Contacts of the helix formed by residues 235 - 239 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393V ARG* 2.8 33.1 + - - +
151X ILE* 3.8 19.6 - - + +
152X VAL 4.6 4.3 - - - +
153X LYS* 4.4 8.5 - - - +
154X LYS* 4.1 9.7 + - - +
230X ASP 4.4 1.6 - - - +
231X ILE* 3.1 16.6 - - + +
232X SER* 2.8 32.4 + - - +
234X GLU* 1.3 88.0 - - - +
236X PHE* 1.3 58.6 + - + +
237X VAL 2.9 2.6 - - - +
238X SER* 2.8 30.3 + - - +
239X ALA* 3.1 3.5 + - - +
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Residues in contact with PHE 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113X LEU* 4.7 14.4 - - + -
114X LYS 4.5 6.9 - - - +
115X GLN* 3.6 17.7 - - - +
116X ASN* 5.1 0.4 - - - -
117X PRO* 3.9 28.7 - - + -
118X LEU* 4.4 17.0 - - + -
127X LEU* 5.5 5.2 - - + -
151X ILE* 4.7 15.5 - - + -
222X MET* 4.2 22.7 - - + -
225X LEU* 3.7 26.9 - - + -
231X ILE* 4.3 4.9 - - + -
232X SER 4.2 3.6 - - - -
233X GLU* 3.0 24.7 - - + +
234X GLU 2.4 21.9 + - - -
235X ASP* 1.3 68.4 - - + +
237X VAL* 1.3 64.3 + - + +
239X ALA* 3.0 29.6 + - + +
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Residues in contact with VAL 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V LYS* 5.7 0.2 - - - +
9V TYR* 4.5 5.2 - - - +
369V PHE* 6.1 3.4 - - + -
371V LYS* 4.8 2.4 - - - +
389V ILE* 3.7 27.3 - - + +
393V ARG* 4.4 8.7 - - + -
403V TRP* 3.9 38.8 - - + -
405V THR* 4.8 6.3 - - + -
115X GLN* 2.9 47.7 + - - +
116X ASN* 4.0 11.4 - - - +
233X GLU 5.7 0.2 - - - +
234X GLU* 4.3 14.8 - - + -
235X ASP 4.6 2.0 - - - +
236X PHE* 1.3 81.1 - - - +
238X SER* 1.3 56.0 + - - +
239X ALA 3.6 2.9 + - - +
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Residues in contact with SER 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386V PRO* 3.4 12.3 - - - +
389V ILE* 3.9 6.7 - - - -
390V ALA* 3.5 33.4 - - - +
393V ARG* 2.6 24.5 + - - +
152X VAL* 2.5 50.9 + - - +
235X ASP 2.8 6.6 + - - -
237X VAL* 1.3 78.6 - - - +
239X ALA* 1.3 57.5 + - - +
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Residues in contact with ALA 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371V LYS* 4.1 12.0 - - - +
386V PRO* 3.8 9.5 - - - +
150X VAL 3.4 7.6 - - - +
151X ILE* 3.8 20.2 - - + +
235X ASP 3.4 8.7 - - - +
236X PHE* 3.0 33.8 + - + +
237X VAL 3.3 1.3 - - - +
238X SER* 1.3 78.0 - - - +
240X GLU* 1.3 70.0 + - - +
241X LEU* 3.9 3.5 + - - +
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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