Contacts of the helix formed by residues 640 - 658 (chain A) in PDB entry 5XA0
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 640 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A ARG* 4.8 6.1 - - - +
604A LYS* 5.1 18.4 - - - -
638A CYS 4.8 0.3 - - - -
639A VAL* 1.3 87.3 + - - +
641A MET* 1.3 66.7 + - - +
642A ASN* 3.2 7.7 + - - +
643A LYS* 4.0 9.5 + - - +
644A SER* 4.5 1.7 + - - -
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Residues in contact with MET 641 (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 SER* 1.3 75.4 - - - +
642A ASN* 1.3 58.7 + - - +
643A LYS 3.4 0.2 - - - -
644A SER* 2.9 31.2 + - - -
645A ILE* 3.4 7.6 + - - +
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Residues in contact with ASN 642 (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 LYS* 4.3 24.9 - - + +
605A LEU* 4.4 7.4 - - - +
611A THR* 5.5 0.7 - - - -
639A VAL* 6.2 0.7 - - + -
640A SER* 3.2 4.7 - - - +
641A MET* 1.3 75.8 - - - +
643A LYS* 1.3 69.5 + - - +
644A SER 3.2 0.3 + - - -
645A ILE* 3.8 3.5 + - - +
646A PRO* 3.7 18.2 - - - +
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Residues in contact with LYS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A THR* 6.2 2.0 - - - -
638A CYS* 2.9 31.2 - - - +
639A VAL* 4.5 4.4 - - + +
640A SER 4.0 7.0 + - - +
642A ASN* 1.3 78.4 - - - +
644A SER* 1.3 53.1 + - - +
646A PRO* 5.4 0.4 - - - -
647A VAL* 2.3 50.4 + - + +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A SER 4.5 1.5 + - - -
641A MET* 2.9 20.7 + - - -
643A LYS* 1.3 78.0 - - - +
645A ILE* 1.3 59.4 + - - -
647A VAL* 4.4 1.6 - - - -
648A THR* 2.5 41.9 + - - +
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Residues in contact with ILE 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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641A MET 3.4 7.9 + - - +
642A ASN* 3.8 4.0 + - - +
643A LYS 3.6 0.2 - - - -
644A SER* 1.3 80.5 - - - +
646A PRO* 1.3 61.9 - - - +
648A THR* 3.8 9.6 - - - -
649A GLN* 4.2 3.3 + - - +
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Residues in contact with PRO 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A THR* 3.3 37.7 - - - +
612A ALA* 4.7 3.6 - - - +
615A ILE* 6.2 0.2 - - - +
642A ASN 3.7 8.8 - - - +
643A LYS 3.3 3.9 - - - +
644A SER 3.2 0.2 - - - -
645A ILE* 1.3 74.7 - - - +
647A VAL* 1.3 68.4 + - - +
648A THR 3.1 2.3 + - - -
649A GLN* 3.2 20.0 + - + +
650A GLU 4.4 0.5 + - - -
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Residues in contact with VAL 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A THR* 4.9 6.6 - - - -
614A GLU* 6.1 3.1 - - - -
643A LYS* 2.3 49.1 + - + +
644A SER* 4.3 1.3 - - - +
646A PRO* 1.3 69.2 - - - +
648A THR* 1.3 63.7 + - - +
649A GLN 2.9 1.7 + - - -
650A GLU* 2.9 24.1 + - - +
651A LEU* 4.1 0.9 + - - +
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Residues in contact with THR 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 SER* 2.5 28.7 + - - +
645A ILE* 3.8 7.2 - - - -
647A VAL* 1.3 71.9 - - - +
649A GLN* 1.3 66.1 + - - +
651A LEU* 2.9 23.4 + - - +
652A ILE 4.1 1.0 + - - -
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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
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615A ILE* 5.3 6.5 - - + -
645A ILE 4.2 3.0 + - - +
646A PRO* 3.2 13.7 + - + +
647A VAL 2.9 0.4 + - - -
648A THR* 1.3 78.5 - - - +
650A GLU* 1.3 66.4 + - - +
651A LEU 2.7 2.1 + - - -
652A ILE* 3.1 15.7 + - - +
653A CYS* 3.6 6.2 + - - +
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Residues in contact with GLU 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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614A GLU 5.2 1.8 - - - +
615A ILE* 4.0 34.3 - - + +
618A PHE* 5.4 8.1 - - + -
646A PRO 4.4 0.4 + - - -
647A VAL* 2.9 14.9 + - + +
649A GLN* 1.3 76.9 - - - +
651A LEU* 1.3 51.1 + - - +
653A CYS* 3.0 11.0 + - - +
654A LYS* 2.8 32.8 + - - +
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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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647A VAL 4.1 0.6 + - - +
648A THR* 2.9 14.8 + - - +
649A GLN 2.7 5.3 + - - -
650A GLU* 1.3 75.9 - - - +
652A ILE* 1.3 65.2 + - - +
654A LYS* 2.9 25.2 + - - +
655A ALA* 3.2 5.2 + - - +
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Residues in contact with ILE 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 THR 4.1 1.0 + - - -
649A GLN* 3.1 9.2 + - - +
651A LEU* 1.3 76.3 - - - +
653A CYS* 1.3 65.2 + - - +
655A ALA* 3.0 22.9 + - - +
656A VAL* 3.8 2.4 + - - +
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Residues in contact with CYS 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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615A ILE* 5.6 5.8 - - + -
619A VAL* 5.6 7.2 - - + -
649A GLN 3.6 3.7 + - - +
650A GLU* 3.0 19.7 + - - +
652A ILE* 1.3 78.1 - - - +
654A LYS* 1.3 62.5 + - - +
655A ALA 2.8 1.6 + - - -
656A VAL* 2.9 8.6 + - - +
657A LEU* 2.9 25.5 + - + +
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Residues in contact with LYS 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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619A VAL* 5.9 3.3 - - - +
650A GLU 2.8 14.8 + - - +
651A LEU* 2.9 18.9 + - - +
653A CYS* 1.3 69.6 - - - +
655A ALA* 1.3 57.3 + - - +
657A LEU* 4.5 3.4 - - - -
658A ASN* 2.4 51.5 + - + +
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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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651A LEU 3.2 4.4 + - - +
652A ILE* 3.0 16.2 + - - +
653A CYS 2.8 2.4 + - - -
654A LYS* 1.3 81.1 - - - +
656A VAL* 1.3 59.8 + - - +
658A ASN* 4.8 1.3 - - - +
659A PRO* 3.7 11.8 - - - +
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Residues in contact with VAL 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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652A ILE 3.8 2.8 + - - +
653A CYS* 2.9 10.3 + - - +
655A ALA* 1.3 75.8 - - - +
657A LEU* 1.3 60.2 + - - +
659A PRO* 3.9 12.3 - - - +
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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 VAL* 4.1 27.1 - - + +
623A ARG* 5.8 4.0 - - - +
653A CYS* 2.9 17.0 + - + +
654A LYS* 4.5 1.3 - - - -
656A VAL* 1.3 76.5 - - - +
658A ASN* 1.3 67.0 + - - +
659A PRO* 3.3 6.8 - - - +
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Residues in contact with ASN 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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654A LYS* 2.4 46.0 + - + +
655A ALA* 4.8 1.6 - - - +
657A LEU* 1.3 65.7 - - - +
659A PRO* 1.3 72.3 - - - +
660A THR* 3.1 12.9 + - - +
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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