Contacts of the strand formed by residues 767 - 770 (chain K) in PDB entry 6R1U
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 TYR 767 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545K TYR* 2.7 36.5 + - - -
546K ALA 3.5 10.8 - - - -
547K CYS 4.1 2.6 - - - +
548K GLY* 3.7 13.5 - - - -
657K GLY* 2.9 25.4 + - - -
659K ILE* 3.2 29.6 - - + +
765K MET* 3.5 6.7 - - - +
766K ALA* 1.3 87.5 - - + +
768K SER* 1.3 64.3 + - - +
795K GLU* 3.7 7.9 - - - +
803K GLN* 3.5 43.5 - - + +
901K FAD 3.7 37.5 - + - -
4M MET* 4.1 16.8 - - + +
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Residues in contact with SER 768 (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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629K LEU* 3.9 18.2 - - - -
654K LEU* 4.8 1.1 - - - -
655K GLY 3.2 12.8 - - - -
765K MET* 4.1 1.3 - - - -
767K TYR* 1.3 75.4 - - - +
769K PHE* 1.3 59.9 + - - +
779K TYR* 2.5 31.6 + - - -
795K GLU* 2.8 32.3 + - - -
796K ALA* 4.0 6.1 - - - -
803K GLN* 2.9 32.7 + - - +
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Residues in contact with PHE 769 (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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547K CYS* 3.3 35.2 - - + +
549K SER* 3.4 31.4 - - - -
553K GLN* 3.9 23.1 - - - -
554K VAL* 4.0 14.1 - - + -
559K TRP 6.2 0.2 - - - +
561K HIS* 6.2 0.2 - - - -
654K LEU* 3.4 7.2 - - - +
655K GLY* 2.7 59.4 + - - -
656K ALA 4.2 1.6 - - - -
657K GLY* 3.7 13.2 - - - -
768K SER* 1.3 75.3 - - - +
770K VAL* 1.3 71.3 + - - +
771K LYS* 3.7 24.0 - - + -
779K TYR* 4.0 7.9 - - - -
803K GLN* 4.7 1.6 - - - +
1M ALA 5.3 2.7 - - - +
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Residues in contact with VAL 770 (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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554K VAL* 3.7 1.6 - - - +
555K SER* 3.0 23.4 + - - -
558K SER* 3.6 22.0 - - - +
559K TRP* 4.9 6.1 + - - +
561K HIS* 3.4 39.3 - - + +
654K LEU* 4.0 17.5 - - + -
769K PHE* 1.3 82.6 - - - +
771K LYS* 1.3 63.1 + - - +
774K GLY* 3.4 37.7 - - - +
775K SER 3.8 7.2 - - - +
779K TYR* 4.2 2.2 - - + -
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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