Contacts of the helix formed by residues 644 - 653 (chain K) in PDB entry 6R1U
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 644 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642K PRO 3.6 2.1 + - - -
643K LEU* 1.3 77.5 - - - +
645K GLU* 1.3 65.0 + - - +
646K LYS* 3.5 9.7 + - - +
647K LYS* 2.9 33.8 + - - +
648K MET* 3.0 21.1 + - - +
786K ILE* 5.7 1.0 - - - +
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Residues in contact with GLU 645 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643K LEU 3.8 0.8 + - - -
644K SER* 1.3 72.8 - - - +
646K LYS* 1.3 63.5 + - - +
648K MET* 3.2 9.1 + - + +
649K LYS* 3.0 52.7 + - + +
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Residues in contact with LYS 646 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644K SER* 3.1 9.3 - - - +
645K GLU* 1.3 80.6 - - - +
647K LYS* 1.3 63.7 + - + +
649K LYS* 3.3 10.8 + - - +
650K ALA* 3.2 20.4 + - - +
777K GLU* 5.3 6.0 + - - -
781K ILE* 3.9 36.7 - - + +
784K GLU* 4.5 12.9 + - - +
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Residues in contact with LYS 647 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643K LEU* 4.5 11.7 - - + -
644K SER* 2.9 31.2 + - - +
646K LYS* 1.3 76.9 - - + +
648K MET* 1.3 57.0 + - - +
650K ALA* 3.2 3.8 + - - +
651K ILE* 2.8 40.2 + - + +
781K ILE* 2.8 41.6 + - + +
782K ILE* 3.2 17.0 + - - +
784K GLU* 2.7 33.1 + - - +
785K ASP 5.0 0.9 - - - -
786K ILE* 3.7 30.7 - - + -
792K PHE* 3.7 11.2 - - + -
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Residues in contact with MET 648 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632K LEU 4.5 15.5 - - - +
633K GLN 5.5 3.6 - - - +
635K GLY* 6.4 0.7 - - - -
643K LEU* 4.0 36.6 - - - +
644K SER 3.0 17.7 + - - +
645K GLU* 3.2 11.0 + - + +
647K LYS* 1.3 76.0 - - - +
649K LYS* 1.3 57.7 + - + +
651K ILE* 3.3 13.3 + - + +
652K ASN* 2.9 54.3 + - - +
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Residues in contact with LYS 649 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645K GLU* 3.0 49.4 + - + +
646K LYS* 3.6 11.0 - - - +
647K LYS 3.3 0.2 - - - -
648K MET* 1.3 75.3 - - - +
650K ALA* 1.3 59.0 + - - +
652K ASN* 3.4 5.4 + - - +
653K SER* 2.9 30.2 + - - -
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Residues in contact with ALA 650 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646K LYS 3.2 3.7 + - - +
647K LYS 3.2 8.8 + - - +
649K LYS* 1.3 76.3 - - - +
651K ILE* 1.3 67.7 + - - +
653K SER* 2.8 23.6 + - - -
654K LEU* 3.5 12.3 + - - +
778K ALA* 3.9 18.7 - - - +
781K ILE* 3.7 38.8 - - + -
782K ILE* 4.1 5.3 - - + +
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Residues in contact with ILE 651 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629K LEU* 3.6 9.9 - - + +
632K LEU* 4.1 26.7 - - + +
633K GLN* 3.0 53.6 + - + +
643K LEU* 4.0 26.7 - - + -
647K LYS* 2.8 24.2 + - + +
648K MET* 3.3 18.4 + - + +
650K ALA* 1.3 76.5 - - - +
652K ASN* 1.3 63.3 - - - +
653K SER 3.5 0.2 + - - -
654K LEU 3.6 4.2 + - - -
782K ILE* 3.8 26.5 - - + -
792K PHE* 6.2 0.7 - - + -
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Residues in contact with ASN 652 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633K GLN* 3.9 28.2 - - - +
648K MET* 2.9 39.3 + - - +
649K LYS* 3.7 5.7 - - - +
651K ILE* 1.3 74.7 - - - +
653K SER* 1.3 57.6 + - - +
654K LEU 3.2 2.9 - - - -
771K LYS* 2.7 32.5 + - - +
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Residues in contact with SER 653 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503K GLN* 6.1 0.7 - - - -
649K LYS 2.9 14.7 + - - -
650K ALA* 2.8 21.1 + - - -
652K ASN* 1.3 79.0 - - - +
654K LEU* 1.3 59.6 + - - +
771K LYS* 3.3 31.8 + - - +
772K THR 5.2 0.4 - - - +
773K GLY 5.3 1.8 - - - -
774K GLY* 4.1 20.2 - - - -
775K SER 4.8 0.9 + - - -
778K ALA* 3.5 17.2 - - - +
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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