Contacts of the strand formed by residues 671 - 677 (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 LYS 671 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B LEU 3.4 3.6 - - - +
655B GLN* 3.5 1.9 - - - -
656B VAL* 2.8 47.1 + - + +
658B THR* 6.2 0.4 - - - +
669B ASP* 3.9 3.2 + - - +
670B ILE* 1.3 71.2 - - - +
672B ARG* 1.3 69.3 + - - +
673B TYR* 3.4 52.9 - - + +
674B PRO* 6.1 0.2 - - - -
721B GLU* 3.3 21.9 + - - +
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Residues in contact with ARG 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B ARG* 4.4 12.5 - - - +
651B THR* 3.8 37.2 + - - +
653B ASP* 3.1 32.5 + - - +
654B LEU 3.2 2.7 - - - -
655B GLN* 4.2 17.0 - - + +
670B ILE* 3.7 9.4 + - + +
671B LYS* 1.3 88.7 - - - +
673B TYR* 1.3 61.7 + - - +
674B PRO* 3.3 11.7 - - + +
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Residues in contact with TYR 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LYS* 5.7 2.3 + - - -
653B ASP* 4.1 3.6 - - - -
654B LEU* 2.9 24.9 + - + +
656B VAL* 3.8 25.1 - - + -
671B LYS* 3.4 41.7 - - + +
672B ARG* 1.3 72.5 - - - +
674B PRO* 1.3 65.5 - - + +
675B GLN* 3.2 2.2 - - + +
676B VAL 3.0 25.6 + - - +
720B GLY 5.1 0.2 + - - -
721B GLU* 3.6 14.5 + - - -
722B LEU* 3.2 66.2 + - + +
724B TRP* 3.4 30.1 - + + +
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Residues in contact with PRO 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 4.0 20.9 - - + +
672B ARG* 3.3 12.1 - - + +
673B TYR* 1.3 84.0 - - + +
675B GLN* 1.3 60.9 + - + +
676B VAL* 3.2 4.5 + - - -
677B LYS* 4.8 10.6 + - - -
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Residues in contact with GLN 675 (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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673B TYR* 3.2 1.3 - - + -
674B PRO* 1.3 78.4 - - + +
676B VAL* 1.3 59.0 + - - +
677B LYS 4.2 1.0 + - - -
712B HIS* 4.6 1.2 + - - -
724B TRP* 3.6 42.1 + - + +
725B LEU 4.9 2.6 + - - -
727B HIS* 3.0 53.3 + - + +
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Residues in contact with VAL 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 3.4 3.6 - - - +
654B LEU* 3.0 52.6 + - + -
673B TYR 3.0 7.0 + - - +
674B PRO 3.2 2.9 - - - -
675B GLN* 1.3 82.3 - - - +
677B LYS* 1.3 69.7 + - - +
698B LEU* 4.2 9.0 - - + -
700B ASN* 4.3 1.6 - - - +
712B HIS* 3.7 43.1 - - + +
724B TRP* 3.7 39.7 - - + +
727B HIS* 4.3 0.7 - - - +
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Residues in contact with LYS 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B GLY 3.6 15.7 - - - +
653B ASP* 4.4 2.9 - - - +
674B PRO 4.9 10.3 - - - -
675B GLN 4.1 2.0 + - - -
676B VAL* 1.3 78.0 - - - +
678B ASP* 1.3 55.9 + - - +
679B VAL* 4.6 13.5 - - + -
700B ASN* 2.7 31.4 + - - +
701B ALA 4.1 3.6 - - - +
702B GLY* 3.9 26.7 - - - +
703B GLY* 6.0 0.4 - - - -
704B PRO* 6.5 0.4 - - + -
712B HIS* 4.7 4.2 + - - +
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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