Contacts of the helix formed by residues 654 - 666 (chain A) in PDB entry 5KZX
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 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A TRP* 4.8 5.4 + - - -
652A ASN 4.0 0.2 + - - -
653A THR* 1.3 81.9 + - - +
655A GLU* 1.3 64.2 + - - +
656A GLU* 3.8 6.6 + - - +
657A LEU* 3.2 24.4 + - - +
658A CYS* 2.9 21.5 + - - +
687A PHE* 4.6 0.9 - - - -
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Residues in contact with GLU 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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654A SER* 1.3 72.9 - - - +
656A GLU* 1.3 58.9 + - - +
658A CYS* 3.2 2.9 + - - +
659A VAL* 2.9 29.7 + - + +
687A PHE* 3.4 26.9 - - + +
688A SER* 2.6 50.0 + - - -
690A PRO* 5.7 0.3 - - - +
691A ALA* 3.4 22.1 + - + +
695A MET* 4.4 0.3 - - - +
811A LEU* 6.1 2.6 - - + +
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Residues in contact with GLU 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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621A TRP* 3.8 14.4 + - + -
654A SER* 3.3 5.3 + - - +
655A GLU* 1.3 78.7 - - - +
657A LEU* 1.3 63.3 + - - +
659A VAL* 3.4 8.0 + - - +
660A ARG* 3.1 26.8 + - + +
757A GLN 4.5 1.0 - - - +
758A ALA* 3.6 17.8 - - - +
759A GLY* 2.7 30.5 + - - -
760A LYS 4.4 4.0 + - - +
811A LEU* 3.9 27.9 - - + +
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Residues in contact with LEU 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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619A SER* 3.5 35.7 - - - +
620A SER* 3.7 12.8 - - - +
621A TRP* 3.5 33.3 - - + +
624A LEU* 3.7 24.7 - - + -
653A THR* 3.7 16.6 - - - +
654A SER* 3.2 20.9 + - - +
656A GLU* 1.3 78.1 - - - +
658A CYS* 1.3 59.0 + - - +
660A ARG* 3.3 1.0 + - - -
661A TRP* 2.8 49.9 + - + +
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Residues in contact with CYS 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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647A CYS* 2.0 48.2 - - - -
653A THR* 3.7 8.3 - - - +
654A SER 2.9 17.0 + - - +
655A GLU 3.8 2.0 - - - +
657A LEU* 1.3 75.7 - - - +
659A VAL* 1.3 57.6 + - - +
662A THR* 2.6 39.8 + - - -
673A ASN* 4.5 0.4 - - - -
682A GLN* 4.0 7.0 - - - -
687A PHE* 3.6 36.8 - - + -
695A MET* 3.8 9.0 - - + -
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Residues in contact with VAL 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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655A GLU* 2.9 20.2 + - + +
656A GLU* 3.6 7.2 - - - +
658A CYS* 1.3 76.0 - - - +
660A ARG* 1.3 58.3 + - - +
662A THR* 3.2 3.3 + - - -
663A GLN* 3.0 38.5 + - - +
691A ALA* 3.7 35.4 - - + +
694A ALA* 3.9 12.6 - - + -
695A MET* 3.7 12.2 - - + +
811A LEU* 3.4 44.2 - - + +
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Residues in contact with ARG 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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621A TRP* 3.6 29.8 - - + -
624A LEU* 4.0 5.0 - - + +
656A GLU* 3.1 17.9 + - + +
657A LEU 3.9 1.1 - - - +
659A VAL* 1.3 78.6 - - - +
661A TRP* 1.3 57.9 + - - +
663A GLN* 3.2 17.1 + - - +
664A LEU* 3.1 28.9 + - - +
754A PRO* 5.6 0.3 - - - +
755A VAL* 3.3 44.3 - - + +
757A GLN 5.0 0.6 + - - -
760A LYS 2.9 20.4 + - - -
809A ALA 2.8 24.2 + - - -
