Contacts of the strand formed by residues 485 - 490 (chain A) in PDB entry 3OPY
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 ASP 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A SER 2.9 14.9 + - - +
396A ARG* 2.8 58.9 + - + +
397A ALA 3.1 11.6 + - - +
480A VAL* 5.1 1.7 - - - +
483A GLY 4.2 1.0 + - - -
484A LEU* 1.3 66.4 - - - +
486A THR* 1.4 61.1 + - - +
487A ARG* 5.4 3.9 + - - -
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Residues in contact with THR 486 (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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396A ARG* 4.4 0.5 + - - -
397A ALA* 3.2 15.5 - - + +
398A PHE 4.3 0.2 - - - +
399A VAL* 3.6 31.2 - - + -
476A LYS* 3.2 44.0 + - + -
479A LEU* 3.4 30.3 - - + +
480A VAL* 3.5 9.8 - - - +
484A LEU 3.1 14.8 + - - -
485A ASP* 1.4 75.8 + - - +
487A ARG* 1.3 69.6 + - - +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ARG* 3.5 20.8 - - - +
397A ALA 3.1 6.3 + - - -
398A PHE* 3.7 23.0 - - + +
399A VAL 3.0 22.4 + - - +
476A LYS* 4.8 7.6 - - - +
485A ASP* 5.4 4.0 + - - -
486A THR* 1.3 79.8 + - - +
488A ILE* 1.4 67.2 + - - +
489A THR* 3.7 3.5 + - - -
375B MET* 3.2 35.6 - - - +
377B ARG* 4.2 14.3 - - - +
432B GLU* 4.0 16.4 + - - -
465B GLY* 3.9 19.9 - - - -
466B HIS* 4.1 13.7 - - + +
469B ARG* 5.2 3.2 - - - +
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Residues in contact with ILE 488 (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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399A VAL* 3.3 13.5 - - + +
401A GLU* 4.7 0.4 - - + -
472A SER* 3.4 39.7 - - - +
473A GLU* 3.3 27.6 - - - +
476A LYS* 3.7 37.2 - - + +
487A ARG* 1.4 75.6 - - - +
489A THR* 1.4 67.1 + - - +
490A ARG* 3.6 38.1 - - + +
463B THR* 3.5 10.4 + - - -
465B GLY* 3.7 11.6 - - - -
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Residues in contact with THR 489 (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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383A LEU* 3.9 25.8 - - + -
387A ILE* 3.5 24.1 - - + +
399A VAL 2.7 11.3 + - - -
400A VAL* 3.4 8.5 - - + +
401A GLU 2.9 24.1 + - - +
487A ARG 4.2 2.4 + - - -
488A ILE* 1.4 74.0 + - - +
490A ARG* 1.3 61.1 + - - +
491A LEU* 4.7 6.7 - - + -
463B THR 3.4 10.3 - - - +
464B LEU 2.9 26.9 + - - +
465B GLY* 3.8 4.3 - - - -
466B HIS 3.9 2.4 + - - -
467B VAL* 3.9 7.2 - - + -
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Residues in contact with ARG 490 (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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383A LEU* 5.4 0.5 - - - +
401A GLU* 3.5 31.6 - - + +
472A SER* 3.4 18.4 + - - -
473A GLU* 4.1 21.4 + - - +
488A ILE* 3.6 26.4 - - + +
489A THR* 1.3 71.7 - - - +
491A LEU* 1.3 64.6 + - - +
492A GLY 3.4 1.1 - - - +
373B GLU* 4.4 14.1 + - - -
461B VAL* 4.1 16.6 - - - +
462B THR* 3.3 4.2 - - - +
463B THR* 2.8 65.6 + - + +
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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