Contacts of the helix formed by residues 1092 - 1100 (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 ASP1092 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5608 LYS 5.9 0.4 - - - +
5618 MET* 4.9 19.7 - - + -
5628 GLY 5.7 1.8 - - - +
1056u MET* 5.8 8.5 - - + -
1088u ILE 5.7 3.1 - - - +
1089u GLY 4.2 4.7 + - - +
1091u HIS* 1.3 77.9 - - - +
1093u VAL* 1.3 61.9 + - - +
1094u LEU 3.1 1.9 + - - -
1095u ALA* 3.7 12.5 + - - +
1096u THR* 3.8 8.3 + - - -
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Residues in contact with VAL1093 (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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1056u MET* 6.6 0.4 - - - -
1059u CYS* 4.8 17.5 - - + -
1081u PHE* 5.6 4.0 - - + +
1084u ILE* 5.7 4.9 - - + -
1085u ALA* 5.1 18.2 - - + +
1089u GLY 4.8 5.6 + - - +
1090u PRO* 6.0 0.9 - - + -
1091u HIS 4.6 1.2 - - - +
1092u ASP* 1.3 75.9 - - - +
1094u LEU* 1.3 58.7 + - - +
1095u ALA 3.4 0.2 - - - -
1096u THR* 3.3 10.4 + - - -
1097u LEU* 2.9 28.9 + - - +
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Residues in contact with LEU1094 (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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1090u PRO* 4.1 22.7 - - + +
1091u HIS* 4.3 10.0 - - - +
1092u ASP 3.1 0.8 - - - +
1093u VAL* 1.3 77.9 - - - +
1095u ALA* 1.3 57.8 + - - +
1097u LEU* 3.2 6.5 + - - +
1098u LEU* 2.9 29.5 + - - +
1127u THR 5.8 1.8 - - - +
1128u VAL* 6.0 6.7 - - + -
1131u ALA* 6.2 4.3 - - + -
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Residues in contact with ALA1095 (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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1091u HIS 4.7 5.5 + - - +
1092u ASP* 3.7 10.5 + - - +
1093u VAL 3.4 0.2 - - - -
1094u LEU* 1.3 78.7 - - - +
1096u THR* 1.3 57.3 + - - +
1098u LEU* 3.4 5.9 + - - +
1099u ASN* 2.9 30.7 + - - +
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Residues in contact with THR1096 (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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1059u CYS* 5.1 17.9 - - - -
1060u PHE* 5.5 5.2 - - - -
1092u ASP 3.8 4.5 + - - -
1093u VAL* 3.3 18.9 + - - -
1094u LEU 3.2 0.4 - - - -
1095u ALA* 1.3 78.8 - - - +
1097u LEU* 1.3 57.5 + - - +
1099u ASN* 3.2 6.9 + - - +
1100u ASN* 3.0 27.0 + - - +
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Residues in contact with LEU1097 (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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1093u VAL 2.9 16.1 + - - +
1094u LEU* 3.2 6.5 + - - +
1096u THR* 1.3 75.8 - - - +
1098u LEU* 1.3 60.9 + - - +
1100u ASN* 3.6 19.6 + - - +
1101u LEU* 4.2 2.6 + - - +
1112u THR* 4.2 22.8 - - - +
1115u ALA* 5.1 9.4 - - + -
1116u ILE* 5.2 10.1 - - + +
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Residues in contact with LEU1098 (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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1094u LEU 2.9 15.6 + - - +
1095u ALA* 4.0 6.7 - - - +
1097u LEU* 1.3 74.3 - - - +
1099u ASN* 1.3 63.8 + - - +
1100u ASN 3.2 2.0 - - - -
1101u LEU* 3.3 20.2 + - - +
1102u LYS 4.9 0.2 + - - -
1135u GLU* 5.6 9.2 - - + -
1143u VAL* 5.7 0.9 - - - +
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Residues in contact with ASN1099 (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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1095u ALA 2.9 19.2 + - - +
1096u THR* 3.2 7.4 + - - +
1098u LEU* 1.3 72.1 - - - +
1100u ASN* 1.3 56.7 + - - +
1101u LEU 3.1 8.7 + - - -
1102u LYS* 3.9 12.5 + - - +
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Residues in contact with ASN1100 (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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1063u LEU* 5.2 14.4 - - + -
1096u THR 3.0 15.9 + - - +
1097u LEU* 3.7 12.1 - - - +
1098u LEU 3.2 0.8 - - - -
1099u ASN* 1.3 76.7 - - - +
1101u LEU* 1.3 57.0 + - - -
1102u LYS 3.5 2.9 + - - -
1103u VAL* 4.6 7.2 - - - +
1108u ASN 3.8 17.7 - - - +
1109u ARG* 4.1 6.8 - - - +
1112u THR* 3.9 19.2 - - - -
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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