Contacts of the strand formed by residues 317 - 322 (chain B) in PDB entry 3O8C
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 LEU 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO* 4.1 11.9 - - + +
192B ALA 4.2 6.7 - - - +
193B VAL* 4.4 4.9 - - + -
194B PRO* 4.0 18.4 - - + -
197B PHE* 4.4 0.6 - - - -
198B GLN* 3.4 12.3 - - + +
200B ALA* 4.0 19.1 - - + -
218B TYR* 3.6 20.4 - - + +
285B ASP 3.3 2.4 + - - +
286B ILE* 3.3 25.5 - - + -
287B ILE 2.9 24.9 + - - -
315B ALA* 3.7 2.5 - - - +
316B ARG* 1.3 82.4 - - + +
318B VAL* 1.3 75.3 + - - +
319B VAL* 3.6 24.2 - - + -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 3.6 15.7 - - + -
198B GLN 2.9 9.8 + - - +
199B VAL* 3.4 8.1 - - + +
200B ALA* 2.7 32.7 + - - +
287B ILE* 3.3 11.9 - - + +
289B CYS* 4.3 3.6 - - - -
306B VAL* 3.8 22.9 - - + +
307B LEU* 4.3 9.9 - - + -
310B ALA* 3.6 31.6 - - + -
315B ALA* 5.3 0.2 - - + -
317B LEU* 1.3 77.4 - - - +
319B VAL* 1.3 58.8 + - - +
320B LEU* 4.0 24.5 - - + -
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PRO* 3.6 17.5 - - + -
200B ALA 3.5 4.3 - - - +
202B LEU* 3.6 36.8 - - + +
214B VAL* 6.1 0.4 - - + -
218B TYR* 4.2 6.5 - - + +
286B ILE* 4.4 9.2 - - + -
287B ILE 2.8 8.9 + - - -
288B ILE* 3.4 18.7 - - + +
289B CYS* 2.7 33.4 + - - +
317B LEU* 3.6 32.1 - - + -
318B VAL* 1.3 73.1 - - - +
320B LEU* 1.3 62.6 + - - +
321B ALA* 3.6 7.1 + - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.6 25.4 - - + -
200B ALA 2.8 12.3 + - - +
201B HIS* 3.5 34.5 + - + +
202B LEU 3.1 21.3 + - - +
203B HIS* 4.6 1.9 - - - -
289B CYS* 3.9 24.9 - - + -
292B CYS* 3.4 18.5 - - + -
303B ILE* 4.4 15.7 - - + -
307B LEU* 4.6 3.6 - - + -
318B VAL* 4.0 15.0 - - + -
319B VAL* 1.3 73.1 - - - +
321B ALA* 1.3 58.2 + - - +
322B THR 4.0 0.2 + - - -
519B THR* 4.1 7.6 - - + -
522B LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 321 (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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202B LEU* 3.4 26.5 - - + +
210B LYS* 4.4 9.0 - - + -
288B ILE* 4.0 21.1 - - + -
289B CYS 2.9 15.3 + - - +
290B ASP* 4.2 11.2 - - - +
291B GLU 2.9 26.3 + - - -
292B CYS* 3.0 8.0 + - - -
319B VAL* 3.6 1.3 + - + -
320B LEU* 1.3 71.3 - - - +
322B THR* 1.3 62.3 + - - +
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Residues in contact with THR 322 (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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202B LEU 3.0 14.4 + - - +
203B HIS* 3.3 28.9 - - + +
204B ALA 3.4 2.4 + - - -
210B LYS* 3.9 10.4 - - - +
291B GLU* 4.8 3.4 - - - +
292B CYS* 3.7 20.0 - - - -
293B HIS* 2.7 35.5 + - + -
321B ALA* 1.3 76.4 - - - +
323B ALA* 1.3 60.7 + - - +
324B THR 3.0 8.7 + - - -
325B PRO* 3.7 27.4 - - + -
326B PRO* 5.6 0.4 - - + -
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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