Contacts of the helix formed by residues 676 - 681 (chain q) 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 ASN 676 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615q PHE* 6.0 2.2 - - - -
616q LEU 4.4 2.4 + - - -
675q THR* 1.3 71.2 - - - +
677q ILE* 1.3 66.3 + - - +
678q ALA 3.0 3.1 - - - -
679q GLU* 2.8 28.4 + - + +
680q THR 4.3 0.7 + - - -
681q SER* 5.2 0.3 + - - -
696q CYS* 5.1 14.8 - - + -
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Residues in contact with ILE 677 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455q ARG* 5.4 8.3 - - + -
457q VAL* 5.2 14.1 - - + -
458q ALA 6.3 0.2 - - - +
648q ILE* 5.8 6.5 - - + +
649q TYR* 5.9 5.8 - - - -
650q ALA* 6.2 0.4 - - - +
674q ALA* 5.8 1.6 - - + -
675q THR* 2.9 11.9 + - - +
676q ASN* 1.3 78.7 - - - +
678q ALA* 1.3 56.8 + - - +
681q SER* 2.9 42.9 + - - -
682q LEU* 3.9 2.1 + - - -
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Residues in contact with ALA 678 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613q LEU* 5.8 7.2 - - + -
674q ALA* 3.7 27.3 - - + +
675q THR 3.3 3.5 + - - +
676q ASN 3.0 0.6 - - - -
677q ILE* 1.3 78.1 - - - +
679q GLU* 1.3 67.4 + - - +
682q LEU* 4.0 17.7 - - - +
726q ARG* 4.9 10.6 - - - +
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Residues in contact with GLU 679 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425q THR* 4.6 6.8 - - - -
676q ASN* 2.8 27.1 + - + +
678q ALA* 1.3 82.8 - - - +
680q THR* 1.3 61.6 + - - +
682q LEU 5.1 0.7 - - - +
719q SER* 5.4 8.3 - - - +
722q GLN* 4.3 31.3 - - + +
723q ARG* 5.3 11.0 - - + +
726q ARG* 5.3 3.7 - - - +
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Residues in contact with THR 680 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425q THR* 3.7 23.2 - - - -
522q GLU* 6.3 3.4 - - - -
554q ALA* 4.6 20.9 - - - -
676q ASN 4.3 0.6 + - - -
677q ILE 4.0 0.4 + - - -
679q GLU* 1.3 80.0 - - - +
681q SER* 1.3 65.6 + - - +
682q LEU* 3.4 3.6 + - - -
722q GLN* 5.7 4.7 - - - -
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Residues in contact with SER 681 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430q THR* 5.7 5.5 - - - -
455q ARG* 4.8 8.5 - - - -
458q ALA* 4.0 29.3 - - - +
522q GLU* 6.1 4.7 - - - -
677q ILE* 2.9 29.7 + - - -
679q GLU 3.8 0.2 - - - -
680q THR* 1.3 79.7 - - - +
682q LEU* 1.3 61.9 + - - +
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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