Contacts of the strand formed by residues 690 - 695 (chain A) in PDB entry 2Y48
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 690 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680A HIS* 4.3 12.6 + - - -
687A SER* 3.2 30.5 + - - +
688A ARG 3.4 0.5 - - - +
689A GLY* 1.3 71.7 - - - +
691A LEU* 1.3 84.2 + - + +
692A PHE* 3.1 2.5 + - - -
707A VAL* 4.5 3.6 - - - -
711A ALA* 3.6 15.5 - - + +
715A MET* 3.7 20.6 - - + +
726A ARG* 3.0 42.7 + - - +
730A ILE* 4.6 1.4 - - - +
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Residues in contact with LEU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A VAL* 4.0 17.0 - - + -
680A HIS* 3.8 9.8 + - - +
689A GLY 3.0 4.4 + - - -
690A GLU* 1.3 89.7 - - + +
692A PHE* 1.3 56.9 + - - +
693A LEU 3.2 5.6 - - - -
694A PHE* 3.2 26.6 - - + -
705A ALA* 3.7 16.6 - - + -
706A LEU 3.1 14.7 + - - -
707A VAL* 4.2 9.4 - - + +
715A MET* 4.4 10.5 - - + -
723A ILE* 4.4 4.0 - - + +
726A ARG* 4.1 26.9 - - + -
727A CYS* 3.1 35.9 - - - +
730A ILE* 4.2 13.0 - - + -
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Residues in contact with PHE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A TRP* 2.8 46.7 + + + -
534A ALA* 3.5 17.5 - - + -
535A ASN* 3.5 23.6 - - + -
538A PHE* 3.6 31.2 - + + -
679A GLY* 3.4 0.2 - - - -
680A HIS* 3.1 26.4 + - - +
688A ARG 3.1 22.9 - - - +
689A GLY 3.3 18.7 + - - +
690A GLU 3.1 2.2 - - - +
691A LEU* 1.3 76.8 - - - +
693A LEU* 1.3 81.5 + - + +
706A LEU* 3.7 24.0 + - + -
708A ALA* 3.9 7.9 - - + -
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A CYS* 4.2 7.4 - - - -
531A TRP* 4.8 2.7 - - + +
535A ASN* 4.7 1.8 - - - +
538A PHE* 4.9 0.4 - - + -
677A LEU* 4.0 14.4 - - + -
678A PHE 3.8 19.5 - - - +
679A GLY* 4.2 2.9 - - - +
691A LEU 3.2 2.2 + - - -
692A PHE* 1.3 111.5 - - + +
694A PHE* 1.3 83.5 + - - +
695A TRP* 4.0 6.7 - - - +
704A LEU 3.6 0.2 - - - +
705A ALA* 3.1 5.9 - - - +
706A LEU* 3.0 47.6 + - + -
6C VAL* 3.7 33.7 - - + -
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Residues in contact with PHE 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A LEU* 4.6 2.7 - - + -
676A ASN 3.8 0.2 - - - +
677A LEU* 3.0 27.2 - - - +
678A PHE* 3.1 46.6 + + + +
680A HIS* 4.4 5.8 - - + -
691A LEU* 3.2 31.0 - - + -
693A LEU* 1.3 85.9 - - - +
695A TRP* 1.3 64.6 + - - +
703A LEU* 4.2 13.0 - - + -
704A LEU 3.1 7.0 - - - -
705A ALA* 3.7 22.9 - - + -
727A CYS* 4.5 14.4 - - - -
730A ILE* 4.2 24.9 - - + -
731A LEU* 3.8 33.7 - - + -
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Residues in contact with TRP 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A MET* 3.6 25.3 - - + +
333A VAL* 4.4 8.7 - - + -
356A ILE* 3.5 30.3 - - + -
538A PHE* 4.4 15.9 - + - -
676A ASN 3.3 3.4 - - - -
677A LEU* 4.5 19.1 - - + -
693A LEU* 4.0 6.4 - - + +
694A PHE* 1.3 79.2 - - - +
696A ASN* 1.3 60.0 + - - +
697A LEU* 3.5 33.4 + - + -
698A TYR* 6.0 0.9 - - - -
702A ILE 3.8 1.4 - - - +
703A LEU* 3.4 9.8 - - - +
704A LEU* 2.6 58.0 + - + +
706A LEU* 3.2 35.4 - - + +
4C PHE 5.7 1.3 - - - -
6C VAL* 4.0 27.8 - - + -
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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