Contacts of the strand formed by residues 711 - 716 (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 HIS 711 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389K ILE 3.6 2.1 + - - +
390K ILE* 3.5 3.1 - - - +
391K ARG* 2.9 71.6 + - + +
392K ASN 5.3 0.6 - - - -
393K GLY 5.4 4.6 - - - +
709K LYS 4.4 0.2 + - - -
710K LEU* 1.3 72.3 - - - +
712K ILE* 1.3 78.5 + - - +
713K ARG* 4.2 17.2 + - + +
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Residues in contact with ILE 712 (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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10K GLN* 5.0 13.7 - - + +
354K THR* 5.2 19.7 - - + +
356K LEU* 4.2 22.2 - - + -
388K ARG* 4.5 16.8 - - + +
389K ILE 3.3 7.2 - - - +
390K ILE* 4.1 23.6 - - + -
710K LEU* 4.0 12.3 + - + +
711K HIS* 1.3 91.0 + - - +
713K ARG* 1.3 68.7 + - - +
714K THR* 4.1 11.4 + - - +
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Residues in contact with ARG 713 (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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388K ARG* 3.6 2.6 - - - -
389K ILE* 2.9 52.5 + - + +
711K HIS* 4.2 16.7 + - + +
712K ILE* 1.3 73.8 - - - +
714K THR* 1.3 68.7 + - - +
715K VAL* 4.9 4.4 - - + +
797K HIS 3.6 25.2 + - - -
798K THR* 3.9 16.4 + - - +
799K PHE* 4.1 21.0 - - - +
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Residues in contact with THR 714 (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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330K ASP* 5.3 4.3 - - - +
386K SER* 4.3 5.4 - - - -
387K LEU 3.8 3.4 - - - +
388K ARG* 3.6 41.1 + - - +
712K ILE* 4.1 7.7 + - - +
713K ARG* 1.3 79.6 + - - +
715K VAL* 1.3 66.6 + - - +
716K PRO* 3.5 23.9 - - + +
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Residues in contact with VAL 715 (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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386K SER* 3.3 2.2 - - - -
387K LEU* 2.9 45.3 + - + +
389K ILE* 3.7 20.6 - - + -
713K ARG* 4.9 7.9 - - + +
714K THR* 1.3 75.7 - - - +
716K PRO* 1.3 72.3 - - + +
717K LEU* 3.3 14.1 + - + +
794K ILE* 5.9 0.4 - - + -
799K PHE* 3.6 45.8 - - + +
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Residues in contact with PRO 716 (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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385K GLY 3.9 7.0 - - - +
386K SER* 4.0 4.9 - - - -
714K THR* 3.5 19.9 - - + +
715K VAL* 1.3 89.4 - - + +
717K LEU* 1.3 63.9 + - - +
718K TYR* 3.7 37.3 - - + +
756K ALA* 5.6 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