Contacts of the helix formed by residues 1012 - 1021 (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 PRO1012 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006u MET 5.5 3.6 - - - +
1009u MET* 3.5 15.5 - - + +
1010u THR 3.5 4.1 - - - +
1011u PRO* 1.3 76.8 - - - +
1013u ILE* 1.3 65.9 + - - +
1014u LYS* 3.2 14.1 + - + +
1015u ASP* 3.4 4.4 + - - +
1016u LEU* 3.3 17.9 + - - +
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Residues in contact with ILE1013 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006u MET* 5.4 7.7 + - + +
1012u PRO* 1.3 72.5 - - - +
1014u LYS* 1.3 64.6 + - - +
1015u ASP 3.3 0.9 + - - -
1016u LEU* 3.6 13.7 + - - -
1017u LEU* 3.8 16.4 + - + +
1018u PRO 5.3 0.2 - - - -
1042u ILE* 5.9 6.1 - - + -
1046u GLY* 4.8 12.6 - - - +
1049u TYR* 3.7 24.3 - - + +
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Residues in contact with LYS1014 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012u PRO* 3.2 9.4 - - + +
1013u ILE* 1.3 78.1 - - - +
1015u ASP* 1.3 59.8 + - + +
1018u PRO* 5.1 6.5 - - - +
1049u TYR* 3.7 22.3 - - + +
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Residues in contact with ASP1015 (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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223t ARG 5.4 3.3 - - - +
224t SER* 5.3 15.9 - - - -
1012u PRO* 3.4 6.0 + - - +
1014u LYS* 1.3 78.4 - - + +
1016u LEU* 1.3 61.7 + - - +
1017u LEU 3.9 0.7 - - - -
1018u PRO* 4.5 9.2 - - - +
1019u ARG* 3.9 15.8 + - - +
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Residues in contact with LEU1016 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011u PRO* 4.4 12.6 - - + +
1012u PRO 3.3 20.3 + - - +
1013u ILE* 3.6 5.5 + - - -
1015u ASP* 1.3 77.9 - - - +
1017u LEU* 1.3 61.8 + - - +
1018u PRO 3.4 0.4 - - - -
1019u ARG* 3.0 9.8 + - - +
1020u LEU* 2.9 24.4 + - - +
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Residues in contact with LEU1017 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013u ILE* 3.8 14.4 + - + +
1016u LEU* 1.3 78.3 - - - +
1018u PRO* 1.4 57.2 - - - +
1020u LEU* 2.9 23.5 + - + +
1021u THR* 3.0 14.4 + - - -
1042u ILE* 5.5 11.7 - - + -
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Residues in contact with PRO1018 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206t LYS 5.6 3.4 - - - +
223t ARG* 4.5 31.1 - - + +
1013u ILE 5.3 0.4 - - - -
1014u LYS 5.1 4.4 - - - +
1015u ASP* 4.8 10.9 - - - +
1016u LEU 3.4 2.4 - - - -
1017u LEU* 1.4 75.1 - - - +
1019u ARG* 1.3 61.1 + - - +
1021u THR* 3.6 17.5 + - - +
1022u PRO* 4.4 4.0 - - - +
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Residues in contact with ARG1019 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223t ARG* 5.4 2.9 - - + +
979u TYR 5.2 9.2 - - - +
1015u ASP 3.9 12.4 + - - +
1016u LEU* 3.0 13.0 + - - +
1018u PRO* 1.3 77.3 - - - +
1020u LEU* 1.3 60.7 + - - +
1021u THR 3.3 0.2 - - - -
1022u PRO* 4.2 8.0 - - - +
1023u ILE* 4.2 8.8 + - - +
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Residues in contact with LEU1020 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016u LEU 2.9 10.9 + - - +
1017u LEU* 2.9 16.6 + - - +
1019u ARG* 1.3 78.3 - - - +
1021u THR* 1.3 58.4 + - - +
1022u PRO 3.5 0.2 - - - -
1023u ILE* 3.2 10.3 + - + +
1024u LEU* 3.1 26.2 + - - +
1035u CYS* 5.4 11.0 - - + +
1038u LEU* 6.5 1.1 - - + -
1039u VAL* 6.2 3.6 - - + -
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Residues in contact with THR1021 (chain u).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209t GLY* 5.4 11.9 - - - +
1017u LEU 3.0 13.1 + - - -
1018u PRO* 3.9 11.4 - - - -
1019u ARG 3.3 1.4 - - - -
1020u LEU* 1.3 77.3 - - - +
1022u PRO* 1.3 60.7 - - - +
1024u LEU* 3.4 19.8 + - - +
1025u LYS* 3.9 4.5 + - - +
1058u ILE* 5.9 7.0 - - - -
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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