Contacts of the helix formed by residues 294 - 298 (chain R) 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 LYS 294 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R ASP* 2.7 15.2 + - - -
110R ARG* 5.1 5.5 - - - +
132R TYR* 3.5 23.1 + - - +
293R ASP* 1.3 102.9 + - - +
295R GLU* 1.3 54.6 + - - -
296R GLU 3.4 0.4 - - - -
297R VAL* 3.2 18.4 - - + +
298R GLY 3.2 6.1 + - - -
299R SER* 2.5 34.2 + - - -
300R ILE* 3.8 27.8 - - + +
303R THR* 4.3 13.7 - - - +
381S CYS 5.9 0.4 - - - +
383S ASP* 3.3 42.1 + - - +
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Residues in contact with GLU 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R HIS* 3.0 53.2 + - + -
107R ASP* 2.9 2.0 + - - -
292R VAL* 5.9 0.4 - - + -
293R ASP 3.0 5.0 - - - +
294R LYS* 1.3 72.7 - - - +
296R GLU* 1.3 88.6 + - - +
297R VAL 2.9 10.2 + - - -
298R GLY* 3.0 11.4 + - - -
299R SER* 3.3 14.1 + - - +
342R ASP* 3.3 13.3 - - - +
417R GLY 4.3 13.6 - - - +
418R THR* 5.1 2.1 - - - -
419R ILE* 3.6 28.7 - - + +
6035R MN 4.0 5.2 + - - -
6036R MN 3.9 3.0 + - - -
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Residues in contact with GLU 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R HIS* 3.9 9.6 - - + -
107R ASP* 3.3 14.1 + - - +
108R SER* 4.3 1.1 - - - -
109R PRO* 3.9 17.5 - - + +
132R TYR* 4.7 3.8 - - + +
133R GLY* 3.3 35.0 - - - +
265R ASP* 3.0 9.9 - - - +
295R GLU* 1.3 90.0 + - - +
297R VAL* 1.3 56.9 + - - +
298R GLY 3.6 0.2 - - - -
441R HIS* 2.7 25.7 + - - -
6035R MN 2.3 36.1 + - - -
6036R MN 2.9 12.0 + - - -
379S SER* 5.8 1.0 - - - -
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Residues in contact with VAL 297 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R TYR* 3.4 24.6 + - + -
133R GLY 4.7 0.2 - - - +
294R LYS* 3.2 40.6 + - + +
295R GLU 2.9 1.0 - - - -
296R GLU* 1.3 79.3 - - - +
298R GLY* 1.3 53.8 + - - +
299R SER 4.3 2.0 - - - +
300R ILE* 4.3 12.1 - - + +
377S GLY 3.5 10.5 - - - +
378S LYS* 2.8 39.9 - - + +
379S SER* 3.5 10.2 + - - +
380S GLY* 2.7 32.3 + - - +
381S CYS 5.1 1.6 - - - +
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Residues in contact with GLY 298 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295R GLU 3.0 7.0 + - - -
296R GLU 3.6 0.4 - - - -
297R VAL* 1.3 79.5 - - - +
299R SER* 1.3 75.0 + - - +
300R ILE* 3.3 6.3 + - - +
305R MET* 5.3 4.2 - - - +
421R TYR* 5.5 2.6 + - - -
379S SER* 5.4 1.1 - - - -
380S GLY* 4.8 5.4 - - - -
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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