Contacts of the helix formed by residues 592 - 607 (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 ARG 592 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B PHE* 1.3 82.5 - - + +
593B PRO* 1.3 66.8 - - - +
594B TRP* 3.1 11.2 + - - -
595B LEU* 3.1 34.6 + - + +
596B ASN* 3.5 8.7 + - - -
769B VAL* 4.0 10.1 - - + -
772B GLN* 4.1 4.4 - - - +
773B SER* 3.0 35.3 + - - +
776B ASP* 3.0 28.1 + - - -
861B TRP* 2.9 65.0 + - + +
1006B ACY 2.9 40.4 + - - +
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Residues in contact with PRO 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B MET* 3.9 16.8 - - + -
590B LEU* 3.4 20.0 - - + +
591B PHE 3.0 9.3 - - - +
592B ARG* 1.3 90.5 - - - +
594B TRP* 1.3 78.7 + - + +
596B ASN* 3.0 14.4 + - - +
597B MET* 3.0 25.8 + - + +
618B LEU* 3.7 22.7 - - + -
863B PHE* 3.5 26.7 - - + -
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Residues in contact with TRP 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B ARG* 3.1 11.4 + - - -
593B PRO* 1.3 80.8 - - + +
595B LEU* 1.3 57.9 + - - +
597B MET* 3.1 9.6 + - - +
598B ASP* 2.9 34.7 + - - +
614B LYS* 4.6 14.6 - - - +
615B LEU* 4.2 17.3 - - + +
618B LEU* 3.7 22.2 - - + +
860B GLU 3.4 22.0 - - - -
861B TRP 3.3 23.8 - - - -
862B MET 3.9 9.2 - - - -
863B PHE* 3.6 31.2 - + + -
1006B ACY 3.4 38.1 - - + -
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B ARG* 3.1 45.6 + - - +
594B TRP* 1.3 73.6 - - - +
596B ASN* 1.3 66.5 + - - +
598B ASP* 3.3 16.3 + - + +
599B ARG* 3.0 25.3 + - - +
769B VAL* 3.9 31.6 - - + +
772B GLN* 4.7 13.5 - - + -
1006B ACY 3.9 26.2 - - + +
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Residues in contact with ASN 596 (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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576B GLU* 3.0 35.0 - - + +
577B GLY 3.1 12.6 - - - +
578B MET* 3.6 38.2 - - + +
591B PHE 4.1 5.1 + - - -
592B ARG 3.5 15.8 + - - -
593B PRO* 3.0 7.3 + - - +
595B LEU* 1.3 77.7 - - - +
597B MET* 1.3 62.2 + - + +
599B ARG* 3.4 10.4 + - - -
600B MET* 2.9 30.7 + - - +
769B VAL* 3.7 16.8 - - - +
813B THR* 5.3 0.5 + - - -
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Residues in contact with MET 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B GLU* 5.4 0.9 - - + -
578B MET* 4.0 17.0 - - + -
593B PRO 3.0 19.7 + - - +
594B TRP* 3.1 10.3 + - - +
596B ASN* 1.3 83.6 - - + +
598B ASP* 1.3 65.2 + - - +
600B MET* 3.3 11.8 + - - +
601B LEU* 3.0 23.7 + - - +
612B PHE* 4.7 4.9 - - + -
614B LYS* 3.8 39.2 - - + +
615B LEU* 6.5 0.2 - - + -
617B LEU* 3.6 33.7 - - + -
618B LEU* 4.2 15.5 - - + -
621B ILE* 3.9 22.2 - - + -
644B PRO* 4.8 5.2 - - + -
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Residues in contact with ASP 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B TRP* 2.9 17.3 + - - +
595B LEU* 3.6 24.2 - - + +
597B MET* 1.3 77.4 - - - +
599B ARG* 1.3 61.7 + - - +
601B LEU* 3.4 8.2 + - - +
602B ARG* 3.1 31.9 + - + +
614B LYS* 2.7 37.9 + - - +
1006B ACY 5.5 1.4 - - - +
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Residues in contact with ARG 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B GLU* 2.8 38.2 + - - +
577B GLY 4.3 3.4 + - - -
595B LEU 3.0 17.1 + - - +
596B ASN* 3.5 9.9 + - - +
598B ASP* 1.3 73.3 - - - +
600B MET* 1.3 60.8 + - - +
602B ARG* 3.2 33.8 + - - +
603B SER* 2.9 36.2 + - - +
700B ASN 5.3 0.7 - - - +
701B TYR* 5.5 0.4 - - - -
702B LYS* 3.7 20.1 - - + +
766B LEU* 3.0 41.6 - - + +
767B PRO* 3.0 22.1 + - - -
768B GLY* 3.6 0.6 - - - -
769B VAL* 3.8 7.2 - - - +
900B ILP 2.7 31.5 + - - -
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Residues in contact with MET 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 3.9 15.0 - - + +
575B PHE 5.6 0.7 - - - -
576B GLU* 3.7 19.2 + - + -
