Contacts of the strand formed by residues 653 - 659 (chain A) 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 ASP 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A THR* 2.7 37.5 + - - -
652A GLY* 1.3 78.1 + - - +
654A LEU* 1.3 62.3 + - - +
655A GLN* 3.5 5.4 + - - +
672A ARG* 2.8 42.2 + - - +
673A TYR 3.6 9.9 - - - +
674A PRO* 3.6 28.9 - - + +
676A VAL 3.4 13.5 - - - +
677A LYS* 4.8 5.8 - - - +
678A ASP* 3.5 16.4 - - - +
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Residues in contact with LEU 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A PHE* 4.0 6.3 - - + -
653A ASP* 1.3 73.0 - - - +
655A GLN* 1.3 68.3 + - - +
656A VAL* 3.8 19.5 - - + -
671A LYS 3.4 1.2 - - - +
672A ARG* 3.1 6.9 - - - -
673A TYR* 2.8 43.1 + - + +
676A VAL* 2.9 29.3 + - + +
678A ASP* 4.6 4.7 - - + -
683A MET* 3.5 35.9 - - + -
698A LEU* 3.9 17.3 - - + -
700A ASN* 5.6 0.9 - - - +
724A TRP* 3.5 34.8 - - + +
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Residues in contact with GLN 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A ARG* 4.7 6.4 + - - -
627A ARG 5.0 2.9 + - - +
629A GLN 4.4 10.4 + - - +
630A ASN* 5.0 4.5 + - - -
645A LEU 3.8 0.2 - - - +
646A PHE* 3.6 1.2 - - - -
647A MET* 3.1 45.6 + - + +
649A GLY* 3.5 30.7 - - - -
650A LEU 3.7 1.8 - - - +
651A THR* 3.5 39.6 + - - +
653A ASP 3.5 3.3 + - - +
654A LEU* 1.3 78.1 - - - +
656A VAL* 1.3 67.0 + - - +
670A ILE* 3.7 26.3 - - + +
671A LYS 3.3 4.7 - - - -
672A ARG* 4.3 8.6 - - + +
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A LYS* 3.9 25.4 - - + +
645A LEU 3.3 10.3 - - - +
646A PHE* 3.5 35.2 - - + -
647A MET* 4.1 0.2 - - - -
654A LEU* 3.8 4.3 - - + -
655A GLN* 1.3 79.0 - - - +
657A ALA* 1.3 69.5 + - - +
658A THR* 4.9 2.0 + - - +
669A ASP 4.3 0.9 - - - +
670A ILE* 3.5 6.5 - - - +
671A LYS* 2.8 42.7 + - + +
673A TYR* 3.5 35.0 - - + +
722A LEU* 4.7 2.9 - - + -
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Residues in contact with ALA 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A VAL* 3.8 40.4 - - + -
643A VAL 3.7 0.3 - - - +
644A LYS* 3.4 4.9 - - - -
645A LEU* 2.8 34.7 + - + +
647A MET* 3.8 7.6 - - + +
656A VAL* 1.3 74.2 - - - +
658A THR* 1.3 66.1 + - - +
666A TRP* 3.8 11.8 - - + -
667A GLU 5.8 1.3 - - - +
669A ASP 4.8 6.1 - - - +
670A ILE* 4.7 3.8 - - + +
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Residues in contact with THR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A ASP* 4.1 27.1 - - + +
643A VAL 3.2 8.3 - - - +
644A LYS* 2.9 32.9 + - - +
656A VAL* 4.9 2.6 + - - +
657A ALA* 1.3 77.9 - - - +
659A SER* 1.3 64.4 + - - +
660A LYS* 4.8 5.4 - - + +
666A TRP* 3.4 6.7 - - - -
667A GLU* 2.8 47.3 + - + +
669A ASP 5.0 5.2 + - - -
671A LYS* 6.2 0.2 - - - +
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Residues in contact with SER 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A GLY 4.6 0.3 - - - +
642A ASP* 3.5 5.0 - - - +
643A VAL* 2.8 42.4 + - - +
658A THR* 1.3 73.5 - - - +
660A LYS* 1.3 61.5 + - - +
661A ASP* 3.0 6.9 + - - -
662A GLY 4.6 0.2 + - - -
663A GLY* 2.8 33.5 + - - -
665A THR 2.8 24.3 + - - -
666A TRP* 3.5 20.8 - - - -
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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