Contacts of the strand formed by residues 464 - 468 (chain B) in PDB entry 6J94
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 ASP 464 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER 4.3 9.7 + - - +
152B PHE* 3.4 21.2 - - + +
153B LEU* 2.8 25.5 + - - +
176B ILE* 3.6 30.6 + - + +
445B ILE* 6.1 0.9 - - + -
446B ARG 3.8 3.4 - - - +
447B ARG* 2.9 39.7 + - - +
462B GLY 3.5 5.9 + - - +
463B GLU* 1.3 73.8 + - - +
465B ILE* 1.3 60.5 + - - +
466B PHE* 4.9 2.0 - - + -
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.4 24.0 - - + +
155B VAL* 3.8 23.6 - - + -
164B ILE* 4.2 15.0 - - + -
172B TYR* 3.6 35.4 - - + -
444B LEU 3.7 0.5 - - - +
445B ILE* 3.4 9.3 - - - +
446B ARG* 2.9 46.7 + - + +
448B SER* 4.4 2.0 - - - +
454B LEU* 4.5 10.1 - - + -
459B ILE* 5.6 0.7 - - + -
463B GLU* 3.7 19.7 - - + +
464B ASP* 1.3 78.5 - - - +
466B PHE* 1.3 70.7 + - - +
467B ILE* 4.3 6.3 - - + -
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Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.1 14.8 - + - -
132B LEU* 5.1 2.9 - - + -
152B PHE* 3.3 46.0 - + + -
153B LEU 2.7 7.9 + - - -
154B ILE* 3.4 20.7 - - + +
155B VAL 2.9 25.3 + - - -
176B ILE* 5.4 2.5 - - + -
289B VAL* 4.2 25.6 - - + -
291B PRO* 3.7 30.5 - - + -
443B VAL* 3.5 14.8 - - + -
444B LEU 3.7 3.8 - - - -
445B ILE* 3.4 30.3 - - + -
464B ASP* 5.1 2.9 - - + -
465B ILE* 1.3 77.3 - - - +
467B ILE* 1.3 62.2 + - - +
468B SER* 3.5 2.1 + - - +
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Residues in contact with ILE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.5 24.9 - - + +
161B ALA* 4.0 12.8 - - + -
164B ILE* 4.1 22.4 - - + -
165B LEU* 3.7 36.8 - - + -
443B VAL* 3.2 3.1 - - - -
444B LEU* 2.8 57.3 + - + +
446B ARG* 4.5 7.0 - - + -
465B ILE* 3.9 9.2 - - + -
466B PHE* 1.3 72.5 - - - +
468B SER* 1.3 59.0 + - - +
469B VAL 3.2 6.3 + - - +
472B LEU* 3.9 24.2 - - + -
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Residues in contact with SER 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 5.1 3.6 - - - +
132B LEU* 5.3 6.6 - - - +
154B ILE* 4.7 9.0 - - - -
155B VAL 3.0 10.9 + - - +
156B SER* 4.0 4.3 - - - -
442B PRO 3.8 4.5 + - - -
443B VAL* 4.4 9.7 - - - +
466B PHE* 3.5 3.0 + - - -
467B ILE* 1.3 69.6 - - - +
469B VAL* 1.3 60.6 + - - +
470B TRP* 3.6 8.1 + - - +
471B ASN* 2.9 45.6 + - - +
472B LEU* 3.1 25.7 + - - +
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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
------------------------------------------------------------
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