Contacts of the strand formed by residues 680 - 684 (chain B) in PDB entry 1D0N
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 680 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B LEU* 4.2 21.1 - - + -
674B LEU 3.8 5.2 - - - +
675B ASP* 4.2 17.7 - - - +
679B GLN* 1.3 80.9 - - - +
681B PHE* 1.3 69.7 + - - +
700B ALA* 4.2 14.4 - - + -
703B TYR* 4.5 12.3 - - + -
704B ILE* 3.6 33.0 - - + -
711B ARG* 4.3 7.6 - - - +
715B THR* 4.5 1.3 - - + -
716B PRO 3.0 8.2 + - - +
717B ILE* 3.4 6.9 - - + +
718B THR* 2.9 25.8 + - - +
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Residues in contact with PHE 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B LEU* 3.3 6.4 - - - +
674B LEU* 2.7 64.5 + - + +
676B THR* 4.4 11.9 - - - -
679B GLN* 3.9 34.1 - - + -
680B VAL* 1.3 74.6 - - - +
682B VAL* 1.3 60.4 + - - +
683B TRP 4.0 0.4 - - - -
718B THR* 3.3 32.5 - - + -
720B VAL* 4.0 15.3 - - + -
726B PRO* 4.5 3.4 - - + -
728B SER* 3.7 41.7 - - - -
729B PHE* 3.9 21.5 - + + -
732B TRP* 4.7 3.4 - - - -
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Residues in contact with VAL 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B VAL* 3.7 27.4 - - + -
672B MET 3.2 4.9 - - - +
673B LEU* 3.7 16.8 - - + -
681B PHE* 1.3 75.0 - - - +
683B TRP* 1.3 56.0 + - - +
684B VAL* 3.9 2.6 + - + -
696B ALA* 4.0 27.8 - - + +
699B SER* 5.7 0.2 - - - -
700B ALA* 4.7 1.1 - - + -
717B ILE* 4.2 13.7 - - + -
718B THR 2.9 10.1 + - - +
719B VAL* 3.5 30.4 - - + +
720B VAL* 2.8 32.2 + - - +
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Residues in contact with TRP 683 (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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666B LEU* 3.7 35.3 - - + +
667B ALA 3.5 16.4 - - - -
668B THR* 4.2 0.7 - - - -
670B ASP 3.9 1.8 - - - -
671B VAL* 3.4 4.3 - - - +
672B MET* 2.7 61.7 + - + +
674B LEU 5.5 0.6 - - - +
681B PHE 4.0 1.2 - - - -
682B VAL* 1.3 71.4 - - - +
684B VAL* 1.3 62.2 + - - +
685B GLY* 3.4 19.5 - - - -
720B VAL* 3.4 15.9 - - + -
722B GLN* 3.4 46.4 - - + +
725B GLU* 3.0 31.5 + - + +
729B PHE* 3.7 34.1 - + + -
741B TRP* 3.9 14.4 - + - -
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Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B ASP 4.2 1.6 - - - -
671B VAL* 4.6 7.4 - - + +
682B VAL* 4.3 9.0 - - + +
683B TRP* 1.3 79.4 - - - +
685B GLY* 1.3 67.3 + - - +
686B LYS* 3.6 1.0 + - - -
688B SER* 4.5 2.2 - - - +
693B LYS* 4.2 31.0 - - + +
696B ALA* 4.2 24.7 - - + -
719B VAL* 4.3 7.4 - - + -
720B VAL 2.9 13.1 + - - +
721B LYS* 3.6 30.7 - - + -
722B GLN* 3.4 18.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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