Contacts of the helix formed by residues 667 - 679 (chain U) in PDB entry 6FF7
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 667 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426U LEU* 5.0 2.7 - - - +
632U ASN* 1.0 89.2 - - - +
633U GLN* 1.2 56.2 - - - +
636U GLN* 4.0 7.7 - - + +
666U PHE* 1.3 73.1 - - - +
668U ALA* 1.3 52.4 + - - +
670U LEU* 3.4 6.2 + - - +
671U GLU* 3.0 28.6 + - - +
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Residues in contact with ALA 668 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531U TRP* 4.4 10.3 - - + -
630U ASP* 6.2 0.2 - - + -
631U PRO* 4.0 8.1 - - + -
632U ASN* 0.2 156.0 - - + +
666U PHE 5.6 0.9 - - - +
667U LYS 2.4 8.3 - - - -
669U VAL* 1.3 55.2 + - - +
671U GLU* 3.4 6.3 + - - +
672U THR* 3.0 27.4 + - - -
1043U ALA 4.7 3.6 - - - +
1044U LEU* 5.2 17.9 - - + +
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Residues in contact with VAL 669 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473U PHE* 6.1 5.4 - - + -
632U ASN* 2.9 1.2 - - - +
666U PHE* 3.3 14.6 + - - +
667U LYS 3.3 0.2 - - - -
668U ALA* 1.3 76.7 - - - +
670U LEU* 1.3 59.0 + - - +
672U THR* 3.2 8.2 + - - -
673U ILE* 2.9 28.8 + - - +
1043U ALA* 5.1 16.2 - - + -
1044U LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 670 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426U LEU* 5.1 16.2 - - + +
470U PHE* 5.8 8.6 - - + +
473U PHE* 6.3 3.8 - - + +
474U ARG* 5.9 8.3 - - + -
666U PHE 2.9 17.6 + - - +
667U LYS* 3.7 6.7 - - - +
669U VAL* 1.3 75.8 - - - +
671U GLU* 1.3 57.8 + - - +
673U ILE* 3.3 8.2 + - - +
674U ARG* 2.9 30.3 + - - +
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Residues in contact with GLU 671 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426U LEU* 5.9 2.6 - - + +
530U ASN* 5.2 14.5 - - + +
531U TRP* 4.8 13.0 - - + +
632U ASN* 5.3 0.2 - - - -
635U GLN* 5.7 4.5 - - + -
667U LYS 3.0 17.5 + - - +
668U ALA* 3.6 8.7 - - - +
669U VAL 3.2 0.2 - - - -
670U LEU* 1.3 76.6 - - - +
672U THR* 1.3 56.0 + - - +
674U ARG* 3.3 6.1 + - - +
675U ASN* 2.9 30.4 + - - +
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Residues in contact with THR 672 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668U ALA 3.0 15.1 + - - -
669U VAL* 3.4 9.6 - - - -
671U GLU* 1.3 77.6 - - - +
673U ILE* 1.3 56.4 + - - +
675U ASN* 3.3 7.4 + - - +
676U LEU* 3.0 27.5 + - - +
1043U ALA* 3.9 21.5 - - - -
1046U ARG* 5.1 10.1 - - - -
1047U HIS 6.1 0.2 - - - -
1074U ILE* 6.3 2.9 - - - -
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Residues in contact with ILE 673 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466U LEU* 5.0 11.6 - - + +
469U ASN* 6.1 0.7 - - + -
470U PHE* 4.7 22.4 - - + +
669U VAL 2.9 15.9 + - - +
670U LEU* 3.7 7.2 - - - +
671U GLU 3.3 0.2 - - - -
672U THR* 1.3 75.9 - - - +
674U ARG* 1.3 62.4 + - - +
676U LEU* 3.3 9.4 + - - +
677U MET* 3.1 21.7 + - - +
1070U ILE* 6.4 2.5 - - + -
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Residues in contact with ARG 674 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421U LEU* 6.0 6.5 - - + +
470U PHE* 6.1 0.2 - - - +
670U LEU 2.9 17.6 + - - +
671U GLU* 3.7 6.5 - - - +
673U ILE* 1.3 75.2 - - - +
675U ASN* 1.3 64.1 + - - +
677U MET* 3.2 10.5 + - - +
678U ASN* 3.1 20.8 + - - +
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Residues in contact with ASN 675 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671U GLU 2.9 17.4 + - - +
672U THR* 3.6 7.9 - - - +
674U ARG* 1.3 72.5 - - - +
676U LEU* 1.3 66.9 + - - +
678U ASN* 2.9 17.8 + - - +
679U THR* 3.0 14.0 + - - -
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Residues in contact with LEU 676 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466U LEU* 5.9 4.0 - - + -
672U THR 3.0 13.8 + - - +
673U ILE* 3.4 13.2 - - - +
675U ASN* 1.3 76.0 - - - +
677U MET* 1.3 56.7 + - - +
679U THR* 2.9 31.1 + - - +
681U CYS* 4.5 11.5 - - + +
1077U LEU* 6.1 4.3 - - + -
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Residues in contact with MET 677 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418U ILE* 5.4 8.0 - - - +
421U LEU* 5.9 7.2 - - + -
463U HIS* 5.9 7.4 - - + +
466U LEU* 4.9 15.4 - - + +
673U ILE 3.1 10.2 + - - +
674U ARG* 3.2 12.3 + - - +
676U LEU* 1.3 78.3 - - - +
678U ASN* 1.3 57.5 + - - +
679U THR 4.0 4.6 - - - +
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Residues in contact with ASN 678 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418U ILE* 6.5 0.7 - - - -
674U ARG 3.1 10.5 + - - +
675U ASN* 2.9 13.6 + - - +
677U MET* 1.3 76.1 - - - +
679U THR* 1.3 61.2 + - - +
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Residues in contact with THR 679 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675U ASN 3.0 8.0 + - - -
676U LEU* 2.9 19.4 + - - +
677U MET 4.0 5.0 - - - +
678U ASN* 1.3 81.5 - - - +
680U ASP* 1.3 61.1 + - - +
681U CYS* 3.0 13.8 + - - +
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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
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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