU* 4.3 15.0 - - + -
235S ASP 4.6 4.5 - - - +
236S PHE* 1.3 79.6 - - - +
238S SER* 1.3 55.6 + - - +
239S ALA 3.6 1.7 + - - +
7T LYS* 5.9 0.9 - - + -
9T TYR* 3.5 24.0 - - - +
369T PHE* 6.0 3.8 - - + -
371T LYS* 4.7 3.5 - - - +
389T ILE* 3.8 26.0 - - + +
393T ARG* 4.7 6.1 - - + -
403T TRP* 3.9 31.6 - - + -
405T THR* 4.6 4.7 - - + -
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Residues in contact with SER 238 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152S VAL* 2.6 42.3 + - - +
235S ASP 2.8 6.5 + - - -
237S VAL* 1.3 77.8 - - - +
239S ALA* 1.3 57.0 + - - +
386T PRO* 3.5 12.1 - - - +
389T ILE* 3.9 8.5 - - - -
390T ALA* 3.7 30.0 - - - +
393T ARG* 2.5 34.8 + - - -
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Residues in contact with ALA 239 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150S VAL 3.4 7.2 - - - +
151S ILE* 3.8 20.2 - - + +
235S ASP 3.4 9.0 - - - +
236S PHE* 2.9 33.5 + - + +
237S VAL 3.3 0.4 - - - -
238S SER* 1.3 79.2 - - - +
240S GLU* 1.3 72.2 + - - +
241S LEU* 3.9 4.0 + - - +
371T LYS* 4.0 12.1 - - - +
386T PRO* 4.0 8.2 - - - +
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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