Contacts of the strand formed by residues 298 - 305 (chain A) in PDB entry 2OCA
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 LYS 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TYR* 5.5 6.1 + - - -
296A GLU 5.1 1.8 - - - +
297A LEU* 1.3 73.8 - - - +
299A ILE* 1.3 58.2 + - - +
300A ASN* 2.9 31.7 + - - +
448A ILE* 5.4 7.6 - - + +
449A ALA 3.0 9.2 + - - +
450A THR* 2.9 24.5 + - + +
451A VAL* 2.6 34.0 + - - +
494A ASN* 3.7 25.4 - - - +
496A VAL* 3.6 27.3 - - - +
498A LYS* 6.0 0.8 - - - +
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Residues in contact with ILE 299 (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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297A LEU* 5.0 8.1 - - + +
298A LYS* 1.3 78.2 - - - +
300A ASN* 1.3 75.0 + - - +
301A SER* 4.4 2.0 - - - +
433A LEU* 3.3 39.7 - - + -
451A VAL* 3.5 11.0 - - + +
453A ASP* 4.5 5.4 - - + -
488A TYR* 3.8 36.1 - - + +
493A PHE* 3.4 29.8 - - + -
494A ASN 2.8 12.0 + - - +
495A TYR* 3.2 11.4 - - + -
496A VAL 2.9 26.0 + - - -
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Residues in contact with ASN 300 (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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298A LYS* 2.9 43.2 + - - +
299A ILE* 1.3 71.7 - - - +
301A SER* 1.3 64.0 + - - +
302A ILE* 3.3 6.6 + - + +
450A THR* 4.2 7.9 - - - +
451A VAL 2.8 13.9 + - - +
452A TRP* 3.5 36.3 - - + -
453A ASP 2.9 23.4 + - - -
496A VAL* 3.7 6.2 - - - +
498A LYS* 3.4 34.8 - - - +
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Residues in contact with SER 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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299A ILE* 4.0 1.9 - - - +
300A ASN* 1.3 70.6 - - - +
302A ILE* 1.3 60.6 + - - +
303A PHE* 3.8 2.6 + - - -
453A ASP* 3.4 13.9 + - - +
455A ILE* 4.4 13.4 - - - +
485A ILE* 3.9 9.9 - - - +
488A TYR* 3.6 27.9 - - - -
495A TYR* 4.9 1.2 - - - -
496A VAL 2.7 17.8 + - - -
497A MET* 3.3 16.0 - - - +
498A LYS 2.8 28.1 + - - +
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Residues in contact with ILE 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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300A ASN* 3.7 13.5 - - + +
301A SER* 1.3 75.5 - - - +
303A PHE* 1.3 66.1 + - - +
304A LEU* 3.4 5.0 + - + +
335A TRP* 4.0 26.7 - - + -
452A TRP* 3.8 27.4 - - + -
453A ASP 2.9 8.3 + - - -
454A LEU* 3.7 18.8 - - + +
455A ILE* 2.8 31.3 + - - +
498A LYS* 3.4 41.5 - - + +
500A VAL* 4.3 16.6 - - + -
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Residues in contact with PHE 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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301A SER* 4.5 5.6 - - - -
302A ILE* 1.3 72.7 - - - +
304A LEU* 1.3 62.3 + - - +
305A ARG* 3.5 1.7 + - + -
455A ILE* 3.7 20.6 - - + -
457A ASP* 4.2 15.0 - - + +
478A LEU* 3.6 31.6 - - + -
482A ILE* 4.7 11.4 - - + -
485A ILE* 3.5 34.3 - - + -
497A MET* 4.6 17.5 - - + -
498A LYS 2.6 18.4 + - - +
499A THR* 3.4 18.5 - - + +
500A VAL 2.8 29.9 + - - +
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Residues in contact with LEU 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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302A ILE* 3.4 5.1 + - + +
303A PHE* 1.3 71.3 - - - +
305A ARG* 1.3 58.7 + - - +
306A TYR* 3.3 15.1 - - + +
332A ARG* 4.4 11.0 - - + +
335A TRP* 3.6 52.5 - - + +
454A LEU* 5.5 8.5 - - + -
455A ILE 2.9 16.4 + - - +
456A ASP* 3.9 16.8 - - - +
457A ASP* 2.8 26.3 + - - +
500A VAL* 3.3 14.6 - - + +
502A LEU* 3.7 34.8 - - + -
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Residues in contact with ARG 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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303A PHE 3.5 3.4 + - - +
304A LEU* 1.3 72.5 - - - +
306A TYR* 1.3 70.6 + - - +
307A PRO* 4.7 0.2 - - - +
308A ASP* 3.5 15.4 + - - -
311A THR* 3.3 14.3 + - - +
457A ASP* 3.1 28.9 + - + +
459A GLY 2.7 26.1 + - - -
461A LYS* 3.3 31.5 - - - +
471A TYR* 3.2 31.2 + - - -
499A THR* 5.0 9.0 - - + -
500A VAL 2.9 11.9 + - - +
501A ASN* 3.7 22.6 - - - +
502A LEU* 2.9 31.0 + - - +
503A LEU 4.7 0.2 + - - -
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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