Contacts of the helix formed by residues 642 - 658 (chain A) in PDB entry 3K57
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 THR 642 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A TRP* 1.3 71.7 - - - +
643A PRO* 1.3 70.1 - - - +
644A LEU* 3.5 7.9 - - - +
645A ALA* 3.1 15.8 + - - +
646A GLN* 3.0 24.6 + - - +
681A ARG 3.3 12.3 - - - -
682A LEU* 3.8 13.7 - - - +
683A VAL 3.8 13.2 - - - +
684A TYR* 3.8 25.8 - - + -
752A TYR* 4.0 5.4 - - + -
756A GLN* 2.9 32.7 + - - +
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Residues in contact with PRO 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A TRP 4.0 3.1 - - - +
642A THR* 1.3 86.2 - - - +
644A LEU* 1.3 62.3 + - - +
646A GLN* 4.0 14.6 - - + +
647A GLN* 2.8 31.4 + - - +
680A ALA 5.0 3.4 - - - +
681A ARG* 3.3 30.3 - - + +
683A VAL* 3.5 16.6 - - + +
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Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A THR* 3.5 3.1 - - - +
643A PRO* 1.3 77.8 - - - +
645A ALA* 1.3 60.0 + - - +
647A GLN* 4.1 1.4 - - - +
648A PHE* 3.1 25.3 + - - +
669A THR* 4.8 4.0 - - + -
673A LEU* 4.1 13.9 - - + -
678A LEU* 4.0 28.0 - - + -
681A ARG* 3.0 42.8 + - + +
682A LEU* 3.4 25.8 - - + -
752A TYR* 4.1 14.8 - - + -
756A GLN* 4.3 8.5 - - + -
757A LEU* 3.8 28.5 - - + -
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Residues in contact with ALA 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A GLU* 5.1 2.0 - - + -
641A TRP* 3.7 19.1 - - + -
642A THR* 3.1 6.8 + - - +
644A LEU* 1.3 79.9 - - - +
646A GLN* 1.3 58.8 + - - +
648A PHE* 3.4 6.3 + - - +
649A GLN* 2.9 32.1 + - - +
756A GLN* 3.6 44.9 - - + +
757A LEU* 5.0 0.4 - - - -
760A VAL* 4.0 8.3 - - + +
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Residues in contact with GLN 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A GLU 3.3 17.7 + - - +
636A THR* 2.9 36.5 + - - +
637A VAL 5.0 0.2 - - - -
638A ARG 2.8 31.3 + - - -
639A THR* 4.5 3.2 - - - +
641A TRP* 3.7 12.9 + - + +
642A THR 3.0 15.1 + - - +
643A PRO* 3.3 15.1 + - + +
645A ALA* 1.3 75.2 - - - +
647A GLN* 1.3 62.2 + - - +
650A GLN* 2.9 27.4 + - - +
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Residues in contact with GLN 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A PRO* 2.8 17.8 + - - +
644A LEU 4.1 2.0 - - - +
646A GLN* 1.3 74.8 - - - +
648A PHE* 1.3 67.2 + - - +
650A GLN* 3.4 10.1 + - - +
651A GLU* 3.0 57.3 + - - +
681A ARG* 3.2 49.2 + - - +
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Residues in contact with PHE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU 3.1 20.4 + - - +
645A ALA 3.6 3.6 - - - +
647A GLN* 1.3 77.3 - - - +
649A GLN* 1.3 56.5 + - - +
651A GLU* 3.9 0.7 - - - +
652A LEU* 2.9 41.8 + - + +
665A TYR* 3.7 26.9 - + - -
666A VAL* 3.9 43.5 - - + -
669A THR* 4.0 20.0 - - + -
681A ARG* 5.8 0.4 - - - +
757A LEU* 3.4 45.8 - - + -
760A VAL* 3.7 28.0 - - + -
761A ALA* 4.1 11.2 - - + -
772A PHE* 4.7 3.6 - + - -
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Residues in contact with GLN 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A PHE* 4.1 6.7 - - + -
634A LEU* 3.6 12.2 - - - +
635A GLU* 2.8 31.5 + - - -
636A THR* 2.8 39.8 + - - +
645A ALA 2.9 18.3 + - - +
646A GLN 3.8 4.3 - - - +
647A GLN 3.2 0.2 - - - -
648A PHE* 1.3 77.4 - - - +
650A GLN* 1.3 57.3 + - - +
652A LEU* 4.6 0.4 - - - -
653A TYR* 2.8 68.9 + - + +
760A VAL* 3.4 25.8 + - + +
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Residues in contact with GLN 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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629A MET* 3.4 11.0 - - + +
631A PHE* 3.7 25.7 - - + -
636A THR* 3.3 22.1 + - + +
646A GLN* 2.9 27.4 + - - +
647A GLN* 3.4 8.0 + - - +
649A GLN* 1.3 78.8 - - - +
651A GLU* 1.3 59.7 + - + +
654A LEU* 2.9 32.2 + - - +
