Contacts of the helix formed by residues 330 - 335 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310G PHE* 3.1 38.6 - - - -
311G GLU* 3.1 63.6 - - + +
314G VAL* 3.7 28.5 - - + +
328G LYS* 3.1 26.4 - - - +
310H PHE* 6.1 4.0 - - - -
328H LYS* 2.5 47.3 + - + +
329H LEU* 1.3 71.9 - - - +
331H LYS* 1.3 59.1 + - + +
332H ALA* 2.6 19.3 + - - +
333H LEU* 3.0 18.0 + - - +
334H TYR 3.7 4.5 + - - -
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Residues in contact with LYS 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311G GLU* 5.2 7.3 + - - +
315G ALA* 3.5 29.5 - - - +
96H TYR* 4.3 15.5 - - + +
329H LEU* 2.7 28.2 + - + +
330H ARG* 1.3 74.3 - - + +
332H ALA* 1.3 63.5 + - - +
333H LEU 3.1 0.4 + - - -
334H TYR* 3.7 15.2 - - + +
335H ASN* 2.9 47.1 + - - +
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H LEU 4.2 5.8 - - - +
96H TYR* 4.1 11.0 + - - -
98H GLY* 3.6 8.3 - - - -
99H PHE* 3.3 20.9 - - + -
313H THR* 5.6 0.7 - - + -
317H ILE* 3.8 25.4 - - + -
328H LYS 5.5 0.4 - - - +
329H LEU* 3.0 22.5 - - + +
330H ARG* 2.6 6.8 + - - +
331H LYS* 1.3 73.8 - - - +
333H LEU* 1.3 63.1 + - + +
335H ASN 3.9 0.3 + - - -
336H SER* 3.0 16.5 + - - -
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Residues in contact with LEU 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311G GLU* 5.8 0.9 - - - +
99H PHE* 4.8 6.1 - - + -
101H ILE* 5.4 2.2 - - + -
309H PHE* 3.7 32.5 - - + -
310H PHE* 4.0 17.9 - - + -
313H THR* 4.4 20.6 - - + +
330H ARG* 3.0 8.9 + - - +
332H ALA* 1.3 75.4 - - + +
334H TYR* 1.3 67.2 + - - +
335H ASN 3.1 2.7 - - - -
336H SER* 2.9 23.1 + - - +
426H TYR* 3.6 50.0 - - + -
428H MET* 3.5 14.5 - - + +
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Residues in contact with TYR 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G ASN 4.8 3.6 + - - -
80G ASN* 3.4 29.4 + - - -
81G ARG* 4.6 5.7 + - - +
308G LYS* 5.2 12.1 + - + -
311G GLU* 3.3 30.2 + - - +
330H ARG 3.7 1.8 + - - -
331H LYS* 3.1 19.5 + - + +
333H LEU* 1.3 78.5 - - - +
335H ASN* 1.3 73.6 + - - +
336H SER 3.3 3.3 + - - +
426H TYR* 3.3 22.8 + - - +
427H GLY* 3.6 36.2 - - - +
428H MET* 4.2 1.2 + - - -
429H GLN* 6.1 0.5 - - - +
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Residues in contact with ASN 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H TYR* 4.3 3.8 + - - -
97H THR 3.0 24.3 + - - +
98H GLY* 3.5 10.4 - - - -
99H PHE 4.1 0.5 + - - +
285H LYS* 5.3 3.3 - - - +
331H LYS* 2.9 44.6 + - - +
333H LEU 3.0 0.2 + - - -
334H TYR* 1.3 92.3 - - - +
336H SER* 1.3 63.3 + - - +
337H GLU* 4.9 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