596B ASN 2.9 18.2 + - - +
597B MET* 3.6 9.6 - - - +
598B ASP 3.3 0.2 - - - -
599B ARG* 1.3 77.9 - - - +
601B LEU* 1.3 58.3 + - - +
603B SER* 3.3 7.6 + - - -
604B ALA* 2.9 27.2 + - - +
612B PHE* 3.9 12.1 - - + -
617B LEU* 3.9 24.2 - - + -
644B PRO* 4.0 27.6 - - + +
645B VAL 4.1 12.3 - - - +
646B LEU* 4.0 25.6 - - + +
663B LEU* 4.2 15.7 - - + -
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Residues in contact with LEU 601 (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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597B MET 3.0 16.1 + - - +
598B ASP* 3.7 7.2 - - - +
600B MET* 1.3 74.4 - - - +
602B ARG* 1.3 67.9 + - + +
604B ALA* 3.3 4.7 + - + +
605B MET* 3.0 34.5 + - + +
611B SER* 3.9 13.2 - - - +
612B PHE* 3.3 62.4 - - + +
614B LYS* 5.1 13.2 - - + +
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Residues in contact with ARG 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ASP* 3.1 20.2 + - + +
599B ARG* 3.2 38.9 + - - +
601B LEU* 1.3 78.9 - - + +
603B SER* 1.3 61.7 + - - +
605B MET* 3.3 7.6 + - - +
606B ARG* 3.1 22.2 + - - +
700B ASN* 3.4 26.7 + - - +
701B TYR* 3.7 21.3 - - + +
767B PRO* 3.8 22.9 + - - +
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Residues in contact with SER 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 3.4 26.5 - - - +
575B PHE 5.8 0.2 - - - -
599B ARG* 2.9 18.3 + - - +
600B MET* 3.6 10.0 - - - -
602B ARG* 1.3 74.8 - - - +
604B ALA* 1.3 62.5 + - - +
606B ARG* 3.1 12.8 + - - +
607B LEU* 3.1 13.3 + - - +
701B TYR* 3.7 13.4 - - - +
702B LYS* 3.1 30.6 + - - +
703B LEU* 3.8 12.2 - - - +
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Residues in contact with ALA 604 (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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574B LEU* 3.3 11.2 - - + +
600B MET 2.9 13.5 + - - +
601B LEU* 3.4 14.8 - - + +
602B ARG 3.2 0.2 - - - -
603B SER* 1.3 76.9 - - - +
605B MET* 1.3 62.7 + - - +
607B LEU 3.3 2.1 + - - -
608B CYS 3.1 3.3 + - - -
609B LEU* 2.8 33.5 + - - +
610B PRO 4.2 12.1 - - - +
612B PHE* 4.8 3.8 - - + -
646B LEU* 3.9 24.0 - - + -
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Residues in contact with MET 605 (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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212A LEU* 4.4 11.1 - - - +
601B LEU* 3.0 23.1 + - + +
602B ARG* 3.3 6.7 + - - +
603B SER 3.3 0.2 - - - -
604B ALA* 1.3 77.5 - - - +
606B ARG* 1.3 63.6 + - - +
608B CYS* 3.2 14.3 + - - +
609B LEU 4.3 11.2 - - - +
611B SER* 4.2 27.6 - - - +
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Residues in contact with ARG 606 (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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190A PHE* 6.3 0.2 - - - -
208A GLY 5.1 0.5 - - - +
209A PRO* 2.4 37.6 + - - +
212A LEU* 3.6 38.7 + - - +
213A VAL* 4.2 10.3 - - - +
602B ARG 3.1 13.5 + - - +
603B SER* 3.1 8.7 + - - +
605B MET* 1.3 78.5 - - - +
607B LEU* 1.3 60.5 + - + +
608B CYS 3.3 1.0 + - - -
696B GLY 5.1 4.9 + - - -
697B GLY 4.7 3.6 + - - -
698B VAL* 3.3 28.2 - - + +
701B TYR* 3.7 47.8 - - + -
703B LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY* 3.5 33.4 - - - +
209A PRO* 3.9 8.1 - - + -
211A VAL* 5.0 3.1 - - - +
571B SER 4.0 5.6 - - - +
572B LEU* 3.8 19.4 - - + +
573B GLN 3.3 43.7 - - - +
574B LEU* 4.4 2.2 - - + -
603B SER 3.1 9.5 + - - +
604B ALA 3.3 0.4 + - - +
605B MET 3.1 0.6 - - - -
606B ARG* 1.3 78.0 - - + +
608B CYS* 1.3 73.1 + - - +
609B LEU* 3.2 22.0 + - + +
658B PRO* 4.7 1.9 - - - +
703B LEU* 3.8 37.2 - - + -
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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
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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