Contacts of the helix formed by residues 235 - 239 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ARG* 2.7 41.0 + - - +
151I ILE* 3.8 17.9 - - + +
152I VAL 4.5 4.7 - - - +
153I LYS* 4.4 9.5 - - - +
154I LYS* 4.1 8.7 + - - +
230I ASP 4.4 0.7 - - - +
231I ILE* 3.1 16.5 - - + +
232I SER* 2.8 34.3 + - - +
234I GLU* 1.3 87.6 - - - +
236I PHE* 1.3 57.8 + - - +
237I VAL 2.9 2.3 - - - +
238I SER* 2.8 30.8 + - - +
239I ALA* 3.1 3.1 + - - +
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Residues in contact with PHE 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LEU* 4.7 14.8 - - + -
114I LYS 4.5 6.7 - - - +
115I GLN* 3.6 18.0 - - - +
116I ASN* 5.1 0.4 - - - -
117I PRO* 3.9 28.9 - - + -
118I LEU* 4.4 17.0 - - + -
127I LEU* 5.5 5.2 - - + -
151I ILE* 4.7 9.6 - - + -
222I MET* 4.2 22.0 - - + -
225I LEU* 3.7 26.9 - - + -
231I ILE* 4.3 10.3 - - + -
232I SER 4.1 3.8 - - - -
233I GLU* 3.0 26.9 - - + +
234I GLU 2.4 17.4 + - - -
235I ASP* 1.3 72.1 - - + +
237I VAL* 1.3 64.0 + - + +
239I ALA* 2.9 30.5 + - + +
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Residues in contact with VAL 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 5.8 0.4 - - + -
9A TYR* 3.8 22.7 - - - +
369A PHE* 6.0 3.4 - - + -
371A LYS* 4.8 1.9 - - - +
389A ILE* 3.7 26.2 - - + +
393A ARG* 4.5 8.3 - - + -
403A TRP* 3.8 35.2 - - + -
405A THR* 4.7 4.7 - - + -
115I GLN* 2.9 45.8 + - - +
116I ASN* 4.1 1.3 - - - +
233I GLU 5.7 0.2 - - - +
234I GLU* 4.3 14.6 - - + -
235I ASP 4.6 1.8 - - - +
236I PHE* 1.3 79.9 - - - +
238I SER* 1.3 56.8 + - - +
239I ALA 3.6 2.4 + - - +
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Residues in contact with SER 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 3.3 16.7 - - - +
389A ILE* 3.8 8.1 - - - -
390A ALA* 3.5 33.5 - - - +
393A ARG* 2.5 33.6 + - - -
152I VAL* 2.5 36.6 + - - +
235I ASP 2.8 5.8 + - - -
237I VAL* 1.3 77.8 - - - +
239I ALA* 1.3 57.1 + - - +
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Residues in contact with ALA 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LYS* 4.0 12.3 - - - +
386A PRO* 3.9 8.3 - - - +
389A ILE* 5.8 0.2 - - - +
150I VAL 3.4 6.5 - - - +
151I ILE* 3.8 20.4 - - + +
235I ASP 3.5 9.2 - - - +
236I PHE* 2.9 34.6 + - + +
237I VAL 3.3 0.8 - - - +
238I SER* 1.3 78.7 - - - +
240I GLU* 1.3 71.5 + - - +
241I 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