Contacts of the helix formed by residues 671 - 681 (chain D) in PDB entry 3F7F
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 ASP 671 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413D SER* 5.3 2.0 - - - -
667D LEU 3.1 10.2 + - - +
669D ARG 3.4 1.0 - - - -
670D GLN* 1.3 85.5 - - + +
672D LYS* 1.3 63.4 + - - +
673D CYS* 3.4 9.0 + - - +
674D LEU* 3.0 40.7 + - + +
675D LEU* 3.0 18.2 + - - +
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Residues in contact with LYS 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLN* 3.4 40.2 - - + +
14D TYR* 3.9 15.7 - - + -
413D SER* 3.2 34.7 + - - +
414D ARG* 4.1 9.4 - - - +
613D ILE* 5.1 0.7 - - + -
616D LEU* 3.7 8.4 - - + +
617D GLU* 3.9 5.8 - - - +
668D TYR* 3.3 59.1 + - + +
669D ARG* 4.4 3.0 - - - +
671D ASP* 1.3 71.2 + - - +
673D CYS* 1.3 64.3 + - - +
675D LEU* 3.2 6.1 + - - +
676D ALA* 2.9 24.1 + - - +
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Residues in contact with CYS 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D TYR* 3.6 48.2 - - + +
15D TYR* 6.0 3.1 - - - -
671D ASP* 3.2 6.7 + - - +
672D LYS* 1.3 78.3 - - - +
674D LEU* 1.3 68.7 + - - +
676D ALA* 3.1 3.0 + - - +
677D GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671D ASP* 3.0 36.7 + - + +
673D CYS* 1.3 77.9 - - - +
675D LEU* 1.3 63.6 + - - +
677D GLU* 3.1 26.8 + - - +
678D VAL* 3.0 36.0 + - + +
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Residues in contact with LEU 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D LEU* 3.7 24.9 - - + -
664D LEU* 4.0 32.3 - - + -
667D LEU* 4.2 25.4 - - + +
668D TYR* 3.6 34.3 - - + +
671D ASP 3.0 12.4 + - - +
672D LYS* 3.5 9.2 - - - +
674D LEU* 1.3 77.7 - - - +
676D ALA* 1.3 65.0 + - - +
678D VAL* 3.2 16.0 - - + +
679D LEU* 2.8 36.6 + - + +
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Residues in contact with ALA 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D TYR* 3.6 31.0 - - + +
612D SER* 4.2 9.2 - - - +
616D LEU* 4.1 11.2 - - + +
672D LYS 2.9 11.6 + - - +
673D CYS* 3.5 7.4 - - - +
675D LEU* 1.3 76.5 - - - +
677D GLU* 1.3 54.4 + - - +
679D LEU* 4.3 2.9 - - - -
680D LEU* 2.7 52.1 + - + +
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Residues in contact with GLU 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D CYS* 2.9 18.9 + - - +
674D LEU* 3.3 29.1 - - - +
675D LEU 3.1 0.2 - - - -
676D ALA* 1.3 76.9 - - - +
678D VAL* 1.3 60.9 + - - +
680D LEU* 3.4 2.7 + - - +
681D LYS* 2.9 43.4 + - + +
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Residues in contact with VAL 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D LEU* 5.8 4.0 - - + -
674D LEU* 3.0 35.7 + - + +
675D LEU* 3.2 24.9 - - + +
677D GLU* 1.3 76.2 - - - +
679D LEU* 1.3 67.8 + - + +
681D LYS* 3.9 5.1 - - - -
682D ASP* 3.4 22.9 + - - +
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Residues in contact with LEU 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D LEU* 4.5 7.2 - - + -
619D LEU* 3.5 31.6 - - + -
664D LEU* 4.4 6.7 - - + -
675D LEU* 2.8 41.0 + - + +
676D ALA* 3.7 4.7 - - - +
678D VAL* 1.3 85.2 - - + +
680D LEU* 1.3 62.8 + - + +
682D ASP* 3.5 25.3 - - - +
683D SER* 4.3 3.1 + - - -
705D LEU* 4.4 22.4 - - + +
708D ASN* 4.8 10.2 + - + -
709D VAL* 4.5 15.9 - - + -
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Residues in contact with LEU 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607D PHE* 4.5 13.2 - - + -
612D SER* 4.1 27.1 - - - +
615D SER* 6.0 2.9 - - - -
616D LEU* 6.3 2.2 - - + +
676D ALA* 2.7 40.9 + - + +
677D GLU* 4.4 2.5 - - - +
679D LEU* 1.3 80.5 - - + +
681D LYS* 1.3 58.1 + - - +
682D ASP 3.1 6.4 + - - -
683D SER* 3.5 14.1 + - - +
686D PHE 3.5 19.9 - - - +
687D SER* 3.6 10.5 - - - +
688D PHE 4.7 1.8 - - - +
689D GLY* 4.2 24.7 - - - +
701D TYR* 4.0 19.3 - - - +
705D LEU* 5.1 8.5 - - + -
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Residues in contact with LYS 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677D GLU* 2.9 30.0 + - + +
678D VAL* 3.9 6.3 - - - +
679D LEU 3.4 0.2 - - - -
680D LEU* 1.3 76.2 - - - +
682D ASP* 1.3 60.5 - - - +
683D SER 3.6 4.3 - - - +
687D SER* 5.1 9.2 - - - +
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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