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Residues in contact with GLU 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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647A GLN* 3.0 47.2 + - + +
650A GLN* 1.3 75.9 - - + +
652A LEU* 1.3 63.4 + - - +
654A LEU* 3.9 7.2 - - + +
655A ARG* 3.1 44.0 + - - +
665A TYR* 2.2 52.0 + - + +
681A ARG* 5.1 1.0 + - - -
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Residues in contact with LEU 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 PHE* 2.9 34.1 + - + +
649A GLN 3.9 2.2 - - - +
651A GLU* 1.3 75.0 - - - +
653A TYR* 1.3 66.5 + - + +
655A ARG* 3.3 4.0 + - - +
656A ILE* 3.0 35.8 + - + +
662A TYR* 3.7 31.0 - - + +
665A TYR* 4.2 10.5 - - + -
666A VAL* 4.0 16.2 - - + -
760A VAL* 4.7 5.6 - - + +
761A ALA* 4.2 19.5 - - + -
764A ILE* 3.7 24.7 - - + -
765A LEU* 4.5 5.4 - - + -
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Residues in contact with TYR 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU* 3.3 33.7 - - + +
604A PRO* 5.5 0.9 - - - +
618A ALA* 3.6 22.7 - - + -
629A MET* 4.3 0.2 - - - -
631A PHE* 3.4 28.7 - + + -
634A LEU* 4.0 13.5 - - + +
649A GLN* 2.8 53.1 + - + +
650A GLN 4.0 0.2 - - - +
652A LEU* 1.3 75.8 - - + +
654A LEU* 1.3 56.7 + - - +
656A ILE* 3.3 0.5 + - - +
657A PHE* 2.7 55.7 + + + -
760A VAL* 4.5 6.3 - - + -
763A GLY* 4.3 9.5 + - - -
764A ILE* 3.8 34.3 - - + +
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Residues in contact with LEU 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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620A LEU* 4.1 13.2 - - + -
627A GLN* 5.9 0.2 - - + -
629A MET* 3.8 33.2 - - + -
650A GLN 2.9 19.2 + - - +
651A GLU* 3.9 8.7 - - + +
653A TYR* 1.3 77.9 - - - +
655A ARG* 1.3 63.3 + - + +
657A PHE* 3.3 2.5 + - - +
658A ARG* 3.0 67.6 + - - +
660A GLU* 5.1 0.4 - - - +
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Residues in contact with ARG 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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651A GLU* 3.1 47.3 + - - +
652A LEU* 3.6 4.7 - - - +
653A TYR 3.2 0.2 - - - -
654A LEU* 1.3 77.1 - - + +
656A ILE* 1.3 60.7 + - - +
658A ARG 3.1 3.1 + - - -
659A ASN 3.1 3.8 + - - -
660A GLU* 2.8 50.3 + - + +
661A PRO 3.4 26.4 + - - +
662A TYR* 4.1 11.7 - - + +
665A TYR* 3.8 41.2 - - - +
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Residues in contact with ILE 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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411A LEU* 3.8 29.4 - - + -
600A ARG* 3.6 9.5 + - - -
652A LEU* 3.0 25.1 + - + +
653A TYR 3.9 2.2 - - - +
655A ARG* 1.3 75.0 - - - +
657A PHE* 1.3 64.0 + - + +
659A ASN* 3.0 15.1 + - - +
660A GLU 4.8 3.1 - - - +
662A TYR* 4.0 16.8 - - + -
764A ILE* 3.7 40.8 - - + -
765A LEU* 4.0 9.0 - - + -
768A ILE* 3.5 34.1 - - + -
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Residues in contact with PHE 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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411A LEU* 4.0 25.8 - - + -
600A ARG* 3.1 41.4 + - + +
601A PHE 4.3 4.9 - - - -
602A LEU* 4.1 13.9 - - + -
618A ALA* 3.9 23.6 - - + -
619A GLY* 3.9 19.3 - - - -
620A LEU* 4.1 23.3 - - + +
629A MET* 3.7 27.6 - - + -
653A TYR* 2.7 48.1 + + - +
654A LEU* 3.7 5.4 - - - +
656A ILE* 1.3 74.4 - - + +
658A ARG* 1.3 60.1 + - - +
659A ASN* 3.2 3.5 + - - -
764A ILE* 5.0 3.6 - - + -
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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
----------------------------------------------------------
620A LEU* 4.8 5.4 - - + -
627A GLN* 2.8 41.0 + - - +
654A LEU* 3.0 53.7 + - + +
655A ARG 3.1 0.4 + - - +
657A PHE* 1.3 76.6 - - - +
659A ASN* 1.3 73.0 + - - +
660A GLU* 3.1 38.8 + - - +
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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