Contacts of the strand formed by residues 643 - 647 (chain B) in PDB entry 2YA6
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 643 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B LEU* 4.1 24.7 - - + -
571B LEU* 3.8 9.4 - - + -
635B VAL* 3.4 33.0 - - + -
636B VAL 3.4 4.9 - - - +
637B GLN* 4.2 7.6 - - + -
641B GLY 4.3 3.1 - - - +
642B ASP* 1.3 77.9 - - - +
644B LYS* 1.3 60.7 + - - +
657B ALA 3.7 0.2 - - - +
658B THR* 3.3 7.3 - - - +
659B SER* 2.9 41.1 + - - +
662B GLY* 4.2 21.8 - - - -
663B GLY* 4.4 1.3 - - - +
666B TRP* 3.7 15.9 - - + -
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Residues in contact with LYS 644 (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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634B THR 3.8 0.9 - - - +
635B VAL* 3.4 7.6 - - - +
636B VAL* 2.7 38.7 + - + +
638B LEU* 3.8 30.7 - - + -
642B ASP* 4.7 1.9 + - - -
643B VAL* 1.3 75.4 - - - +
645B LEU* 1.3 59.2 + - - +
646B PHE* 3.8 26.1 - - + -
656B VAL* 3.8 17.0 - - + +
657B ALA 3.4 1.3 - - - -
658B THR* 2.7 40.6 + - - +
673B TYR* 5.7 2.0 + - - -
696B ILE* 5.0 0.9 - - + -
719B ASN 5.4 0.4 + - - -
720B GLY* 3.2 33.1 + - - -
721B GLU* 5.2 1.4 + - - +
722B LEU* 4.8 7.4 - - + +
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Residues in contact with LEU 645 (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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573B PRO* 4.8 1.1 - - + -
589B SER* 3.9 15.0 - - - -
590B ARG* 4.4 8.7 - - - +
591B VAL* 4.3 12.1 - - + -
607B VAL* 3.8 25.6 - - + -
633B SER* 3.2 29.6 - - - +
634B THR 3.8 11.4 - - - +
635B VAL* 3.9 22.4 - - + -
644B LYS* 1.3 72.7 - - - +
646B PHE* 1.3 61.8 - - - +
647B MET* 3.6 6.6 + - + +
656B VAL* 3.3 4.9 - - - -
657B ALA* 2.8 36.4 + - + +
666B TRP* 3.5 27.1 - - + -
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Residues in contact with PHE 646 (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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633B SER* 3.0 4.0 - - - -
634B THR* 2.8 58.7 + - + +
636B VAL* 3.9 21.1 - - + -
644B LYS* 3.8 24.5 - - + -
645B LEU* 1.3 71.4 - - - +
647B MET* 1.3 59.9 + - - +
648B ARG 4.1 0.5 + - - -
654B LEU* 4.0 7.6 - - + -
655B GLN 3.5 3.6 - - - -
656B VAL* 3.5 21.5 - - + -
683B MET* 3.9 15.8 - - - +
685B ALA* 4.0 12.8 - - + -
696B ILE* 4.1 17.5 - - + -
698B LEU* 3.5 22.9 - - + -
722B LEU* 3.7 32.8 - - + -
724B TRP* 4.5 3.1 - + - -
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Residues in contact with MET 647 (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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589B SER* 3.5 15.9 - - - +
607B VAL* 3.8 23.1 - - - -
630B ASN* 3.6 34.8 - - + +
632B GLU 3.8 3.8 - - - -
633B SER* 3.7 9.4 - - - -
645B LEU* 3.7 8.1 - - + +
646B PHE* 1.3 74.7 - - - +
648B ARG* 1.3 65.2 + - - +
649B GLY* 3.2 3.1 + - - -
655B GLN* 2.9 38.7 + - + +
657B ALA* 3.7 31.2 - - + +
670B ILE* 3.9 30.3 - - + -
678B ASP* 4.0 4.3 - - - +
683B MET* 3.9 6.5 - - - +
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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