Contacts of the strand formed by residues 707 - 715 (chain C) in PDB entry 2OYQ
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 ARG 707 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702C TRP* 3.8 0.2 - - - -
703C THR* 2.9 39.2 + - - +
704C GLY 3.2 9.5 + - - +
705C LYS 2.9 7.4 + - - +
706C LYS* 1.3 90.8 + - - +
708C TYR* 1.3 64.4 + - - +
728C MET 3.5 1.8 - - - -
729C GLY* 3.2 33.9 + - - +
730C LEU* 3.7 12.9 - - + +
731C GLU* 5.3 3.6 + - - -
734C LYS* 3.8 27.1 - - - +
10I A 4.9 8.7 + - - +
11I T 3.0 64.2 + - - -
12I G 4.1 14.2 - - - -
111J T 5.5 3.0 + - - -
112J A 5.3 10.5 + - - -
113J A 6.2 0.6 - - - -
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Residues in contact with TYR 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C TYR* 3.8 22.2 - + - -
626C TYR* 2.7 29.1 + + - -
701C PHE* 3.3 17.0 - - - +
702C TRP* 3.2 41.7 - + + -
703C THR 4.6 0.4 - - - +
706C LYS* 4.9 2.0 - - - -
707C ARG* 1.3 83.8 - - - +
709C ALA* 1.3 71.1 + - - +
710C LEU* 4.2 21.1 - - + -
726C LYS* 4.3 10.3 - - - -
727C ILE* 3.5 4.9 - - - +
728C MET* 2.9 60.9 + - + +
730C LEU* 3.7 8.5 - - - +
114J G 3.1 14.4 + - - -
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Residues in contact with ALA 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700C GLY* 3.2 5.0 - - - -
701C PHE* 2.9 60.0 + - + +
708C TYR* 1.3 78.1 - - - +
710C LEU* 1.3 64.0 + - - +
726C LYS 3.4 6.1 - - - -
727C ILE* 4.0 13.7 - - + -
730C LEU* 4.3 0.2 - - + -
749C ILE* 3.9 20.2 - - + -
753C LEU* 3.8 3.3 - - + +
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Residues in contact with LEU 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C VAL* 3.8 24.9 - - + -
409C SER* 5.4 0.7 - - - +
626C TYR* 4.2 15.7 - - + -
687C ALA* 4.9 7.0 - - + -
689C ALA* 3.8 14.6 - - + -
699C GLY 4.0 2.0 - - - -
700C GLY* 4.6 4.5 - - - -
702C TRP* 3.3 38.8 - - + -
708C TYR* 4.2 19.3 - - + -
709C ALA* 1.3 76.4 - - - +
711C ASN* 1.3 59.2 + - - +
712C VAL* 3.4 9.6 + - + -
725C LEU* 3.7 3.5 - - - -
726C LYS* 2.8 49.9 + - + +
753C LEU* 3.6 6.0 - - - +
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Residues in contact with ASN 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689C ALA* 3.1 3.9 - - - +
690C GLY 2.8 43.6 + - - +
691C PRO* 4.5 0.4 - - - +
692C PRO* 4.2 2.6 - - - +
699C GLY 3.0 21.4 + - - +
710C LEU* 1.3 70.2 - - - +
712C VAL* 1.3 60.9 + - - +
713C TRP* 3.4 29.9 - - - +
723C PRO* 3.5 12.5 - - - +
724C LYS 4.2 1.3 - - - +
725C LEU* 3.8 8.3 - - - +
753C LEU* 3.6 14.3 - - + +
754C GLN* 2.9 39.8 + - - +
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Residues in contact with VAL 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687C ALA* 3.9 23.6 - - + -
688C ILE 3.5 6.3 - - - +
689C ALA* 4.3 1.1 - - + +
710C LEU* 4.0 10.5 - - + +
711C ASN* 1.3 73.2 - - - +
713C TRP* 1.3 59.9 + - - +
714C ASP 3.1 33.0 - - - +
715C MET* 4.4 7.2 - - + -
720C TYR* 3.5 15.9 - - + -
723C PRO* 3.3 5.8 - - - +
724C LYS* 3.0 37.6 + - + +
726C LYS* 3.6 31.4 - - + -
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Residues in contact with TRP 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C THR* 3.6 33.7 - - + -
645C ASN* 6.1 2.9 - - - -
647C TRP* 3.7 15.3 - + - -
648C VAL* 3.6 22.7 - - + -
688C ILE 2.8 10.3 + - - +
690C GLY 2.8 31.9 + - - -
692C PRO* 3.8 27.4 - - + -
711C ASN* 3.4 29.7 - - - +
712C VAL* 1.3 72.8 - - - +
714C ASP* 1.3 60.4 + - - +
719C ARG* 3.7 7.4 - - - -
720C TYR* 3.0 41.4 + - - +
721C ALA 5.8 1.3 - - - -
722C GLU* 5.6 0.2 - - - -
723C PRO* 3.6 36.1 - - + -
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Residues in contact with ASP 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648C VAL* 3.8 17.9 - - + -
652C ASP* 4.7 0.2 - - - +
685C ARG* 2.6 36.0 + - - +
687C ALA* 3.3 1.6 - - - -
688C ILE* 2.9 30.8 + - + -
712C VAL* 3.1 9.7 - - - +
713C TRP* 1.3 81.8 - - - +
715C MET* 1.3 60.4 + - - +
717C GLY* 2.9 24.3 + - - +
718C THR 3.3 8.2 - - - -
719C ARG* 2.7 38.9 + - - +
720C TYR* 4.6 0.7 - - - -
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Residues in contact with MET 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686C GLU* 3.2 39.3 - - + +
687C ALA* 4.0 17.9 - - + -
712C VAL* 4.4 8.1 - - + -
714C ASP* 1.3 72.5 + - - +
716C GLU* 1.3 69.8 + - - +
717C GLY 3.0 1.3 - - - -
718C THR* 2.6 42.2 + - - +
720C TYR* 3.3 29.1 - - + +
726C LYS* 4.2 28.0 - - + +
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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