Contacts of the strand formed by residues 361 - 365 (chain K) in PDB entry 6R90
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 361 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359K ILE* 3.6 3.4 - - - +
360K VAL* 1.3 82.6 - - - +
362K MET* 1.3 82.5 + - - +
363K CYS* 5.0 0.9 - - - -
377K THR* 3.5 2.4 - - - -
378K CYS* 2.9 31.6 + - - +
722K ARG 3.6 14.8 - - - +
723K LYS* 3.1 28.5 + - + +
724K ILE* 2.9 30.9 + - - +
1006K VAL* 3.9 17.9 - - - +
1007K PHE 5.7 0.5 - - - +
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Residues in contact with MET 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359K ILE* 4.2 9.0 - - + -
361K ASP* 1.3 87.6 + - - +
363K CYS* 1.3 74.6 + - - +
375K LEU* 3.6 28.5 - - + -
376K VAL 3.2 13.7 - - - +
377K THR* 3.7 8.3 - - + -
724K ILE* 4.1 3.6 - - - -
1006K VAL* 4.6 8.4 - - + +
1007K PHE 5.2 0.2 - - - -
1008K CYS* 3.4 38.1 - - + +
1029K LEU* 3.5 34.3 - - + +
1030K PHE* 3.5 13.2 - - - +
1031K GLY* 3.8 17.7 - - - +
1037K ILE* 5.2 2.9 - - + -
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Residues in contact with CYS 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361K ASP* 5.0 1.6 - - - -
362K MET* 1.3 84.4 - - - +
364K VAL* 1.3 62.7 + - - +
365K VAL* 4.1 7.5 + - + -
374K GLN 3.9 0.7 - - - +
375K LEU* 3.1 8.8 - - - +
376K VAL* 2.9 36.6 + - + +
724K ILE* 3.2 35.2 - - + -
725K CYS* 4.3 10.1 - - - -
726K TYR* 5.3 3.6 - - + +
733K PHE* 5.9 1.6 - - + -
1008K CYS* 4.7 6.1 - - - -
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Residues in contact with VAL 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K CYS* 1.3 76.3 - - - +
365K VAL* 1.3 71.8 + - - +
373K GLY* 4.0 21.1 - - - -
374K GLN 3.4 10.3 - - - +
375K LEU* 3.9 16.8 - - + -
1008K CYS* 4.4 7.4 - - - -
1009K HIS 4.0 23.0 + - - +
1010K GLY* 4.0 13.5 - - - -
1011K SER 4.2 13.5 - - - +
1012K LEU* 5.0 1.3 - - + -
1029K LEU* 4.5 9.0 - - + -
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Residues in contact with VAL 365 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K CYS* 4.1 5.6 + - + +
364K VAL* 1.3 82.6 - - - +
366K ASP* 1.3 76.8 + - - +
367K LEU* 3.1 25.5 + - + +
373K GLY* 4.4 2.5 - - - -
374K GLN* 2.9 34.6 + - - +
376K VAL* 5.3 2.0 - - + -
726K TYR* 3.5 60.8 - - + -
733K PHE* 3.8 13.0 - - + -
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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