Contacts of the helix formed by residues 643 - 658 (chain B) 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 LYS 643 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B GLU* 5.8 8.5 - - + -
638B CYS* 4.6 18.2 - - + -
639B VAL 5.0 0.4 - - - +
640B SER* 3.2 30.6 + - - +
641B MET 3.1 1.0 - - - -
642B ASN* 1.3 78.1 - - - +
644B SER* 1.3 60.6 + - - +
646B PRO* 3.5 10.9 - - - +
647B VAL* 3.4 16.6 + - - +
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Residues in contact with SER 644 (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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640B SER 3.9 2.4 + - - -
641B MET* 2.9 17.7 + - - -
643B LYS* 1.3 76.6 - - - +
645B ILE* 1.3 68.2 + - - +
647B VAL* 2.8 25.5 + - - +
648B THR* 3.6 5.0 + - - -
706B GLU* 5.7 9.4 - - - -
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Residues in contact with ILE 645 (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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641B MET 4.4 0.4 + - - -
642B ASN* 3.4 10.8 + - - +
644B SER* 1.3 77.0 - - - +
646B PRO* 1.3 62.9 - - - +
648B THR* 3.9 10.8 + - - -
649B GLN* 4.7 0.7 + - - +
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Residues in contact with PRO 646 (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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607B GLU* 5.8 8.1 - - + +
611B THR* 5.4 14.8 - - - -
642B ASN 4.3 1.9 - - - +
643B LYS* 3.5 13.3 - - - +
644B SER 3.1 0.2 - - - -
645B ILE* 1.3 77.1 - - - +
647B VAL* 1.3 66.0 + - - +
649B GLN* 3.0 24.8 + - + +
650B GLU* 4.1 1.0 + - - +
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Residues in contact with VAL 647 (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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643B LYS 3.4 9.2 + - - +
644B SER* 2.8 21.9 + - - +
646B PRO* 1.3 73.5 - - - +
648B THR* 1.3 63.2 + - - +
650B GLU* 3.0 23.4 + - - +
651B LEU* 4.0 1.7 + - - +
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Residues in contact with THR 648 (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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644B SER 3.6 4.6 + - - -
645B ILE* 4.3 9.6 - - - -
646B PRO 3.0 1.0 + - - -
647B VAL* 1.3 77.5 - - - +
649B GLN* 1.3 64.6 + - - +
651B LEU* 3.0 22.5 + - - +
652B ILE 4.4 0.3 + - - -
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Residues in contact with GLN 649 (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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615B ILE* 6.3 2.5 - - + -
645B ILE 4.7 1.0 + - - +
646B PRO* 3.0 13.8 + - + +
648B THR* 1.3 77.8 - - - +
650B GLU* 1.3 64.6 + - - +
651B LEU 2.9 1.7 + - - -
652B ILE* 3.0 19.8 + - - +
653B CYS* 4.2 1.0 + - - +
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Residues in contact with GLU 650 (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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615B ILE* 5.6 11.4 - - - +
618B PHE* 5.8 8.7 - - + -
646B PRO 4.1 1.0 + - - +
647B VAL* 3.0 16.2 + - - +
649B GLN* 1.3 78.6 - - - +
651B LEU* 1.3 63.9 + - - +
653B CYS* 2.9 13.4 + - + +
654B LYS* 2.8 19.8 + - - +
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Residues in contact with LEU 651 (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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647B VAL 4.0 1.2 + - - +
648B THR* 3.0 15.6 + - - +
649B GLN 2.9 0.8 + - - -
650B GLU* 1.3 78.1 - - - +
652B ILE* 1.3 51.6 + - - +
654B LYS* 2.9 13.2 - - + +
655B ALA* 2.5 37.2 + - - +
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Residues in contact with ILE 652 (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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648B THR 4.4 0.4 + - - -
649B GLN 3.0 12.8 + - - +
651B LEU* 1.3 77.4 - - - +
653B CYS* 1.3 51.2 + - - +
655B ALA* 3.0 9.8 + - - +
656B VAL* 2.7 34.9 + - - +
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Residues in contact with CYS 653 (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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615B ILE* 4.7 15.5 - - + +
619B VAL* 4.4 20.8 - - + +
649B GLN 4.2 1.0 + - - +
650B GLU* 2.9 13.9 + - + +
652B ILE* 1.3 76.9 - - - +
654B LYS* 1.3 50.9 + - - +
656B VAL* 3.0 11.3 + - + +
657B LEU* 2.3 40.4 + - - +
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Residues in contact with LYS 654 (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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650B GLU 2.8 7.3 + - - +
651B LEU* 2.9 24.4 + - + +
653B CYS* 1.3 74.9 - - - +
655B ALA* 1.3 56.6 + - - +
657B LEU 2.7 3.2 + - - -
658B ASN* 1.9 56.6 + - + +
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Residues in contact with ALA 655 (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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651B LEU 2.5 15.4 + - - +
652B ILE* 3.5 10.3 - - - +
654B LYS* 1.3 72.1 - - - +
656B VAL* 1.3 60.8 + - - +
658B ASN* 3.6 6.5 + - - +
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Residues in contact with VAL 656 (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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652B ILE 2.7 17.6 + - - +
653B CYS* 3.0 17.7 - - - +
655B ALA* 1.3 75.7 - - - +
657B LEU* 1.3 56.4 + - + +
658B ASN 4.2 0.2 + - - -
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Residues in contact with LEU 657 (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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619B VAL* 4.7 20.6 - - + +
653B CYS 2.3 26.2 + - - +
654B LYS* 2.7 5.8 + - - -
656B VAL* 1.3 69.6 - - + -
658B ASN* 1.4 56.7 + - - -
659B PRO* 3.4 5.3 - - - +
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Residues in contact with ASN 658 (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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654B LYS* 1.9 50.0 + - + +
655B ALA* 3.6 7.8 + - - +
656B VAL 3.7 1.4 + - - -
657B LEU* 1.4 68.7 - - - +
659B PRO* 1.3 64.7 - - - +
660B THR* 3.2 5.5 + - - -
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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