810A PRO 3.0 16.9 + - - -
811A LEU* 3.4 25.3 + - + +
813A THR 2.9 28.1 + - - -
814A ILE* 5.6 0.2 - - - +
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Residues in contact with TRP 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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617A VAL* 4.0 13.0 - - + -
618A TRP 3.4 21.5 - - - -
620A SER 3.5 22.9 - - - -
623A GLN 3.9 6.1 - - - -
624A LEU* 3.7 38.7 - - + +
644A ALA* 4.6 3.6 - - + -
645A ASP 3.7 20.5 + - - -
646A VAL* 3.7 7.9 - - + +
647A CYS* 3.3 34.5 - - - +
648A GLY* 3.6 13.9 - - - -
657A LEU* 2.8 41.6 + - + +
658A CYS 4.1 0.9 - - - +
660A ARG* 1.3 71.5 - - - +
662A THR* 1.3 59.8 + - - +
665A GLY* 2.8 26.3 + - - -
668A TYR* 2.9 31.2 + + - -
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Residues in contact with THR 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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371A PHE* 6.1 2.0 - - + -
646A VAL* 3.8 10.0 - - + +
647A CYS* 3.6 13.0 - - - -
658A CYS* 2.6 25.9 + - - -
659A VAL 3.7 2.9 - - - -
661A TRP* 1.3 77.2 - - - +
663A GLN* 1.3 56.4 + - - +
665A GLY 3.8 0.2 - - - -
666A ALA* 2.9 29.5 + - - +
671A MET* 3.9 14.9 - - + +
673A ASN* 5.3 1.2 + - - -
684A PRO* 5.8 4.9 - - + +
695A MET* 3.9 41.0 - - + +
698A ALA* 3.9 8.2 - - + +
699A LEU* 4.9 5.4 - - + -
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Residues in contact with GLN 663 (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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659A VAL* 3.0 25.4 + - + +
660A ARG* 3.2 35.9 + - - +
662A THR* 1.3 78.7 - - - +
664A LEU* 1.3 62.2 + - - +
666A ALA* 3.6 7.3 + - - +
667A PHE* 3.6 17.8 - - - -
694A ALA* 4.3 9.2 + - - +
698A ALA* 4.1 16.6 - - + +
755A VAL* 5.7 0.5 + - - +
811A LEU 2.9 25.5 + - - -
812A ASP* 3.4 7.1 + - - +
813A THR 3.4 24.3 - - - +
814A ILE* 3.7 27.6 - - + +
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Residues in contact with LEU 664 (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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624A LEU* 4.0 16.8 - - + -
627A SER* 3.8 9.2 - - - +
628A VAL* 4.1 15.3 - - + -
660A ARG 3.1 15.1 + - - +
663A GLN* 1.3 78.7 - - - +
665A GLY* 1.3 54.4 + - - +
667A PHE* 2.8 33.5 + - - +
668A TYR* 3.4 39.0 + - + +
744A LEU* 3.8 24.7 - - + -
752A ILE* 4.7 3.8 - - + -
754A PRO* 3.8 35.9 - - + -
756A LEU* 4.4 1.1 - - + -
814A ILE* 4.0 5.8 - - - +
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Residues in contact with GLY 665 (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 VAL* 4.1 3.8 - - - -
661A TRP 2.8 24.2 + - - -
662A THR 3.8 0.9 - - - -
664A LEU* 1.3 69.9 - - - +
666A ALA* 1.3 55.2 + - - +
667A PHE 3.0 5.4 - - - -
668A TYR* 2.9 50.5 + - - +
671A MET* 3.4 19.4 - - - +
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Residues in contact with ALA 666 (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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662A THR 2.9 19.0 + - - +
663A GLN 3.7 8.3 - - - +
664A LEU 3.2 0.6 - - - -
665A GLY* 1.3 75.5 - - - +
667A PHE* 1.3 63.2 + - + +
671A MET* 3.6 19.7 - - + +
698A ALA* 3.6 29.2 - - + +
702A ARG* 2.8 35.4 + - + +
746A TRP* 3.9 4.9 - - - -
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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