Contacts of the strand formed by residues 676 - 682 (chain B) in PDB entry 5N06
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 LYS 676 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A GLN* 3.4 37.3 + - - +
674B ILE* 3.7 3.4 - - - +
675B SER* 1.3 86.4 - - - +
677B TYR* 1.3 65.6 + - - +
678B VAL* 4.4 10.5 - - + -
694B ASP* 2.8 32.4 + - + +
695B VAL 3.3 17.5 - - - +
696B ASP* 4.2 4.9 - - - +
698B PRO* 4.0 7.3 - - - +
720B ALA* 3.8 1.9 - - - +
721B SER* 3.3 34.1 + - - +
723B GLN* 4.8 10.5 + - + +
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Residues in contact with TYR 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B PRO* 3.8 22.0 - - + -
664B TRP* 3.7 26.2 - + + -
666B HIS* 2.9 25.4 + + - -
667B PRO* 3.3 18.6 - - + +
674B ILE* 3.5 16.5 - - + +
676B LYS* 1.3 76.5 - - - +
678B VAL* 1.3 62.4 + - - +
679B VAL* 3.9 0.7 + - - +
694B ASP* 3.2 1.7 - - - -
695B VAL* 2.8 45.2 + - + +
697B ARG 5.1 2.0 - - - -
698B PRO* 3.2 30.3 - - + +
700B GLU 4.1 0.7 - - - -
718B MET* 3.7 26.0 - - + -
719B ARG 3.6 14.6 - - - -
720B ALA* 4.0 16.8 - - + -
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A GLN* 5.0 0.9 - - - +
725A LEU* 4.9 9.9 - - + -
728A TRP* 4.5 3.3 - - + -
676B LYS* 4.4 17.3 - - + -
677B TYR* 1.3 74.1 - - - +
679B VAL* 1.3 66.7 + - - +
680B GLU 4.4 0.2 + - - -
692B TRP* 3.5 44.6 - - + -
694B ASP* 3.9 18.4 - - + +
717B ARG 4.1 0.3 - - - +
718B MET* 3.4 5.9 - - - +
719B ARG* 3.0 49.6 + - + +
721B SER* 4.6 11.9 - - - -
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Residues in contact with VAL 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B LEU* 3.7 28.3 - - + -
677B TYR 4.1 6.3 - - - +
678B VAL* 1.3 85.4 - - - +
680B GLU* 1.3 69.5 + - - +
681B VAL* 4.7 1.8 - - + -
692B TRP* 3.4 3.0 - - - -
693B ILE* 2.8 53.7 + - + +
695B VAL* 4.4 11.2 - - + -
703B THR* 4.9 4.0 - - + -
705B ILE* 4.5 9.6 - - + -
716B PHE* 4.7 4.0 - - + -
717B ARG 3.7 9.9 - - - +
718B MET* 3.8 26.2 - - + -
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Residues in contact with GLU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A TRP* 3.9 13.6 - - + -
678B VAL 4.3 0.4 + - - -
679B VAL* 1.3 73.6 - - - +
681B VAL* 1.3 69.9 + - - +
682B GLN* 3.6 17.1 + - + -
690B PRO* 3.6 22.4 - - + +
691B LEU 3.6 3.6 - - - +
692B TRP* 3.0 36.4 + - + +
715B LEU 4.0 0.5 - - - +
716B PHE* 3.8 9.7 - - - -
717B ARG* 2.8 67.0 + - + +
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Residues in contact with VAL 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B VAL* 4.7 3.4 - - + -
680B GLU* 1.3 80.8 - - - +
682B GLN* 1.3 63.9 + - - +
683B VAL* 4.1 4.8 + - + +
690B PRO* 3.8 2.3 - - - +
691B LEU* 3.0 36.4 + - + +
693B ILE* 3.8 29.8 - - + -
705B ILE* 4.0 8.1 - - + -
714B TYR* 4.1 28.0 - - + -
715B LEU 4.3 2.9 - - - +
716B PHE* 3.7 26.9 - - + -
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Residues in contact with GLN 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B GLU* 3.6 26.2 + - + +
681B VAL* 1.3 75.9 - - - +
683B VAL* 1.3 69.1 + - - +
690B PRO* 4.4 21.5 - - + +
714B TYR* 3.6 15.5 - - - -
715B LEU* 3.6 40.2 + - + +
717B ARG* 3.9 12.7 - - - +
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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