Contacts of the strand formed by residues 655 - 662 (chain A) in PDB entry 2QKT
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 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A ASP* 4.1 23.8 + - + +
587A LEU 3.2 15.0 - - - +
588A MET* 3.1 28.9 - - + -
633A ASN* 3.7 13.5 + - - +
653A ASN 3.9 3.7 + - - +
654A GLY* 1.3 71.5 - - - -
656A VAL* 1.3 67.8 + - - +
657A SER* 4.7 7.5 - - - -
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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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585A VAL 3.6 1.0 - - - +
586A ASP* 3.2 6.4 - - - +
587A LEU* 2.6 54.3 + - + +
589A LYS* 4.4 13.5 - - + -
595A LEU* 4.7 9.4 - - + -
632A PHE* 3.2 35.9 - - + -
633A ASN* 3.7 4.0 - - - +
652A ALA* 4.6 19.7 - - + +
653A ASN 5.6 0.2 - - - -
654A GLY 4.0 8.1 - - - +
655A LYS* 1.3 76.3 - - - +
657A SER* 1.3 59.5 + - - +
658A MET* 4.0 19.9 - - + +
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Residues in contact with SER 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A VAL 3.6 0.2 - - - -
586A ASP* 3.1 21.1 + - - -
631A LYS* 3.9 1.7 - - - +
632A PHE* 3.6 4.0 - - - -
633A ASN* 2.9 43.3 + - - +
634A GLY 5.0 2.1 + - - -
655A LYS* 4.7 9.0 - - - -
656A VAL* 1.3 74.3 - - - +
658A MET* 1.3 64.1 + - - +
659A GLU* 5.8 2.1 - - - +
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Residues in contact with MET 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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584A ASN* 3.3 7.1 - - - +
585A VAL* 2.8 61.5 + - + +
586A ASP* 4.4 0.6 + - - +
587A LEU* 4.5 14.4 - - + -
595A LEU* 4.9 5.4 - - + -
597A LEU* 4.8 9.0 - - + -
619A ILE* 5.3 0.4 - - + -
623A LEU* 4.4 20.2 - - + -
629A ILE* 3.9 29.4 - - + -
631A LYS 3.4 5.8 - - - +
632A PHE* 3.7 23.1 - - + -
649A PHE* 4.8 2.0 - - - -
656A VAL* 4.0 17.3 - - + -
657A SER* 1.3 79.3 + - - +
659A GLU* 1.3 63.7 + - - +
660A VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 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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583A PHE 4.7 0.2 - - - +
584A ASN* 2.9 24.6 - - - +
629A ILE* 3.5 4.9 - - - -
630A THR* 2.8 39.9 + - - +
631A LYS* 3.0 49.3 + - + +
657A SER* 5.8 2.0 - - - +
658A MET* 1.3 74.4 - - - +
660A VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 660 (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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581A GLU 3.9 0.2 - - - +
582A LYS* 3.2 6.1 - - - +
583A PHE* 2.8 65.6 + - + +
585A VAL* 4.4 4.5 - - + -
623A LEU* 4.0 18.2 - - + -
627A ASP* 3.6 28.0 - - + -
628A ILE 3.3 12.3 - - - +
629A ILE* 4.4 9.2 - - + -
630A THR* 4.6 1.6 - - - -
658A MET* 4.2 18.2 - - + -
659A GLU* 1.3 80.3 - - - +
661A THR* 1.3 67.4 + - - +
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Residues in contact with THR 661 (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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580A LEU* 3.9 31.2 - - + -
581A GLU 3.4 4.3 - - - +
582A LYS* 3.6 22.5 - - - +
604A ILE* 4.4 18.3 - - + +
627A ASP* 3.7 1.7 - - - -
628A ILE* 2.8 43.2 + - + +
630A THR* 3.8 18.8 + - - +
660A VAL* 1.3 73.3 - - - +
662A ARG* 1.3 66.1 + - - +
663A PRO* 3.8 5.4 - - + +
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Residues in contact with ARG 662 (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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580A LEU* 3.2 3.8 - - - -
581A GLU* 2.6 66.8 + - + +
583A PHE* 4.2 18.5 - - + -
622A LYS* 3.3 17.4 + - - +
624A GLN* 3.6 36.0 + - - +
625A ARG 6.0 0.2 - - - -
627A ASP* 2.6 41.7 + - - +
661A THR* 1.3 75.4 - - - +
663A PRO* 1.3 75.8 - - + +
613B GLN* 3.8 9.5 + - - +
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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