Contacts of the helix formed by residues 330 - 335 (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 ARG 330 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310R PHE* 6.1 3.8 - - - -
328R LYS* 2.5 47.0 + - + +
329R LEU* 1.3 75.6 - - - +
331R LYS* 1.3 55.5 + - + +
332R ALA* 2.6 19.9 + - - +
333R LEU* 3.0 18.9 + - - +
334R TYR 3.7 4.5 + - - -
310T PHE* 3.3 35.6 + - - -
311T GLU* 3.0 66.1 - - + +
314T VAL* 3.5 30.0 - - + +
315T ALA* 6.3 1.1 - - + +
328T LYS* 3.1 26.0 - - - +
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Residues in contact with LYS 331 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R TYR* 4.3 15.9 - - + +
329R LEU* 2.7 33.4 + - + +
330R ARG* 1.3 74.3 - - + +
332R ALA* 1.3 65.4 + - - +
334R TYR* 3.7 15.0 - - + +
335R ASN* 2.9 46.5 + - - +
311T GLU* 5.2 5.1 + - - +
315T ALA* 3.3 31.7 - - - +
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Residues in contact with ALA 332 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R LEU 4.2 6.3 - - - +
96R TYR* 4.1 12.1 + - - -
98R GLY* 3.6 8.3 - - - -
99R PHE* 3.3 21.2 - - + -
313R THR* 5.6 0.7 - - + -
317R ILE* 3.8 24.7 - - + -
328R LYS 5.6 0.2 - - - +
329R LEU* 3.0 23.0 - - + +
330R ARG* 2.6 7.3 + - - +
331R LYS* 1.3 72.7 - - - +
333R LEU* 1.3 62.6 + - + +
335R ASN 3.9 0.3 + - - -
336R SER* 3.0 16.1 + - - -
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Residues in contact with LEU 333 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R PHE* 4.8 6.3 - - + -
101R ILE* 5.4 2.5 - - + -
309R PHE* 3.7 31.6 - - + -
310R PHE* 4.0 18.6 - - + -
313R THR* 4.3 21.1 - - + +
314R VAL* 6.4 1.1 - - + -
330R ARG* 3.0 9.4 + - - +
332R ALA* 1.3 76.6 - - + +
334R TYR* 1.3 67.4 + - - +
335R ASN 3.1 2.2 - - - -
336R SER* 2.9 24.0 + - - +
426R TYR* 3.7 48.7 - - + -
428R MET* 3.6 14.7 - - + +
311T GLU* 5.6 0.9 - - - +
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Residues in contact with TYR 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330R ARG 3.7 1.8 + - - -
331R LYS* 3.1 18.8 + - + +
333R LEU* 1.3 78.9 - - - +
335R ASN* 1.3 73.8 + - - +
336R SER 3.3 3.0 + - - +
426R TYR 3.4 20.0 + - - +
427R GLY* 3.6 36.6 - - - +
428R MET* 4.2 1.6 + - - -
429R GLN* 6.1 0.3 - - - +
79T ASN 4.6 4.3 + - - -
80T ASN* 3.4 30.8 + - - -
81T ARG* 4.6 3.8 + - - +
308T LYS* 5.0 13.7 + - + -
311T GLU* 3.2 30.9 + - - +
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Residues in contact with ASN 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R TYR* 4.3 3.6 + - - -
97R THR 3.0 23.5 + - - +
98R GLY* 3.5 11.3 - - - -
99R PHE 4.1 0.9 + - - +
285R LYS* 5.3 3.8 - - - +
331R LYS* 2.9 46.0 + - - +
334R TYR* 1.3 90.4 - - - +
336R SER* 1.3 62.6 + - - +
337R GLU* 4.9 3.8 - - - +
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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