Contacts of the helix formed by residues 235 - 239 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393M ARG* 2.7 41.7 + - - +
151U ILE* 3.8 18.2 - - + +
152U VAL 4.5 4.3 - - - +
153U LYS* 4.4 7.9 - - - +
154U LYS* 4.2 8.0 + - - +
230U ASP 4.4 1.6 - - - +
231U ILE* 3.1 16.4 - - + +
232U SER* 2.8 33.2 + - - +
234U GLU* 1.3 88.0 - - - +
236U PHE* 1.3 57.7 + - + +
237U VAL 2.9 2.6 - - - +
238U SER* 2.8 22.7 + - - +
239U ALA* 3.1 11.1 + - - +
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Residues in contact with PHE 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113U LEU* 4.7 14.8 - - + -
114U LYS 4.5 3.2 - - - +
115U GLN* 3.6 21.1 - - - +
116U ASN* 5.1 0.9 - - - -
117U PRO* 3.9 28.0 - - + -
118U LEU* 4.4 19.1 - - + -
127U LEU* 5.5 5.4 - - + -
151U ILE* 4.7 9.9 - - + -
222U MET* 4.2 21.3 - - + -
225U LEU* 3.7 27.1 - - + -
231U ILE* 4.4 9.9 - - + -
232U SER 4.1 3.8 - - - -
233U GLU* 3.0 26.0 - - + +
234U GLU 2.4 17.8 + - - -
235U ASP* 1.3 72.0 - - - +
237U VAL* 1.3 64.8 + - - +
239U ALA* 2.9 30.2 + - + +
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Residues in contact with VAL 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369M PHE* 6.0 4.0 - - + -
371M LYS* 4.7 3.6 - - - +
389M ILE* 3.7 25.9 - - + +
393M ARG* 4.6 7.9 - - + -
403M TRP* 3.9 37.9 - - + -
405M THR* 4.7 7.9 - - + -
115U GLN* 2.9 46.2 + - - +
116U ASN* 4.0 11.9 - - - +
233U GLU 5.7 0.2 - - - +
234U GLU* 4.3 14.1 - - + -
235U ASP 4.6 2.0 - - - +
236U PHE* 1.3 80.1 - - - +
238U SER* 1.3 56.2 + - - +
239U ALA 3.6 1.2 + - - -
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Residues in contact with SER 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M PRO* 3.3 19.1 - - - +
389M ILE* 3.8 10.5 - - - -
390M ALA* 3.5 31.7 - - - +
393M ARG* 2.6 30.6 + - - -
152U VAL* 2.6 37.1 + - - +
235U ASP 2.8 6.3 + - - -
237U VAL* 1.3 77.7 - - - +
239U ALA* 1.3 57.1 + - - +
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Residues in contact with ALA 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371M LYS* 4.0 12.1 - - - +
386M PRO* 3.8 8.1 - - - +
150U VAL 3.4 7.0 - - - +
151U ILE* 3.8 20.2 - - + +
235U ASP 3.4 8.7 - - - +
236U PHE* 2.9 34.2 + - + +
237U VAL 3.3 0.6 - - - -
238U SER* 1.3 79.4 - - - +
240U GLU* 1.3 70.4 + - - +
241U LEU* 3.9 4.1 + - - +
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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