Contacts of the helix formed by residues 683 - 691 (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 LEU 683 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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679u ILE 2.9 10.7 + - - +
680u LEU* 3.0 24.3 + - + +
681u PRO 3.3 0.6 - - - -
682u HIS* 1.3 76.1 - - - +
684u ARG* 1.3 55.6 + - - +
686u LEU* 3.0 7.9 + - - +
687u VAL* 2.8 36.4 + - - +
716u ALA* 6.3 2.9 - - + -
720u GLY* 6.4 2.2 - - - -
723u SER* 5.9 3.8 - - - -
217v LEU* 6.2 1.8 - - + -
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Residues in contact with ARG 684 (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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681u PRO 5.1 1.2 + - - +
682u HIS 3.6 0.2 - - - -
683u LEU* 1.3 78.3 - - - +
685u SER* 1.3 58.2 + - - +
687u VAL* 3.0 6.0 + - - +
688u GLU* 2.9 32.7 + - - +
723u SER* 4.6 20.4 - - - -
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Residues in contact with SER 685 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645u LEU* 6.1 1.4 - - - +
682u HIS* 4.1 12.4 + - - -
683u LEU 3.4 0.2 - - - -
684u ARG* 1.3 77.6 - - - +
686u LEU* 1.3 58.0 + - - +
688u GLU* 4.4 8.3 + - - +
689u ILE* 4.7 5.5 + - - +
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Residues in contact with LEU 686 (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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668u VAL* 6.0 4.0 - - + +
682u HIS 3.4 19.3 + - - +
683u LEU* 3.0 7.4 + - - +
685u SER* 1.3 79.6 - - - +
687u VAL* 1.3 61.9 + - - +
688u GLU 3.3 0.7 - - - -
689u ILE* 3.5 19.3 - - - +
690u ILE* 4.1 4.2 + - - +
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Residues in contact with VAL 687 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683u LEU* 2.8 20.4 + - + +
684u ARG* 3.0 5.1 + - - +
686u LEU* 1.3 70.0 - - - +
688u GLU* 1.3 59.7 + - - +
689u ILE 3.1 2.5 - - - -
690u ILE* 2.9 29.0 + - + +
691u GLU* 3.8 6.1 + - - +
712u LEU* 6.1 5.4 - - + -
723u SER* 4.8 15.9 - - - +
724u PHE* 6.0 1.3 - - - -
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Residues in contact with GLU 688 (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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684u ARG 2.9 16.2 + - - +
685u SER* 4.8 6.5 - - - +
686u LEU 3.3 0.4 - - - -
687u VAL* 1.3 74.0 - - - +
689u ILE* 1.3 64.2 + - - +
690u ILE 3.4 0.2 - - - -
691u GLU* 4.4 7.2 + - - +
692u HIS* 4.9 2.1 + - - +
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Residues in contact with ILE 689 (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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648u LEU 5.8 1.1 - - - +
649u LYS* 5.5 11.4 - - + -
652u CYS* 5.1 16.1 - - + +
685u SER 4.7 4.2 + - - +
686u LEU* 3.5 14.4 + - - +
687u VAL 3.1 0.4 - - - -
688u GLU* 1.3 79.5 - - - +
690u ILE* 1.3 58.9 + - + +
692u HIS* 3.0 30.5 + - - +
693u GLY 4.4 0.5 + - - -
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Residues in contact with ILE 690 (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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686u LEU 4.7 2.7 - - - +
687u VAL* 2.9 18.6 + - + +
689u ILE* 1.3 78.9 - - + +
691u GLU* 1.3 58.2 + - - +
692u HIS 3.2 0.2 - - - -
693u GLY* 3.1 22.4 + - - +
694u LEU* 5.2 1.9 - - - +
705u SER* 5.0 16.5 - - - +
708u ALA* 5.8 7.0 - - + -
709u ILE* 6.1 5.4 - - + +
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Residues in contact with GLU 691 (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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687u VAL 3.8 6.7 + - - +
688u GLU* 4.4 5.1 + - - +
689u ILE 3.1 1.6 + - - -
690u ILE* 1.3 76.2 - - - +
692u HIS* 1.3 61.2 + - - +
693u GLY 3.2 10.4 - - - +
694u LEU* 6.0 1.1 - - - -
726u SER* 4.1 29.6 - - - +
727u VAL* 5.7 2.7 - - + -
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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