Contacts of the helix formed by residues 330 - 335 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 6.1 3.8 - - - -
328B LYS* 2.5 48.2 + - + +
329B LEU* 1.3 73.6 - - - +
331B LYS* 1.3 59.6 + - + +
332B ALA* 2.6 19.4 + - - +
333B LEU* 3.0 18.3 + - - +
334B TYR 3.7 4.3 + - - -
310D PHE* 3.2 39.4 + - - -
311D GLU* 3.3 54.2 - - + +
314D VAL* 3.8 28.5 - - + +
328D LYS* 2.9 31.9 - - - +
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR* 4.3 16.4 - - + +
329B LEU* 2.7 33.6 + - + +
330B ARG* 1.3 73.6 - - + +
332B ALA* 1.3 63.8 - - - +
333B LEU 3.2 0.2 - - - -
334B TYR* 3.7 14.1 - - + +
335B ASN* 2.9 46.2 + - - +
311D GLU* 5.3 5.4 + - - +
315D ALA* 3.5 30.1 - - - +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU 4.2 6.3 - - - +
96B TYR* 4.1 12.1 + - - -
98B GLY* 3.6 8.3 - - - -
99B PHE* 3.3 20.2 - - + -
313B THR* 5.6 0.4 - - + -
317B ILE* 3.8 26.2 - - + -
328B LYS 5.5 0.4 - - - +
329B LEU* 3.0 22.1 - - + +
330B ARG* 2.6 7.0 + - - +
331B LYS* 1.3 73.7 - - - +
333B LEU* 1.3 63.1 + - + +
335B ASN 3.9 0.3 + - - -
336B SER* 3.0 16.5 + - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 4.8 6.1 - - + -
101B ILE* 5.4 2.2 - - + -
309B PHE* 3.7 32.1 - - + -
310B PHE* 4.0 18.8 - - + -
313B THR* 4.4 20.4 - - + +
314B VAL* 6.4 1.1 - - + -
330B ARG* 3.0 9.2 + - - +
332B ALA* 1.3 76.5 - - + +
334B TYR* 1.3 67.0 + - - +
335B ASN 3.1 2.0 - - - -
336B SER* 2.9 23.7 + - - +
426B TYR* 3.6 48.9 - - + -
428B MET* 3.6 14.3 - - + +
311D GLU* 5.9 0.7 - - - +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ARG 3.7 2.0 + - - -
331B LYS* 3.1 18.3 + - + +
333B LEU* 1.3 77.9 - - - +
335B ASN* 1.3 75.5 + - - +
336B SER 3.5 3.5 + - - +
426B TYR* 3.4 21.8 + - - +
427B GLY* 3.6 35.8 - - - +
428B MET* 4.2 1.2 + - - -
429B GLN* 6.1 0.5 - - - +
79D ASN 4.8 3.3 + - - -
80D ASN* 3.5 28.6 + - - -
81D ARG* 4.8 3.6 + - - +
308D LYS* 5.2 13.3 + - + -
311D GLU* 3.2 31.3 + - - +
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR* 4.3 3.6 + - - -
97B THR 3.1 24.4 + - - +
98B GLY* 3.5 11.5 - - - -
99B PHE 4.1 0.5 + - - +
285B LYS* 5.3 3.6 - - - +
331B LYS* 2.9 45.5 + - - +
333B LEU 3.0 0.4 + - - -
334B TYR* 1.3 91.5 - - - +
336B SER* 1.3 61.3 + - - +
337B GLU* 4.9 4.0 - - - +
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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