Contacts of the helix formed by residues 1086 - 1094 (chain F) in PDB entry 3F5P
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 ASP1086 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1085F GLY* 1.3 74.6 - - - -
1087F LEU* 1.3 65.4 + - - +
1088F LYS* 3.1 13.0 + - - +
1089F SER* 2.7 46.0 + - - -
1090F TYR* 2.9 20.9 + - - +
1139F ARG* 3.7 21.5 - - - +
1141F CYS 3.1 12.3 - - - +
1142F MET* 4.2 8.6 - - - +
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Residues in contact with LEU1087 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085F GLY 3.8 1.2 + - - -
1086F ASP* 1.3 72.2 - - - +
1088F LYS* 1.3 54.9 + - - +
1090F TYR* 4.1 5.4 - - + -
1091F LEU* 2.8 54.1 + - + +
1115F MET* 4.1 20.6 - - - -
1119F ILE* 3.7 29.6 - - + -
1138F ALA* 3.2 25.7 + - + +
1141F CYS* 2.9 26.1 + - + +
1143F VAL* 3.9 24.2 - - + +
1149F VAL* 4.1 5.6 - - + -
1201F VAL* 4.7 1.6 - - + -
1205F ILE* 4.4 13.0 - - + -
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Residues in contact with LYS1088 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086F ASP* 3.1 10.6 + - - +
1087F LEU* 1.3 74.4 - - - +
1089F SER* 1.3 57.4 + - - +
1091F LEU* 2.9 9.3 + - - +
1092F ARG* 2.8 56.1 + - + +
1138F ALA* 3.3 12.6 + - + -
1139F ARG* 4.0 30.6 - - + +
1178F TRP* 5.5 9.9 - - - -
1204F GLU* 4.8 8.9 + - - +
1209F ALA* 3.8 20.6 - - + -
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Residues in contact with SER1089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084F ARG 5.8 1.3 - - - -
1085F GLY* 5.9 0.7 - - - -
1086F ASP* 2.7 43.0 + - - -
1088F LYS* 1.3 73.3 - - - +
1090F TYR* 1.3 64.3 + - - +
1092F ARG* 3.1 10.2 + - - +
1093F SER* 2.9 23.0 + - - -
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Residues in contact with TYR1090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084F ARG* 4.2 20.1 + - + +
1086F ASP 2.9 13.6 + - - +
1087F LEU* 3.6 20.9 - - + +
1089F SER* 1.3 76.3 - - - +
1091F LEU* 1.3 68.1 + - + +
1093F SER* 2.6 30.2 + - - -
1094F LEU* 3.5 40.6 + - + +
1111F LYS* 6.1 1.0 - - - +
1115F MET* 4.0 22.2 - - + +
1143F VAL* 4.0 24.2 - - + -
1147F PHE* 3.6 39.3 - + + -
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Residues in contact with LEU1091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087F LEU* 2.8 51.3 + - + +
1088F LYS 3.3 4.3 - - - +
1090F TYR* 1.3 77.2 - - + +
1092F ARG* 1.3 61.9 + - - +
1094F LEU* 3.2 26.9 + - + +
1095F ARG* 3.7 0.5 - - - +
1107F PRO* 4.8 2.2 - - + -
1115F MET* 4.7 4.3 - - - -
1138F ALA* 4.3 10.1 - - + -
1204F GLU 3.5 23.3 - - - +
1205F ILE* 3.7 39.5 - - + +
1208F LEU* 3.6 28.4 - - + +
1209F ALA* 4.0 13.0 - - + +
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Residues in contact with ARG1092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088F LYS* 2.8 35.7 + - + +
1089F SER* 3.5 11.4 - - - +
1091F LEU* 1.3 68.2 - - - +
1093F SER* 1.3 57.6 + - - +
1094F LEU 3.0 5.6 - - - -
1095F ARG* 2.7 60.6 + - - +
1208F LEU 2.9 18.6 - - - -
1209F ALA* 3.2 24.0 + - + -
1210F GLU* 5.9 0.4 - - - +
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Residues in contact with SER1093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F SER 2.9 11.5 + - - -
1090F TYR* 2.6 31.8 + - - -
1092F ARG* 1.3 75.1 - - - +
1094F LEU* 1.3 64.5 + - - +
1095F ARG 3.2 7.7 + - - +
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Residues in contact with LEU1094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090F TYR* 3.6 51.1 - - + +
1091F LEU* 3.5 12.3 - - + +
1092F ARG 3.0 1.6 - - - -
1093F SER* 1.3 85.9 - - - +
1095F ARG* 1.3 61.1 + - - +
1096F PRO* 4.5 0.9 - - - +
1105F ALA 5.2 1.4 - - - +
1107F PRO* 4.2 24.9 - - + -
1115F MET* 5.5 0.4 - - + -
1208F LEU* 3.9 18.9 - - + +
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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