Contacts of the helix formed by residues 1055 - 1063 (chain A) 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 LEU1055 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812A THR* 6.1 3.8 - - - +
815A HIS* 6.3 2.9 - - + -
816A TRP* 6.3 4.0 - - + -
1050A LEU* 5.6 2.0 - - + -
1054A GLY* 1.3 74.5 - - - -
1056A HIS* 1.3 64.2 + - - +
1057A ARG 3.7 0.4 - - - -
1058A ALA* 4.3 1.9 - - - +
1059A SER* 3.3 23.3 + - - -
191R ASP* 5.3 9.9 + - + +
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Residues in contact with HIS1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A GLY* 4.6 0.2 - - - -
1055A LEU* 1.3 78.4 - - - +
1057A ARG* 1.3 60.5 + - - +
1059A SER* 3.3 6.6 + - - -
1060A GLU* 2.9 25.9 + - - +
191R ASP* 4.9 17.0 - - + +
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Residues in contact with ARG1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053A LEU* 3.7 22.2 + - + +
1056A HIS* 1.3 76.0 - - - +
1058A ALA* 1.3 60.3 + - - +
1060A GLU* 3.1 9.5 + - - +
1061A MET* 2.9 28.2 + - - +
1083A HIS* 4.7 20.4 - - + -
1085A ILE 6.2 0.4 - - - +
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Residues in contact with ALA1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A ASP 6.2 0.2 - - - -
1050A LEU* 5.5 6.7 - - + -
1053A LEU* 4.4 14.2 + - + +
1054A GLY 3.9 18.2 - - - +
1055A LEU* 4.3 3.7 + - - +
1056A HIS 3.4 0.4 - - - -
1057A ARG* 1.3 77.8 - - - +
1059A SER* 1.3 57.4 + - - +
1061A MET* 3.9 6.2 - - - +
1062A ALA* 2.9 33.6 + - - +
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Residues in contact with SER1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A SER* 6.5 0.9 - - - -
1055A LEU 3.3 19.3 + - - -
1056A HIS* 3.3 7.1 + - - -
1057A ARG 3.3 0.6 - - - -
1058A ALA* 1.3 75.4 - - - +
1060A GLU* 1.3 60.6 + - - +
1062A ALA* 5.4 0.4 - - - -
1063A GLY* 3.1 31.2 + - - +
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Residues in contact with GLU1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056A HIS 2.9 13.1 + - - +
1057A ARG* 3.1 12.5 + - - +
1059A SER* 1.3 79.9 - - - +
1061A MET* 1.3 62.9 + - - +
1063A GLY* 3.7 6.2 + - - -
1074A PHE* 5.4 5.0 - - - +
1075A GLN 5.4 6.4 + - - +
1079A THR* 5.5 15.3 - - - +
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Residues in contact with MET1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057A ARG 2.9 15.5 + - - +
1058A ALA* 3.3 7.1 + - - +
1060A GLU* 1.3 79.8 - - - +
1062A ALA* 1.3 60.9 + - - +
1063A GLY* 3.5 0.3 + - - -
1069A ASN* 3.5 17.5 - - - +
1070A ASP 5.1 1.4 - - - +
1073A SER 4.2 5.7 - - - +
1074A PHE* 5.4 3.7 - - - -
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Residues in contact with ALA1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937A PRO* 4.2 27.8 - - + -
938A PRO* 5.2 4.5 - - - -
1058A ALA 2.9 16.3 + - - +
1059A SER* 5.4 0.4 - - - -
1061A MET* 1.3 77.3 - - - +
1063A GLY* 1.3 65.0 + - - +
1064A PRO 4.3 0.5 - - - +
1068A PRO* 3.9 6.6 - - - +
1069A ASN* 3.6 22.4 + - - -
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Residues in contact with GLY1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A SER* 3.1 26.1 + - - +
1060A GLU 3.7 6.0 + - - -
1061A MET 3.3 3.6 - - - -
1062A ALA* 1.3 82.9 - - - +
1064A PRO* 1.3 64.1 - - - +
1065A PRO 3.9 0.3 - - - -
1067A MET 4.5 4.9 - - - -
1069A ASN* 5.2 3.6 - - - -
1075A GLN* 6.5 1.3 - - - -
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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