Contacts of the helix formed by residues 235 - 239 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N ARG* 2.6 42.0 + - - +
151P ILE* 3.8 19.2 - - + +
152P VAL 4.5 3.8 - - - +
153P LYS* 4.4 8.2 - - - +
154P LYS* 4.1 8.1 + - - +
230P ASP 4.4 1.7 - - - +
231P ILE* 3.1 16.6 - - + +
232P SER* 2.8 32.5 + - - +
234P GLU* 1.3 88.0 - - - +
236P PHE* 1.3 54.4 + - + +
237P VAL 2.9 3.0 - - - +
238P SER* 2.8 34.1 + - - +
239P ALA* 3.0 3.1 + - - +
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Residues in contact with PHE 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P LEU* 4.7 15.0 - - + -
114P LYS 4.6 3.4 - - - +
115P GLN* 3.6 21.4 - - - +
116P ASN* 5.1 1.1 - - - -
117P PRO* 3.9 28.0 - - + -
118P LEU* 4.4 17.9 - - + -
127P LEU* 5.4 5.6 - - + -
151P ILE* 4.7 9.4 - - + -
222P MET* 4.2 21.5 - - + -
225P LEU* 3.7 26.2 - - + -
231P ILE* 4.4 11.0 - - + -
232P SER 4.2 3.6 - - - -
233P GLU* 3.0 25.4 - - + +
234P GLU 2.5 12.9 + - - -
235P ASP* 1.3 72.6 - - + +
237P VAL* 1.3 63.4 + - - +
239P ALA* 3.0 30.4 + - + +
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Residues in contact with VAL 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N TYR* 3.5 24.2 - - - +
369N PHE* 6.0 3.4 - - + -
371N LYS* 4.8 1.9 - - - +
389N ILE* 3.7 25.3 - - + +
393N ARG* 4.6 7.4 - - + -
403N TRP* 3.7 31.9 - - + -
405N THR* 4.6 5.2 - - + -
115P GLN* 2.9 45.4 + - - +
116P ASN* 4.0 2.7 - - - +
234P GLU* 4.4 15.3 - - + -
235P ASP 2.9 2.4 - - - +
236P PHE* 1.3 80.2 - - + +
238P SER* 1.3 57.3 + - - +
239P ALA 3.6 2.4 + - - +
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Residues in contact with SER 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386N PRO* 3.5 10.8 - - - +
389N ILE* 3.7 7.6 - - - -
390N ALA* 3.5 32.9 - - - +
393N ARG* 2.4 35.8 + - - +
152P VAL* 2.5 41.2 + - - +
235P ASP 2.8 5.8 + - - -
237P VAL* 1.3 79.2 - - - +
239P ALA* 1.3 56.9 + - - +
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Residues in contact with ALA 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371N LYS* 4.0 12.0 - - - +
386N PRO* 3.9 8.2 - - - +
150P VAL 3.4 7.9 - - - +
151P ILE* 3.8 20.9 - - + +
235P ASP 3.4 8.5 - - - +
236P PHE* 3.0 33.7 + - + +
237P VAL 3.4 0.8 - - - +
238P SER* 1.3 78.8 - - - +
240P GLU* 1.3 69.1 + - - +
241P LEU* 3.9 4.7 + - - +
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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