Contacts of the strand formed by residues 282 - 291 (chain A) in PDB entry 3OJW
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 PHE 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLN* 3.3 21.5 - - + -
276A PHE* 3.4 31.1 - + + +
280A ASN 3.7 0.8 + - - -
281A PRO* 1.3 72.3 - - - +
283A LEU* 1.3 77.7 + - - +
284A ALA* 3.1 9.9 + - + -
306A ASP 3.5 22.2 - - - -
307A ILE* 3.7 9.0 - - - -
308A SER 3.7 20.2 - - - -
309A ASP* 4.9 2.7 - - + -
310A SER* 3.5 26.7 - - - -
312A ILE* 3.6 16.4 - - + -
511A MET* 2.8 40.5 + - - +
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Residues in contact with LEU 283 (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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269A TYR* 3.8 50.7 - - + +
272A GLN* 2.7 33.3 + - + +
281A PRO 4.0 3.1 - - - +
282A PHE* 1.3 88.3 - - - +
284A ALA* 1.3 62.5 + - - +
285A ALA 3.8 1.2 + - - -
508A LEU* 3.9 41.7 - - + +
509A VAL 3.6 3.4 - - - -
510A PRO* 4.0 22.7 - - + -
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Residues in contact with ALA 284 (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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282A PHE* 3.1 6.6 + - + -
283A LEU* 1.3 70.6 - - - +
285A ALA* 1.3 63.8 + - - +
286A VAL 3.7 0.5 + - - -
305A LEU* 3.7 25.7 - - + +
306A ASP 3.4 18.8 - - - +
307A ILE* 4.2 1.6 - - + -
508A LEU* 3.5 1.6 - - - -
509A VAL* 2.8 38.2 + - - +
511A MET* 3.7 25.4 - - + -
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Residues in contact with ALA 285 (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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283A LEU 3.8 2.2 + - - -
284A ALA* 1.3 72.9 - - - +
286A VAL* 1.3 62.9 + - - +
287A THR 3.2 1.6 + - - -
305A LEU* 3.4 1.4 - - - -
306A ASP* 2.7 43.6 + - + +
506A ARG* 3.6 43.3 - - + +
507A ALA 3.7 6.1 - - - +
508A LEU* 3.7 13.9 - - + -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA* 1.3 70.4 - - - +
287A THR* 1.3 60.3 + - - +
288A ALA 3.6 24.9 - - - +
289A ASN* 4.2 0.7 - - + -
303A LEU* 4.2 13.7 - - + -
304A GLU 3.6 6.5 - - - +
305A LEU* 3.8 9.4 - - + -
497A LYS* 3.9 29.8 - - + +
499A PRO* 3.5 20.7 - - + +
500A ALA 4.7 1.0 + - - -
506A ARG* 5.4 1.9 + - - -
507A ALA* 3.0 27.5 + - + +
509A VAL* 3.7 28.7 - - + -
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Residues in contact with THR 287 (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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285A ALA 3.8 1.3 - - - +
286A VAL* 1.3 73.5 - - - +
288A ALA* 1.3 62.1 + - - +
304A GLU* 2.9 31.1 + - - +
306A ASP* 3.6 33.9 + - + +
468A SER* 4.8 2.6 + - - -
499A PRO* 3.8 12.3 - - - +
506A ARG* 4.2 16.8 - - - +
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Residues in contact with ALA 288 (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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286A VAL* 3.5 5.4 - - - +
287A THR* 1.3 83.3 + - - +
289A ASN* 1.3 63.5 + - - +
290A ARG* 5.6 7.2 - - - -
302A HIS* 4.2 3.8 - - - +
303A LEU* 3.1 7.2 - - - +
304A GLU* 3.0 54.3 + - + +
499A PRO* 3.8 5.8 - - - -
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Residues in contact with ASN 289 (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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286A VAL* 4.2 1.1 - - + -
288A ALA* 1.3 77.7 - - - +
290A ARG* 1.3 61.6 + - - +
299A HIS* 5.3 2.3 + - - -
301A MET* 4.1 12.6 - - - +
302A HIS 3.3 4.9 - - - -
303A LEU* 3.5 23.3 - - + +
494A LEU 3.0 23.0 + - - -
495A ARG* 3.6 12.9 + - - +
497A LYS 2.7 29.4 + - - +
499A PRO* 3.9 14.9 - - + +
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Residues in contact with ARG 290 (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 ALA* 5.6 7.4 - - - +
289A ASN* 1.3 77.0 - - - +
291A LYS* 1.3 69.3 + - - +
292A LEU* 3.5 27.5 + - - +
299A HIS* 5.6 0.9 - - - -
301A MET* 3.4 5.7 - - - -
302A HIS* 3.0 59.6 + - + +
304A GLU* 5.3 1.2 + - - -
575A TYR* 4.1 5.9 - - - -
578A GLU* 3.4 24.4 + - - -
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Residues in contact with LYS 291 (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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290A ARG* 1.3 82.7 + - - +
292A LEU* 1.3 60.0 + - - +
293A ASN* 2.9 45.1 + - - +
294A GLN 4.7 1.1 - - - -
295A GLY 3.2 22.1 + - - -
296A THR* 4.8 3.0 - - - +
298A ARG 3.1 20.6 + - - -
299A HIS* 3.9 28.8 + - + +
300A LEU 3.5 6.5 - - - +
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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