Contacts of the helix formed by residues 1086 - 1093 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 5.4 7.0 - - - +
1084S ARG 4.1 0.9 - - - +
1085S GLY* 1.3 75.1 - - - -
1087S LEU* 1.3 57.0 + - - +
1088S LYS* 3.0 17.8 - - - +
1089S SER* 2.9 44.4 + - - -
1090S TYR* 3.1 20.4 + - - +
1139S ARG* 3.6 24.6 - - - +
1141S CYS 3.1 8.7 - - - +
1142S MET* 4.0 10.3 - - - -
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Residues in contact with LEU1087 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085S GLY 3.8 0.4 + - - -
1086S ASP* 1.3 70.3 - - - +
1088S LYS* 1.3 60.3 + - - +
1090S TYR* 3.8 4.7 - - + -
1091S LEU* 2.9 38.8 + - + +
1115S MET* 4.0 29.8 - - + -
1119S ILE* 4.0 26.9 - - + -
1138S ALA* 3.5 22.2 + - + +
1141S CYS* 2.7 25.6 + - + +
1143S VAL* 3.7 24.9 - - + +
1149S VAL* 4.2 9.2 - - + -
1201S VAL* 5.9 0.7 - - + -
1205S ILE* 4.2 17.0 - - + -
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Residues in contact with LYS1088 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086S ASP* 3.0 14.9 + - - +
1087S LEU* 1.3 81.4 - - - +
1089S SER* 1.3 62.0 + - - +
1091S LEU 3.4 0.2 + - - -
1092S ARG* 3.2 54.6 + - - +
1138S ALA* 3.5 20.5 + - + -
1139S ARG* 3.7 30.4 - - + +
1178S TRP* 5.6 8.5 - - - -
1204S GLU* 4.1 6.8 + - - +
1209S ALA* 3.5 26.8 - - + +
1210S GLU 5.7 1.8 - - - -
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Residues in contact with SER1089 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S 741 5.6 14.6 - - - -
1086S ASP* 2.9 26.9 + - - -
1088S LYS* 1.3 76.8 - - - +
1090S TYR* 1.3 64.5 + - - +
1092S ARG* 3.1 9.7 + - - +
1093S SER* 2.9 23.1 + - - -
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Residues in contact with TYR1090 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 5.9 2.2 - - - -
1084S ARG* 4.2 25.2 + - + +
1086S ASP 3.1 17.9 + - - +
1087S LEU* 3.7 17.5 - - + +
1089S SER* 1.3 76.7 - - - +
1091S LEU* 1.3 67.8 + - + +
1093S SER* 3.0 27.7 + - - -
1094S LEU* 3.5 36.0 - - + +
1115S MET* 3.8 22.9 - - + +
1143S VAL* 4.0 23.1 - - + -
1147S PHE* 3.1 42.8 - + - -
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Residues in contact with LEU1091 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087S LEU* 2.9 46.0 + - + +
1088S LYS 3.6 5.4 - - - +
1089S SER 3.2 0.2 - - - -
1090S TYR* 1.3 82.8 - - + +
1092S ARG* 1.3 57.1 + - - +
1094S LEU* 3.0 28.1 + - + +
1095S ARG 4.0 0.2 + - - -
1107S PRO* 5.3 2.2 - - + -
1115S MET* 4.6 6.5 - - + -
1138S ALA* 4.6 5.4 - - + -
1204S GLU* 3.3 31.2 - - + +
1205S ILE* 3.5 30.7 - - + +
1208S LEU* 3.8 32.0 - - + +
1209S ALA* 3.8 13.5 - - + +
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Residues in contact with ARG1092 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088S LYS* 3.2 38.4 + - - +
1089S SER* 3.1 12.3 + - - +
1091S LEU* 1.3 72.2 - - - +
1093S SER* 1.3 58.9 + - - +
1094S LEU 2.9 5.8 - - - -
1095S ARG* 2.8 66.9 + - - +
1208S LEU 3.9 0.7 - - - +
1209S ALA* 2.9 27.5 + - + -
1210S GLU* 4.8 5.7 - - - +
1211S GLN* 5.0 3.6 - - - +
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Residues in contact with SER1093 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S 741 4.7 14.6 + - - -
1089S SER 2.9 12.0 + - - -
1090S TYR* 3.0 24.7 + - - -
1091S LEU 3.2 0.4 - - - -
1092S ARG* 1.3 75.7 - - - +
1094S LEU* 1.3 67.1 + - - +
1095S ARG 3.3 8.2 + - - +
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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
------------------------------------------------------------
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