Contacts of the strand formed by residues 397 - 403 (chain A) in PDB entry 4OG2
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 TYR 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN* 4.7 4.0 - - - +
301A ALA* 3.5 2.9 - - - +
302A GLN* 2.8 32.0 + - + +
304A TYR* 3.8 19.7 - - - -
305A SER* 3.5 37.7 - - - -
308A TYR* 4.4 16.6 - - - +
395A ASP* 3.8 31.6 + - + +
396A PHE* 1.3 84.3 - - - +
398A VAL* 1.3 72.2 + - - +
414A PHE* 3.8 22.7 - + + -
415A LEU 5.6 5.8 - - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.5 39.3 - - + +
180A SER* 3.9 7.0 - - - +
183A ALA* 3.9 23.8 - - + -
299A LEU* 4.1 7.2 - - + -
300A ILE 3.8 16.2 - - - +
301A ALA* 4.4 2.5 - - - -
302A GLN* 4.4 1.8 - - - +
397A TYR* 1.3 82.4 - - - +
399A ALA* 1.3 71.1 + - - +
414A PHE* 3.7 4.2 - - - +
415A LEU* 2.9 41.9 + - + +
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LEU* 3.5 3.7 - - - -
300A ILE 2.9 33.0 + - - -
302A GLN* 3.9 25.9 - - + +
398A VAL* 1.3 77.7 - - - +
400A GLN* 1.3 61.2 + - - +
412A PHE* 4.1 17.7 - - + -
413A THR 3.2 18.6 - - - +
414A PHE* 4.0 13.2 - - + -
415A LEU* 4.4 0.7 - - - +
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 2.9 39.2 + - - -
297A GLY* 2.9 39.4 + - - +
298A VAL 3.3 3.4 - - - +
299A LEU* 3.6 15.6 - - + +
399A ALA* 1.3 75.6 - - - +
401A ILE* 1.3 70.2 + - - +
402A LYS* 3.3 1.4 + - + +
412A PHE* 4.5 2.7 - - - -
413A THR* 2.8 41.5 + - - +
415A LEU* 3.9 9.4 - - + +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL* 4.0 19.5 - - + -
288A PHE* 3.7 21.3 - - + -
291A CYS* 5.7 0.2 - - - -
295A CYS* 3.6 22.7 - - + +
296A ASP* 3.6 1.0 - - - +
297A GLY* 2.8 28.6 + - - -
298A VAL* 2.9 34.4 + - + +
300A ILE* 4.4 7.9 - - + -
400A GLN* 1.3 74.5 - - - +
402A LYS* 1.3 61.2 + - - +
403A MSE 3.6 31.2 - - + -
411A LYS 3.5 5.6 - - - +
412A PHE* 3.7 25.3 - - + +
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASP* 3.4 15.0 + - - +
400A GLN 3.3 1.1 + - - +
401A ILE* 1.3 73.2 - - - +
403A MSE 1.3 71.6 + - - +
404A GLU* 4.1 0.5 + - - +
410A GLY* 3.2 2.3 - - - -
411A LYS* 2.9 52.7 + - + +
413A THR* 3.8 20.6 - - - +
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Residues in contact with MSE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 3.8 31.6 - - + +
292A LYS 3.4 24.5 - - - +
293A ALA* 4.0 7.6 - - + +
295A CYS* 3.9 2.0 - - + -
296A ASP* 2.9 42.1 + - + +
401A ILE* 3.6 21.1 - - + -
402A LYS* 1.3 87.4 + - - +
404A GLU* 1.3 70.1 + - - +
405A LYS* 3.8 1.0 + - - -
407A GLY 3.4 24.9 - - - +
408A SER 4.8 0.2 - - - -
409A GLN 3.4 22.9 - - - +
410A GLY* 4.0 6.1 - - - -
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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