Contacts of the helix formed by residues 643 - 658 (chain A) in PDB entry 4KHS
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 ASP 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A PHE* 4.2 1.2 - - - +
642A ARG* 1.3 86.2 + - - +
644A THR* 1.3 68.5 + - - +
645A ASN* 3.8 11.1 - - - +
646A HIS* 3.0 41.2 + - - +
647A TRP* 3.6 9.2 + - - -
693A LEU* 3.6 15.2 - - - +
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Residues in contact with THR 644 (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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643A ASP* 1.3 74.9 - - - +
645A ASN* 1.3 65.5 + - - +
646A HIS 3.0 1.6 + - - -
647A TRP* 3.1 38.4 + - + +
648A VAL* 3.2 12.1 + - + +
692A PRO* 3.7 5.2 - - - +
693A LEU* 2.9 26.7 + - - +
713A TRP* 3.5 51.4 - - + -
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Residues in contact with ASN 645 (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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643A ASP* 3.3 11.5 + - - +
644A THR* 1.3 78.9 - - - +
646A HIS* 1.3 62.2 + - - +
648A VAL* 3.7 7.8 - - - +
649A ASP* 3.1 36.8 + - - +
713A TRP* 6.3 0.7 - - - -
719A ARG* 2.9 35.0 + - - +
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Residues in contact with HIS 646 (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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640A LYS 3.5 20.0 - - - -
641A PHE* 3.3 16.3 - + + -
642A ARG* 3.0 62.3 + - + +
643A ASP* 3.0 29.0 + - - +
644A THR 3.0 0.6 + - - -
645A ASN* 1.3 77.5 - - - +
647A TRP* 1.3 62.0 + - - +
649A ASP* 3.5 7.9 + - + +
650A PHE* 3.1 19.3 + - + +
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Residues in contact with TRP 647 (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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406A TYR* 3.6 35.5 + + - -
633A ILE* 4.1 7.0 - - + -
638A GLU* 6.2 0.4 - - + -
641A PHE* 3.6 35.9 - + + -
643A ASP 3.6 7.5 + - - -
644A THR* 3.1 47.4 + - + +
646A HIS* 1.3 76.0 - - - +
648A VAL* 1.3 65.2 + - + +
650A PHE* 3.3 1.6 + - - +
651A LEU* 2.9 52.5 + - + +
688A ILE* 3.8 14.6 - - + -
689A ALA 3.9 2.9 - - - -
690A GLY* 3.7 15.9 - - - -
691A PRO 3.5 24.0 + - - -
693A LEU* 4.3 19.1 - - + +
713A TRP* 3.8 15.7 - + - -
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Residues in contact with VAL 648 (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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644A THR* 3.2 19.8 + - + +
645A ASN* 3.7 10.5 - - - +
646A HIS 3.2 0.2 - - - -
647A TRP* 1.3 94.1 - - + +
649A ASP* 1.3 59.2 + - - +
651A LEU 3.3 0.9 + - - -
652A ASP* 2.8 30.9 + - - +
688A ILE* 3.5 20.1 - - + +
713A TRP* 3.7 28.0 - - + -
714A ASP* 4.2 7.0 - - + -
719A ARG* 3.6 33.4 - - - +
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Residues in contact with ASP 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ASN* 3.1 29.8 + - - +
646A HIS* 3.7 9.9 - - + +
648A VAL* 1.3 75.4 - - - +
650A PHE* 1.3 58.1 + - - +
652A ASP* 3.3 6.5 + - - +
653A LYS* 2.8 31.5 + - - +
656A ARG* 5.0 0.7 + - - -
719A ARG* 2.7 37.2 + - - -
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Residues in contact with PHE 650 (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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632A ILE* 3.9 35.9 - - + -
633A ILE* 4.5 2.7 - - + -
636A VAL* 4.2 18.2 - - + -
641A PHE* 3.7 31.0 - + + -
646A HIS* 3.1 16.1 + - + +
647A TRP 3.4 7.9 - - - +
648A VAL 3.2 0.2 - - - -
649A ASP* 1.3 76.7 - - - +
651A LEU* 1.3 68.2 + - + +
653A LYS* 3.4 6.1 + - + +
654A PHE* 2.8 42.5 + + + +
