Contacts of the helix formed by residues 330 - 335 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310Q PHE* 3.3 34.1 + - - -
311Q GLU* 3.0 65.5 - - + +
314Q VAL* 3.7 28.9 - - + +
315Q ALA* 6.6 0.2 - - + -
328Q LYS* 3.2 26.1 - - - +
310U PHE* 6.1 4.3 - - - -
328U LYS* 2.5 48.4 + - + +
329U LEU* 1.3 76.1 - - - +
331U LYS* 1.3 56.8 + - + +
332U ALA* 2.6 20.2 + - - +
333U LEU* 3.0 18.6 + - - +
334U TYR 3.7 4.4 + - - -
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Residues in contact with LYS 331 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311Q GLU* 5.3 4.3 + - - +
315Q ALA* 3.6 28.5 - - - +
96U TYR* 4.3 16.1 - - + +
329U LEU* 2.8 28.8 + - + +
330U ARG* 1.3 74.3 - - + +
332U ALA* 1.3 64.8 + - - +
333U LEU 3.1 0.4 + - - -
334U TYR* 3.7 14.1 - - + +
335U ASN* 2.9 45.4 + - - +
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Residues in contact with ALA 332 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U LEU 4.2 5.8 - - - +
96U TYR* 4.1 11.6 + - - -
98U GLY* 3.6 8.1 - - - -
99U PHE* 3.2 20.9 - - + -
313U THR* 5.6 0.4 - - + -
317U ILE* 3.9 24.5 - - + -
329U LEU* 3.0 23.2 - - + +
330U ARG* 2.6 7.8 + - - +
331U LYS* 1.3 74.1 - - - +
333U LEU* 1.3 62.9 + - + +
335U ASN 4.0 0.3 + - - -
336U SER* 3.0 16.5 + - - -
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Residues in contact with LEU 333 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311Q GLU* 5.8 0.9 - - - +
99U PHE* 4.8 6.3 - - + -
101U ILE* 5.4 2.2 - - + -
309U PHE* 3.7 31.2 - - + -
310U PHE* 4.0 18.6 - - + +
313U THR* 4.4 20.2 - - + +
330U ARG* 3.0 7.7 + - - +
332U ALA* 1.3 76.0 - - + +
334U TYR* 1.3 67.2 + - - +
335U ASN 3.1 2.5 - - - -
336U SER* 2.9 23.6 + - - +
426U TYR* 3.6 51.4 - - + -
428U MET* 3.6 14.5 - - + +
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Residues in contact with TYR 334 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q ASN 4.7 5.7 + - - -
80Q ASN* 3.6 26.3 + - - -
81Q ARG* 4.6 6.8 + - - +
308Q LYS* 5.3 11.9 + - + -
311Q GLU* 3.4 27.0 + - - +
330U ARG 3.7 2.0 + - - -
331U LYS* 3.1 20.1 + - + +
333U LEU* 1.3 77.6 - - - +
335U ASN* 1.3 73.5 + - - +
336U SER 3.3 3.2 + - - +
426U TYR 3.4 24.8 + - - +
427U GLY* 3.5 36.8 - - - +
428U MET* 4.2 1.6 + - - -
429U GLN* 6.1 0.3 - - - +
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Residues in contact with ASN 335 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U TYR* 4.4 3.6 + - - -
97U THR 3.1 23.5 + - - +
98U GLY* 3.5 10.2 - - - -
99U PHE 4.1 0.7 + - - +
285U LYS* 5.3 3.3 - - - +
331U LYS* 2.9 45.1 + - - +
334U TYR* 1.3 92.1 - - - +
336U SER* 1.3 62.5 + - - +
337U 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