Contacts of the helix formed by residues 235 - 239 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ARG* 2.9 34.5 + - - +
151D ILE* 3.8 17.9 - - + +
152D VAL 4.6 3.4 - - - +
153D LYS* 4.3 9.2 - - - +
154D LYS* 4.1 8.3 + - - +
230D ASP 4.4 1.6 - - - +
231D ILE* 3.1 16.1 - - + +
232D SER* 2.8 32.3 + - - +
234D GLU* 1.3 88.2 - - - +
236D PHE* 1.3 58.2 + - + +
237D VAL 2.9 2.8 - - - +
238D SER* 2.8 31.4 + - - +
239D ALA* 3.0 3.3 + - - +
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Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.7 14.8 - - + -
114D LYS 4.5 3.3 - - - +
115D GLN* 3.5 20.9 + - - +
116D ASN* 5.1 0.4 - - - -
117D PRO* 3.9 28.7 - - + -
118D LEU* 4.4 17.5 - - + -
127D LEU* 5.5 4.7 - - + -
151D ILE* 4.7 10.3 - - + -
222D MET* 4.2 21.5 - - + -
225D LEU* 3.7 27.1 - - + -
231D ILE* 4.3 9.9 - - + -
232D SER 4.1 4.3 - - - -
233D GLU* 3.0 26.0 - - - +
234D GLU 2.5 12.9 + - - -
235D ASP* 1.3 72.5 - - + +
237D VAL* 1.3 63.8 + - + +
239D ALA* 2.9 30.1 + - + +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 4.5 5.2 - - + +
369B PHE* 6.1 2.5 - - + -
371B LYS* 4.7 4.3 - - - +
389B ILE* 3.9 26.6 - - + +
393B ARG* 4.8 4.5 - - + -
403B TRP* 3.9 37.5 - - + -
405B THR* 4.7 7.6 - - + -
115D GLN* 2.9 46.2 + - - +
116D ASN* 4.0 12.6 - - - +
234D GLU* 4.3 16.6 - - + -
235D ASP 4.6 3.6 - - - +
236D PHE* 1.3 79.6 - - + +
238D SER* 1.3 56.3 + - - +
239D ALA 3.6 1.4 + - - +
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Residues in contact with SER 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PRO* 3.5 15.4 - - - +
389B ILE* 3.9 10.8 - - - -
390B ALA* 3.7 27.7 - - - +
393B ARG* 2.6 22.3 + - - +
152D VAL* 2.6 51.3 + - - +
235D ASP 2.8 6.9 + - - -
237D VAL* 1.3 77.2 - - - +
239D ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B LYS* 4.1 11.1 - - - +
386B PRO* 4.1 8.2 - - - +
150D VAL 3.4 7.6 - - - +
151D ILE* 3.8 20.6 - - + +
235D ASP 3.4 8.7 - - - +
236D PHE* 2.9 32.1 + - + +
237D VAL 3.3 0.6 - - - +
238D SER* 1.3 79.3 - - - +
240D GLU* 1.3 70.2 + - - +
241D LEU* 3.9 3.9 + - - +
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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