Contacts of the strand formed by residues 699 - 705 (chain D) in PDB entry 5Y7K
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 GLU 699 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648D LYS* 3.0 39.9 + - + +
649D CYS* 3.1 16.5 - - + +
650D GLY 2.9 28.1 + - - +
698D VAL* 1.3 78.5 - - - +
700D TYR* 1.3 59.5 + - - +
731D GLN* 6.4 0.2 - - + -
758D PHE* 3.6 10.3 - - + -
761D GLN* 3.1 29.7 + - - +
762D CYS* 4.7 2.3 - - - -
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Residues in contact with TYR 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637D SER* 2.9 27.6 + - - -
640D LEU* 3.4 21.1 - - + -
650D GLY 3.7 0.9 - - - -
652D ALA* 3.3 23.1 - - + +
695D PHE* 3.4 39.3 - + + -
698D VAL* 3.9 5.7 + - + +
699D GLU* 1.3 74.6 - - - +
701D LEU* 1.3 64.5 + - - +
702D LEU* 3.3 32.4 - - + +
719D ILE* 4.0 12.3 - - + +
723D LEU* 3.9 29.4 - - + -
728D VAL* 6.6 0.2 - - + -
729D ASP 5.4 1.5 + - - +
730D PHE* 3.6 17.8 - - + +
731D GLN* 2.8 30.7 + - - +
758D PHE* 4.2 2.0 - - - -
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Residues in contact with LEU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650D GLY 3.0 14.1 + - - +
651D ILE* 3.4 22.9 - - + +
652D ALA* 2.8 29.5 + - - +
700D TYR* 1.3 75.2 - - - +
702D LEU* 1.3 61.4 + - - +
703D ILE* 3.9 24.7 - - + -
731D GLN* 3.3 28.5 - - + +
732D ALA* 4.0 7.0 - - - +
754D HIS* 4.5 20.6 - - + +
755D MET* 4.5 3.8 - - + -
758D PHE* 3.8 39.5 - - + -
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Residues in contact with LEU 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C TRP* 4.1 15.2 - - + -
652D ALA 3.6 6.7 - - - +
655D PRO* 3.6 27.6 - - + -
700D TYR* 3.3 30.5 - - + +
701D LEU* 1.3 71.4 - - - +
703D ILE* 1.3 63.6 + - - +
716D SER* 3.6 39.5 - - - +
719D ILE* 3.8 20.0 - - + -
720D SER* 4.3 8.3 - - - +
730D PHE* 4.9 5.8 - - + -
731D GLN 2.9 11.6 + - - +
732D ALA* 3.3 4.1 - - - +
733D MET 2.9 25.8 + - - +
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Residues in contact with ILE 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D ILE* 4.2 6.3 - - + -
652D ALA 2.9 13.4 + - - +
653D VAL* 4.3 9.4 - - + -
654D ALA 2.7 30.0 + - - -
655D PRO* 3.8 2.3 - - - +
701D LEU* 3.9 20.6 - - + -
702D LEU* 1.3 81.5 - - - +
704D HIS* 1.3 62.8 + - - +
733D MET* 3.2 25.4 - - + +
735D TYR* 3.7 16.4 - - + -
742D ILE* 4.4 1.8 - - + -
751D ILE* 3.6 31.9 - - + -
754D HIS* 4.8 5.8 - - + -
755D MET* 3.9 28.9 - - + -
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Residues in contact with HIS 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C TRP* 5.0 1.7 - - + -
654D ALA* 3.3 26.0 - - - +
655D PRO* 3.6 14.1 - - - +
703D ILE* 1.3 78.9 - - - +
705D GLY* 1.3 90.3 + - - +
706D THR 3.8 0.2 + - - -
708D ASP* 3.4 9.7 + - - +
711D VAL* 2.6 31.1 + - + -
712D HIS 3.6 12.9 + - - -
713D PHE* 3.8 22.0 - + + -
716D SER* 2.6 35.9 + - - +
733D MET 3.2 3.8 + - - -
734D TRP* 3.4 8.5 - - - +
735D TYR 3.2 21.0 + - - -
742D ILE* 4.6 5.2 - - - -
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Residues in contact with GLY 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D ALA* 5.2 0.6 - - - +
704D HIS* 1.3 91.6 - - - +
706D THR* 1.3 66.0 + - - +
707D ALA 3.2 3.4 - - - -
708D ASP* 3.2 12.9 + - - +
713D PHE* 3.9 3.5 - - - +
735D TYR* 3.6 13.5 - - - -
738D GLU* 3.4 18.4 - - - -
739D ASP 4.5 5.3 + - - -
742D ILE* 4.2 8.7 - - - +
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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