Contacts of the helix formed by residues 235 - 239 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F ARG* 2.7 42.1 + - - +
151H ILE* 3.7 18.3 - - + +
152H VAL 4.5 4.0 - - - +
153H LYS* 4.5 8.4 - - - +
154H LYS* 4.1 8.3 + - - +
230H ASP 4.4 1.7 - - - +
231H ILE* 3.1 16.4 - - + +
232H SER* 2.7 36.2 + - - +
234H GLU* 1.3 85.3 - - - +
236H PHE* 1.3 58.9 + - + +
237H VAL 2.9 2.4 - - - +
238H SER* 2.8 31.0 + - - +
239H ALA* 3.0 3.3 + - - +
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Residues in contact with PHE 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H LEU* 4.7 14.8 - - + -
114H LYS 4.5 3.7 - - - +
115H GLN* 3.6 20.9 - - - +
116H ASN* 5.1 1.1 - - - -
117H PRO* 3.9 28.3 - - + -
118H LEU* 4.4 18.2 - - + -
127H LEU* 5.5 5.4 - - + -
151H ILE* 4.7 10.1 - - + -
222H MET* 4.2 21.3 - - + -
225H LEU* 3.7 27.4 - - + -
231H ILE* 4.3 10.3 - - + -
232H SER 4.1 4.0 - - - -
233H GLU* 3.0 26.2 - - + +
234H GLU 2.5 12.7 + - - -
235H ASP* 1.3 71.6 - - + +
237H VAL* 1.3 63.9 + - - +
239H ALA* 2.9 29.1 + - + +
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Residues in contact with VAL 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LYS* 6.2 0.4 - - + -
9F TYR* 4.0 7.6 - - - +
369F PHE* 5.9 4.3 - - + -
371F LYS* 4.6 4.2 - - - +
389F ILE* 3.6 26.6 - - + +
393F ARG* 4.6 7.9 - - + -
403F TRP* 3.9 36.8 - - + -
405F THR* 4.6 5.4 - - + -
115H GLN* 2.9 47.1 + - - +
116H ASN* 4.0 12.3 - - - +
234H GLU* 4.3 13.9 - - + -
235H ASP 4.6 2.5 - - - +
236H PHE* 1.3 79.9 - - + +
238H SER* 1.3 56.5 + - - +
239H ALA 3.6 1.6 + - - -
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Residues in contact with SER 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F PRO* 3.2 19.1 - - - +
389F ILE* 3.7 11.0 - - - -
390F ALA* 3.5 33.2 - - - +
393F ARG* 2.6 29.5 + - - -
152H VAL* 2.6 36.6 + - - +
235H ASP 2.8 6.0 + - - -
237H VAL* 1.3 77.7 - - - +
239H ALA* 1.3 57.2 + - - +
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Residues in contact with ALA 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371F LYS* 3.9 12.6 - - - +
386F PRO* 3.8 8.4 - - - +
150H VAL 3.4 6.7 - - - +
151H ILE* 3.8 20.4 - - + +
235H ASP 3.4 9.0 - - - +
236H PHE* 2.9 33.0 + - + +
237H VAL 3.3 0.6 - - - -
238H SER* 1.3 79.4 - - - +
240H GLU* 1.3 71.3 + - - +
241H LEU* 3.9 4.0 + - - +
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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
------------------------------------------------------------
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