Contacts of the strand formed by residues 339 - 345 (chain D) in PDB entry 4OBZ
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 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D TYR* 3.3 60.5 + - + +
198D LEU 3.2 19.7 - - - +
199D ASN* 4.2 11.0 - - - +
200D VAL* 3.8 3.5 - - - +
206D TRP* 3.7 3.8 - - - -
334D ASP* 2.8 58.3 + - + +
337D ASN* 3.5 34.3 + - + +
338D ASN* 1.3 74.4 - - - +
340D VAL* 1.3 64.7 + - - +
341D GLY 4.3 0.2 - - - -
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Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D SER 3.8 1.2 - - - +
197D TYR* 3.4 2.6 - - - -
198D LEU* 2.8 39.9 + - - +
200D VAL* 4.0 8.7 - - + -
206D TRP* 3.5 35.4 - - + -
208D VAL* 4.1 16.6 - - + -
230D VAL* 3.9 17.0 - - + -
331D THR* 3.8 22.9 - - + -
332D VAL 3.2 13.0 - - - +
333D PHE* 4.4 4.0 - - + -
339D ARG* 1.3 77.0 - - - +
341D GLY* 1.3 59.8 + - - +
342D PHE* 4.0 12.0 - - + -
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Residues in contact with GLY 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 4.3 5.8 - - - -
196D SER 3.4 5.8 - - - -
197D TYR* 3.4 30.4 - - - -
330D TYR 3.6 0.5 - - - +
331D THR* 3.5 5.0 - - - +
332D VAL* 2.7 39.6 + - - +
339D ARG 4.3 0.2 - - - -
340D VAL* 1.3 73.3 - - - +
342D PHE* 1.3 63.5 + - - -
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Residues in contact with PHE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D SER 3.8 2.3 - - - +
195D LEU* 3.4 4.3 - - - -
196D SER* 3.0 32.2 + - - +
198D LEU* 3.7 33.7 - - + -
208D VAL* 5.3 1.3 - - + -
230D VAL* 4.2 16.8 - - + -
278D LEU* 4.6 9.4 - - + -
283D TYR* 3.7 32.8 + + + +
321D LEU* 4.5 5.4 - - + -
325D PHE* 3.3 34.8 - + - -
329D TYR* 4.0 8.7 - - + -
330D TYR 3.4 3.1 - - - -
331D THR* 3.7 33.7 - - + -
340D VAL* 4.0 18.4 - - + -
341D GLY* 1.3 75.8 - - - -
343D ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D TYR* 3.6 28.7 - - + -
192D LYS 3.8 7.0 - - - +
194D SER 4.0 9.9 - - - +
195D LEU* 3.4 20.0 - - + -
283D TYR* 5.9 0.4 - - - -
329D TYR* 3.3 8.8 - - - -
330D TYR* 2.8 34.1 + - - +
342D PHE* 1.3 75.4 - - - +
344D GLU* 1.3 63.1 + - - +
345D ALA 3.0 0.3 + - - -
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D TYR* 3.4 0.9 - - - -
192D LYS* 2.7 76.4 + - + +
328D ARG* 3.0 29.7 + - - -
329D TYR* 3.7 22.1 + - + -
343D ALA* 1.3 67.9 - - - +
345D ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D TYR* 5.0 10.3 - - + -
190D TYR 3.6 10.3 - - - +
191D TYR* 4.3 0.7 - - - +
192D LYS* 3.6 14.2 + - - -
326D ILE 5.0 0.4 - - - +
327D GLY 3.6 18.6 - - - +
328D ARG* 3.1 24.0 + - - +
330D TYR* 3.9 11.4 - - + +
343D ALA 3.0 7.0 + - - -
344D GLU* 1.3 78.2 - - - +
346D ALA* 1.3 61.4 + - - +
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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