Contacts of the strand formed by residues 708 - 713 (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 VAL 708 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427K PHE* 4.1 24.9 - - + -
428K LYS 5.3 2.0 - - - +
430K VAL* 4.2 17.5 - - + -
432K VAL* 3.9 23.3 - - + -
663K ALA* 4.8 2.5 - - + -
664K LEU 3.2 13.7 - - - +
665K GLN* 4.3 10.5 - - + +
671K TRP* 3.9 2.0 - - - -
698K TYR 3.8 0.2 - - - +
699K ASP* 4.0 4.7 + - - +
700K MET* 3.0 42.8 + - + +
701K ASP* 5.7 1.4 - - + +
706K HIS* 3.8 7.9 + - + +
707K SER* 1.3 83.5 - - - +
709K LEU* 1.3 73.2 + - - +
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Residues in contact with LEU 709 (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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663K ALA* 3.4 2.8 - - - -
664K LEU* 2.8 39.5 + - + +
666K PHE* 4.2 13.2 - - + -
670K PHE* 4.0 16.4 - - + -
671K TRP* 3.8 48.0 - - + +
681K PHE* 4.2 22.7 - - + -
697K PHE* 4.3 11.4 - - + -
698K TYR 3.4 23.3 - - - +
699K ASP* 4.0 3.8 - - - +
700K MET* 4.3 0.2 - - - -
707K SER 4.2 0.4 - - - -
708K VAL* 1.3 76.6 - - - +
710K MET* 1.3 60.3 + - - +
737K LEU* 4.2 17.9 - - + -
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Residues in contact with MET 710 (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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432K VAL* 4.9 9.2 - - + -
433K GLY 5.2 0.9 - - - +
437K GLN* 5.7 0.9 - - + +
438K ILE* 5.5 7.2 - - + -
574K LEU* 5.9 1.8 - - + -
661K LYS* 3.9 41.3 - - + +
662K ILE 3.3 13.5 - - - +
663K ALA* 4.8 4.5 - - + -
664K LEU* 5.5 0.4 - - - -
697K PHE* 3.3 5.9 - - - +
698K TYR* 2.7 73.8 + - + +
700K MET* 3.7 30.7 - - + -
709K LEU* 1.3 75.9 - - - +
711K SER* 1.3 76.1 + - - +
712K VAL* 4.0 4.0 - - + -
753K PHE* 5.9 0.4 - - + -
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Residues in contact with SER 711 (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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661K LYS* 3.4 4.7 - - - -
662K ILE* 2.9 37.5 + - - +
664K LEU* 5.3 0.4 - - - +
694K PHE* 3.3 32.8 - - - +
696K VAL 2.8 21.6 + - - -
697K PHE* 3.7 22.8 - - - -
710K MET* 1.3 79.9 - - - +
712K VAL* 1.3 70.6 + - - +
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Residues in contact with VAL 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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545K TYR* 3.7 38.8 - - + +
659K ILE* 3.9 13.7 - - + -
660K GLU 3.4 9.2 - - - +
661K LYS* 4.3 12.3 - - + -
692K GLY 3.7 1.9 - - - +
694K PHE* 3.1 27.0 + - - -
695K ALA 4.1 2.8 + - - +
696K VAL* 4.0 5.1 + - + +
698K TYR* 4.3 11.9 - - + +
710K MET* 4.0 15.3 - - + -
711K SER* 1.3 84.2 + - - +
713K ILE* 1.3 78.3 + - - +
714K ALA* 4.1 3.4 - - + +
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Residues in contact with ILE 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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659K ILE* 3.3 5.0 - - - +
660K GLU* 2.8 51.3 + - + +
661K LYS 5.4 0.4 - - - -
662K ILE* 5.4 5.4 - - + -
692K GLY 3.4 2.9 - - - +
693K LEU* 4.4 7.2 - - + -
694K PHE* 3.8 19.3 - - + -
712K VAL* 1.3 77.8 - - - +
714K ALA* 1.3 62.1 + - - +
717K ALA* 3.4 38.1 - - + +
718K VAL* 3.3 15.0 - - + +
721K VAL* 4.4 15.7 - - + -
729K VAL* 3.9 28.0 - - + -
754K VAL* 5.1 5.8 - - + -
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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