Contacts of the helix formed by residues 330 - 335 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E PHE* 3.1 37.7 - - - -
311E GLU* 3.0 64.4 - - + +
314E VAL* 3.7 27.7 - - + +
328E LYS* 3.1 25.3 - - - +
310I PHE* 6.1 4.7 - - - -
328I LYS* 2.6 47.5 + - + +
329I LEU* 1.3 71.9 - - - +
331I LYS* 1.3 56.6 + - + +
332I ALA* 2.6 20.8 + - - +
333I LEU* 3.0 19.1 + - - +
334I TYR 3.7 4.2 + - - -
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Residues in contact with LYS 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E GLU* 5.2 6.0 + - - +
315E ALA* 3.5 29.9 - - - +
96I TYR* 4.3 15.9 - - + +
329I LEU* 2.7 33.1 + - + +
330I ARG* 1.3 73.8 - - + +
332I ALA* 1.3 64.3 + - - +
333I LEU 3.2 0.2 - - - -
334I TYR* 3.1 15.3 + - + -
335I ASN* 2.9 45.5 + - - +
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Residues in contact with ALA 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I LEU 4.2 6.1 - - - +
96I TYR* 4.1 11.2 - - - -
98I GLY* 3.6 7.8 - - - -
99I PHE* 3.3 20.4 - - + -
313I THR* 5.6 0.4 - - + -
317I ILE* 3.8 24.9 - - + -
328I LYS 5.5 0.4 - - - +
329I LEU* 3.0 22.9 - - + +
330I ARG* 2.6 7.2 + - - +
331I LYS* 1.3 73.3 - - - +
333I LEU* 1.3 62.4 + - + +
335I ASN 3.9 0.5 + - - -
336I SER* 3.0 16.5 + - - -
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Residues in contact with LEU 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E GLU* 5.8 0.9 - - - +
99I PHE* 4.8 6.1 - - + -
101I ILE* 5.4 2.5 - - + -
309I PHE* 3.7 31.4 - - + -
310I PHE* 4.0 18.2 - - + +
313I THR* 4.3 21.8 - - + +
314I VAL* 6.4 1.1 - - + -
330I ARG* 3.0 8.9 + - - +
332I ALA* 1.3 76.1 - - + +
334I TYR* 1.3 68.1 + - - +
335I ASN 3.1 1.8 - - - -
336I SER* 2.9 23.6 + - - +
426I TYR* 3.7 48.7 - - + -
428I MET* 3.5 14.1 - - + +
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Residues in contact with TYR 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ASN 4.7 3.6 + - - -
80E ASN* 3.4 29.8 + - - -
81E ARG* 4.6 7.1 + - - +
308E LYS* 5.1 12.8 + - + -
311E GLU* 3.3 28.9 + - - +
330I ARG 3.7 2.2 + - - -
331I LYS* 3.1 20.5 + - + +
333I LEU* 1.3 78.7 - - - +
335I ASN* 1.3 73.3 + - - +
336I SER 3.5 2.9 + - - +
426I TYR 3.4 20.8 + - - +
427I GLY* 3.6 36.5 - - - +
428I MET* 4.2 1.4 + - - -
429I GLN* 6.1 0.3 - - - +
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Residues in contact with ASN 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I TYR* 4.3 3.2 + - - -
97I THR 3.0 23.9 + - - +
98I GLY* 3.5 10.9 - - - -
99I PHE 4.1 0.9 + - - +
285I LYS* 5.3 4.0 - - - +
331I LYS* 2.9 45.0 + - - +
334I TYR* 1.3 91.7 - - - +
336I SER* 1.3 61.5 + - - +
337I 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