Contacts of the strand formed by residues 639 - 648 (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 SER 639 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B LYS* 3.3 34.9 + - - +
580B ALA 3.3 14.6 - - - -
581B PHE* 3.9 20.8 - - - +
632B VAL* 5.1 0.4 - - - -
633B PRO* 3.4 18.2 - - - +
637B GLY 5.3 0.7 + - - -
638B THR* 1.3 81.4 + - - +
640B LEU* 1.3 56.3 + - - +
670B VAL* 2.6 40.2 + - - +
671B GLY 5.5 0.5 + - - -
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Residues in contact with LEU 640 (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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535B THR* 4.0 20.9 - - + -
579B LYS* 3.4 4.8 - - - -
580B ALA* 2.9 40.3 + - + +
625B ILE* 3.8 29.2 - - + -
628B ASP 5.6 1.3 - - - +
631B TRP* 4.2 18.8 - - + -
632B VAL* 4.0 17.5 - - + +
633B PRO* 4.2 0.4 - - - +
639B SER* 1.3 74.8 - - - +
641B TYR* 1.3 65.3 + - - +
642B VAL* 3.7 8.1 + - + +
667B LEU* 4.0 27.8 - - + -
668B CYS 3.6 17.7 - - - +
669B PRO* 4.1 5.8 - - + -
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Residues in contact with TYR 641 (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* 4.1 15.0 - - + -
530B PHE* 3.8 29.8 - + - -
577B GLY* 3.3 18.9 - - - -
578B MET 3.6 9.6 - - - -
579B LYS* 4.2 16.8 - - + -
640B LEU* 1.3 72.4 - - - +
642B VAL* 1.3 63.9 + - - +
643B ARG* 2.9 41.1 + - + -
666B ILE 4.1 0.2 - - - +
667B LEU* 3.4 7.6 - - - +
668B CYS* 2.7 42.9 + - + +
670B VAL* 3.5 17.4 - - + +
813B THR* 4.1 13.2 - - + -
814B ALA* 5.5 3.4 - - + -
900B ILP 2.4 37.5 + - - +
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Residues in contact with VAL 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLY* 3.5 4.2 - - - -
578B MET* 2.8 50.7 + - + +
580B ALA 4.6 0.2 - - - +
590B LEU* 4.4 10.1 - - + -
621B ILE* 4.0 18.2 - - + -
625B ILE* 3.7 24.5 - - + -
640B LEU* 3.8 11.7 - - + +
641B TYR* 1.3 77.8 - - - +
643B ARG* 1.3 61.7 - - - +
644B PRO* 3.4 11.9 - - + +
665B VAL* 4.0 13.5 - - + -
666B ILE 3.9 2.5 - - - -
667B LEU* 3.9 17.0 - - + -
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Residues in contact with ARG 643 (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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69A HIS* 3.0 43.7 + - + -
70A TYR* 2.8 36.3 + - - -
153A LEU* 3.8 26.2 + - + +
575B PHE* 3.4 15.3 - - - -
576B GLU 2.9 23.2 + - - -
641B TYR* 2.9 33.3 + - + -
642B VAL* 1.3 73.7 - - - +
644B PRO* 1.4 69.2 - - - +
645B VAL* 3.9 2.0 + - - +
664B PHE 3.9 0.7 - - - +
665B VAL* 3.5 3.0 - - - -
666B ILE* 2.9 42.7 + - + +
900B ILP 3.1 18.0 - - - +
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Residues in contact with PRO 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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575B PHE* 3.3 2.0 - - - +
576B GLU* 3.0 49.6 + - + +
578B MET* 5.0 3.8 - - + -
597B MET* 4.8 5.4 - - + -
600B MET* 4.0 24.7 - - + -
617B LEU* 5.1 1.3 - - + -
621B ILE* 4.1 23.6 - - + -
642B VAL* 3.4 14.4 - - + +
643B ARG* 1.4 86.5 - - - +
645B VAL* 1.3 64.9 + - - +
664B PHE 3.3 7.0 - - - +
665B VAL* 3.7 13.0 - - + -
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Residues in contact with VAL 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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68A LEU 4.4 11.4 - - - +
69A HIS* 3.3 35.2 - - + +
574B LEU 3.5 13.9 - - - +
575B PHE* 4.2 3.8 - - + +
600B MET* 4.1 4.4 - - - +
643B ARG* 3.9 8.7 - - + +
644B PRO* 1.3 81.0 - - - +
646B LEU* 1.3 63.8 + - - +
647B ILE* 3.8 17.5 - - + -
662B LEU 4.6 0.4 - - - -
663B LEU* 3.3 7.1 - - - +
664B PHE* 2.8 64.8 + - + +
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Residues in contact with LEU 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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548B TRP* 4.1 13.2 - - + -
573B GLN* 3.5 1.6 - - - -
574B LEU* 3.0 48.4 + - + +
600B MET* 4.0 5.8 - - + -
604B ALA* 3.9 19.5 - - + -
609B LEU* 3.9 31.4 - - + +
610B PRO* 4.0 11.7 - - + +
612B PHE* 4.5 13.5 - - + -
645B VAL* 1.3 73.7 - - - +
647B ILE* 1.3 63.3 + - - +
661B ALA* 4.4 11.9 - - + -
662B LEU 3.5 18.8 - - - +
663B LEU* 3.8 17.7 - - + -
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Residues in contact with ILE 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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68A LEU* 4.1 19.5 - - + +
559B LEU* 5.0 0.2 - - + -
561B LEU* 4.3 20.6 - - + -
567B SER* 3.7 22.0 - - - +
572B LEU 3.3 6.3 - - - +
573B GLN* 3.8 20.0 - - + -
609B LEU* 4.3 4.9 - - - -
645B VAL* 3.8 17.5 - - + -
646B LEU* 1.3 81.3 - - - +
648B GLY* 1.3 67.8 + - - +
649B ASN* 5.0 1.1 - - - +
661B ALA* 3.2 5.0 - - - +
662B LEU* 2.9 59.6 + - + +
664B PHE* 4.6 9.0 - - + -
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Residues in contact with GLY 648 (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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565B SER* 3.6 0.3 + - - -
566B SER* 3.7 9.2 - - - -
567B SER* 3.1 22.7 + - - -
572B LEU* 2.8 26.2 + - - -
609B LEU* 3.7 20.6 - - - +
647B ILE* 1.3 77.7 - - - +
649B ASN* 1.3 60.9 + - - +
658B PRO* 4.0 5.8 - - - -
660B ARG 4.0 1.6 - - - -
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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