Contacts of the strand formed by residues 300 - 306 (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 LEU 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A LYS* 3.5 6.1 - - - +
292A LEU* 2.8 34.6 + - + -
293A ASN* 2.9 23.7 + - + +
298A ARG* 3.9 31.6 - - + +
299A HIS* 1.3 78.6 - - - +
301A MET* 1.3 60.4 + - - +
472A THR* 6.3 0.2 - - + -
473A ALA 3.5 4.7 - - - +
474A VAL* 3.7 28.0 - - + -
534A GLY* 5.8 1.8 - - - -
535A THR* 4.5 10.5 - - + +
572A ASP* 4.2 15.3 - - + -
574A LEU* 3.5 36.1 - - + -
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Residues in contact with MET 301 (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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289A ASN* 4.1 7.4 - - - +
290A ARG 3.4 10.1 - - - +
292A LEU* 3.6 6.6 - - - +
299A HIS* 3.9 19.1 - - - +
300A LEU* 1.3 77.2 - - - +
302A HIS* 1.3 59.7 + - - +
303A LEU* 3.5 20.3 - - + +
471A ILE 3.8 0.3 - - - +
472A THR* 3.5 4.9 - - - -
473A ALA* 2.8 53.2 + - + +
475A ALA* 4.5 7.6 - - - -
491A THR* 3.4 44.9 - - + +
494A LEU* 4.2 8.5 - - + -
495A ARG* 3.8 29.6 - - + +
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Residues in contact with HIS 302 (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* 3.9 2.0 - - - +
289A ASN* 3.3 3.5 + - - -
290A ARG* 3.0 59.7 + - + +
292A LEU* 3.6 22.0 - - + -
301A MET* 1.3 74.1 - - - +
303A LEU* 1.3 62.5 + - - +
304A GLU* 2.9 42.7 - - + +
459A ALA* 5.6 1.3 + - + -
470A HIS* 3.7 22.6 + - + +
471A ILE 3.3 12.1 - - - -
472A THR* 4.5 0.4 - - - -
575A TYR* 2.8 32.6 - + - +
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Residues in contact with LEU 303 (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 14.4 - - + -
288A ALA 3.1 7.0 - - - +
289A ASN* 3.5 32.8 - - - +
301A MET* 3.5 38.6 - - + +
302A HIS* 1.3 76.1 - - - +
304A GLU* 1.3 66.6 + - - +
305A LEU* 4.8 11.4 - - + -
469A VAL 4.6 0.7 - - - -
470A HIS* 3.2 5.7 - - - +
471A ILE* 2.9 52.3 + - + +
473A ALA* 5.8 0.2 - - + -
494A LEU* 3.8 30.3 - - + +
497A LYS* 4.9 1.6 - - + -
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Residues in contact with GLU 304 (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* 3.6 3.8 - - - -
287A THR* 2.9 42.4 + - - +
288A ALA* 3.0 27.1 + - + +
290A ARG* 5.3 1.0 + - - -
302A HIS* 2.9 29.1 - - + -
303A LEU* 1.3 76.9 - - - +
305A LEU* 1.3 62.3 + - - +
468A SER* 3.8 5.1 + - - +
469A VAL 3.7 4.3 - - - -
470A HIS* 3.4 31.5 + - + -
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Residues in contact with LEU 305 (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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284A ALA* 3.7 11.9 - - + +
285A ALA 3.4 2.7 - - - +
286A VAL* 3.8 31.0 - - + -
287A THR* 5.0 0.2 - - - -
303A LEU* 4.8 11.2 - - + -
304A GLU* 1.3 77.6 - - - +
306A ASP* 1.3 62.5 + - - +
307A ILE* 3.3 3.7 + - + +
320A VAL* 4.7 9.4 - - + -
322A VAL* 4.7 0.4 - - + -
468A SER* 3.2 7.0 - - - -
469A VAL* 2.9 44.6 + - + +
471A ILE* 4.0 25.1 - - + -
494A LEU* 5.6 0.9 - - + -
509A VAL* 4.1 30.7 - - + -
511A MET* 4.2 16.2 - - + -
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Residues in contact with ASP 306 (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* 3.5 5.0 - - - -
284A ALA* 3.4 20.6 - - - -
285A ALA* 2.7 26.8 + - + +
287A THR* 3.6 21.5 - - + +
304A GLU 4.0 0.6 + - - -
305A LEU* 1.3 70.6 - - - +
307A ILE* 1.3 58.6 + - - +
308A SER* 2.8 33.2 + - - -
467A ASN 3.3 8.4 - - - +
468A SER* 4.7 1.6 - - - +
506A ARG* 4.4 13.7 + - - -
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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