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Residues in contact with LEU 651 (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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406A TYR* 4.8 4.0 - - + -
407A VAL 5.5 0.7 - - - +
408A MET* 3.5 31.6 - - + +
629A ALA* 4.4 12.8 - - + -
632A ILE* 4.0 20.4 - - + -
633A ILE* 4.0 18.2 - - + -
647A TRP* 2.9 47.0 + - + +
648A VAL 3.9 3.1 - - - +
650A PHE* 1.3 88.5 - - + +
652A ASP* 1.3 60.4 + - - +
654A PHE* 3.7 2.4 - - + +
655A ALA* 2.9 33.6 + - - +
688A ILE* 3.8 15.3 - - + -
689A ALA 5.1 1.3 - - - +
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Residues in contact with ASP 652 (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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648A VAL 2.8 18.2 + - - +
649A ASP* 3.4 10.5 - - - +
651A LEU* 1.3 78.0 - - - +
653A LYS* 1.3 61.0 + - - +
655A ALA* 4.1 1.9 - - - +
656A ARG* 3.2 43.9 + - - +
685A ARG* 3.7 25.5 + - - +
688A ILE* 3.6 11.3 - - + +
714A ASP* 3.8 10.4 - - - +
717A GLY* 5.5 1.4 - - - -
719A ARG* 3.2 20.5 + - - +
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Residues in contact with LYS 653 (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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649A ASP 2.8 18.1 + - - +
650A PHE* 3.7 6.7 - - + +
652A ASP* 1.3 75.6 - - - +
654A PHE* 1.3 59.1 + - - +
656A ARG* 3.5 15.0 - - - +
657A GLU* 2.8 64.3 + - - +
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Residues in contact with PHE 654 (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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408A MET* 4.6 3.4 - - + -
604A TYR* 5.1 0.9 - + - -
605A LEU* 4.0 11.4 - - + -
608A VAL* 4.3 17.5 - - + -
609A CYS* 5.9 0.4 - - - -
632A ILE* 3.5 47.1 - - + -
650A PHE* 2.8 31.6 + + + +
651A LEU* 3.7 8.5 - - - +
653A LYS* 1.3 77.2 - - - +
655A ALA* 1.3 63.8 + - - +
658A ARG* 3.0 44.9 + - + +
659A MET* 3.2 36.1 + - + -
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Residues in contact with ALA 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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408A MET* 3.8 11.7 - - - -
410A PHE* 3.7 26.2 - - + -
651A LEU 2.9 17.3 + - - +
652A ASP 4.1 2.9 - - - +
654A PHE* 1.3 77.2 - - - +
656A ARG* 1.3 58.1 + - + +
659A MET* 3.5 12.4 + - - +
660A GLU* 2.9 37.3 + - - +
685A ARG* 4.1 15.0 - - + -
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Residues in contact with ARG 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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649A ASP 5.0 0.6 + - - -
652A ASP* 3.2 34.0 + - - +
653A LYS* 3.2 29.5 + - - +
654A PHE 3.2 0.4 - - - -
655A ALA* 1.3 81.2 - - - +
657A GLU* 1.3 78.8 + - + +
658A ARG 3.6 0.2 - - - -
660A GLU* 4.2 21.6 - - - +
661A PRO* 3.7 13.5 - - - +
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Residues in contact with GLU 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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653A LYS* 2.8 40.9 + - + +
656A ARG* 1.3 96.1 + - + +
658A ARG* 1.3 80.8 + - + +
661A PRO* 3.6 15.5 - - - +
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Residues in contact with ARG 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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604A TYR* 3.3 30.4 + - + +
654A PHE* 3.0 35.6 + - + +
656A ARG 3.6 0.6 - - - -
657A GLU* 1.3 98.7 + - + +
659A MET* 1.3 65.3 + - - +
660A GLU 3.6 0.4 - - - -
661A PRO* 3.6 3.7 - - - +
662A ALA* 3.5 17.3 + - - +
665A ARG* 5.2 1.0 + - - -
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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