Contacts of the strand formed by residues 661 - 670 (chain B) in PDB entry 1KT8
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 ALA 661 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542B GLU* 3.8 4.7 - - - +
543B TRP* 3.0 34.0 + - + +
609B LEU* 4.4 5.8 - - + -
610B PRO* 3.7 37.2 - - + -
646B LEU* 4.4 5.2 - - + -
647B ILE 3.2 15.3 - - - +
649B ASN* 4.0 7.2 + - - -
660B ARG* 1.3 78.9 - - - +
662B LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 662 (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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540B MET* 3.3 38.6 - - + -
541B VAL 3.4 17.5 - - - +
542B GLU* 3.7 15.9 - - + +
548B TRP* 5.4 0.4 - - - -
559B LEU* 4.1 10.1 - - + -
561B LEU* 4.9 1.8 - - + -
645B VAL 4.0 0.5 - - - +
646B LEU* 3.5 4.5 - - - +
647B ILE* 2.9 53.9 + - + +
649B ASN* 4.7 9.0 - - - +
661B ALA* 1.3 76.0 - - - +
663B LEU* 1.3 61.7 + - - +
664B PHE* 4.0 18.5 + - + -
1001B ACY 3.5 26.7 - - + -
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Residues in contact with LEU 663 (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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505B PHE* 4.4 15.0 - - + -
539B LEU* 4.8 1.1 - - + -
540B MET* 3.3 2.9 - - - -
541B VAL* 2.8 51.8 + - + +
548B TRP* 3.9 25.3 - - + -
600B MET* 4.2 16.4 - - + -
612B PHE* 4.2 20.0 - - + -
617B LEU* 4.1 22.9 - - + -
645B VAL 3.3 12.8 - - - +
646B LEU* 3.8 11.9 - - + -
662B LEU* 1.3 75.2 - - - +
664B PHE* 1.3 76.3 + - - +
665B VAL* 4.4 5.2 - - + -
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Residues in contact with PHE 664 (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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63A PRO* 3.3 31.6 - - + -
68A LEU* 4.7 5.4 - - + -
69A HIS* 4.1 4.3 - + - -
538B MET* 4.3 17.5 - - + -
539B LEU 3.0 17.0 - - - +
540B MET* 4.3 11.4 - - - -
559B LEU* 3.7 22.7 - - + -
643B ARG 3.9 0.2 - - - +
645B VAL* 2.8 74.6 + - + +
647B ILE* 4.6 10.8 - - + -
662B LEU* 4.0 22.9 - - + -
663B LEU* 1.3 77.9 - - - +
665B VAL* 1.3 66.0 + - - +
666B ILE* 4.3 9.4 - - + -
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Residues in contact with VAL 665 (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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538B MET* 3.3 10.6 - - - +
539B LEU* 2.9 54.9 + - + -
617B LEU* 4.7 0.9 - - + -
621B ILE* 4.2 15.7 - - + -
624B LEU* 3.8 16.5 - - + +
642B VAL* 4.0 26.7 - - + -
643B ARG 3.5 8.1 - - - +
644B PRO* 3.7 17.9 - - + -
663B LEU* 4.4 6.1 - - + -
664B PHE* 1.3 81.1 - - - +
666B ILE* 1.3 69.0 + - - +
667B LEU* 4.1 0.4 - - + -
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Residues in contact with ILE 666 (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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63A PRO* 3.9 33.9 - - + +
64A ALA* 3.9 11.2 - - + +
69A HIS* 4.1 11.4 - - + -
153A LEU* 4.1 5.1 - - + +
534B PHE* 3.9 26.2 - - + -
537B HIS 5.0 0.7 - - - -
538B MET* 4.0 17.3 - - + +
556B PHE* 3.5 26.5 - - + -
643B ARG* 2.9 46.0 + - + +
664B PHE* 4.3 5.8 - - + -
665B VAL* 1.3 77.9 - - - +
667B LEU* 1.3 66.2 + - - +
668B CYS* 5.6 0.2 - - - -
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Residues in contact with LEU 667 (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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534B PHE* 3.4 7.3 - - - +
535B THR* 3.1 52.0 + - + +
537B HIS 4.8 2.5 + - - +
556B PHE* 5.4 1.0 - - - -
621B ILE* 5.7 0.2 - - + -
624B LEU* 3.5 37.7 - - + -
625B ILE* 4.3 15.7 - - + -
628B ASP* 4.2 11.4 - - + +
640B LEU* 4.0 19.1 - - + -
641B TYR 3.4 4.7 - - - +
642B VAL* 3.9 34.8 - - + -
665B VAL* 4.1 1.1 - - + -
666B ILE* 1.3 85.1 - - - +
668B CYS* 1.3 63.9 + - - +
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Residues in contact with CYS 668 (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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153A LEU* 3.6 22.4 - - - -
530B PHE* 5.4 0.4 - - + -
531B GLY* 4.0 19.3 - - - +
533B THR 3.3 12.1 - - - +
534B PHE* 3.3 35.9 - - - -
640B LEU* 3.6 4.0 - - - -
641B TYR* 2.7 48.0 + - + -
667B LEU* 1.3 72.8 - - - +
669B PRO* 1.4 70.8 - - - +
670B VAL* 3.4 3.1 + - + +
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Residues in contact with PRO 669 (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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522B PRO* 5.0 9.4 - - + -
528B LEU* 3.8 20.6 - - + +
529B VAL 5.4 2.1 - - - +
530B PHE* 5.7 0.5 - - - -
531B GLY 5.6 1.7 + - - -
533B THR* 3.2 28.2 - - + +
535B THR* 4.1 11.0 - - + -
631B TRP* 3.5 50.5 - - + +
633B PRO* 4.2 9.0 - - + -
639B SER 3.7 6.1 - - - +
640B LEU* 4.1 5.2 - - + -
668B CYS* 1.4 86.8 - - - +
670B VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B LEU* 3.4 8.9 - - - +
530B PHE* 4.0 34.8 - - + +
579B LYS* 4.9 13.2 - - - +
633B PRO* 4.0 1.4 - - - +
638B THR* 3.2 8.0 - - - -
639B SER* 2.6 43.1 + - - +
641B TYR* 3.5 24.0 - - + +
668B CYS* 3.5 17.7 - - + +
669B PRO* 1.3 75.0 - - - +
671B GLY* 1.3 74.8 + - - +
673B TYR* 5.6 2.5 - - + +
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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