Contacts of the helix formed by residues 1109 - 1120 (chain A) in PDB entry 1F5T
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 SER1109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1078A LYS* 3.9 1.6 - - - -
1107A VAL 3.7 0.6 + - - -
1108A MET* 1.3 76.6 - - - +
1110A ASP* 1.3 65.9 + - - +
1111A GLU* 3.5 15.2 + - - +
1112A VAL* 3.1 19.2 + - - +
1113A GLU* 2.9 19.4 + - - +
2092B LEU* 5.3 0.2 - - - +
2100B GLU* 2.4 32.4 + - - +
2103B ARG* 4.4 9.9 - - - +
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Residues in contact with ASP1110 (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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1074A ALA* 6.0 0.7 - - - +
1078A LYS* 3.0 24.9 + - - +
1109A SER* 1.3 72.7 - - - +
1111A GLU* 1.3 63.7 + - - +
1113A GLU* 2.8 24.3 + - - +
1114A ARG* 3.0 41.5 + - - +
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Residues in contact with GLU1111 (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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1109A SER* 3.5 14.4 + - - +
1110A ASP* 1.3 80.4 + - - +
1112A VAL* 1.3 58.8 + - - +
1114A ARG* 3.1 33.5 + - - +
1115A ARG* 3.0 33.1 + - + +
2092B LEU* 4.2 17.5 - - + -
2096B LYS* 4.1 30.4 + - + +
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Residues in contact with VAL1112 (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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1108A MET* 3.7 20.4 - - + -
1109A SER* 3.1 23.3 + - - +
1111A GLU* 1.3 76.6 - - - +
1113A GLU* 1.3 57.0 + - - +
1115A ARG* 4.1 7.9 - - - +
1116A LEU* 3.1 28.6 + - + +
2086B LEU* 4.2 5.8 - - + -
2090B ILE* 4.4 13.2 - - + +
2092B LEU* 3.7 31.6 - - + -
2100B GLU* 3.5 15.0 - - + +
2104B TRP* 3.8 19.5 - - + -
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Residues in contact with GLU1113 (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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1074A ALA* 4.9 0.7 - - - +
1077A ARG* 3.0 39.7 + - - +
1078A LYS* 2.8 30.4 + - + +
1081A LEU* 3.4 25.8 - - + +
1108A MET* 3.4 21.3 - - + -
1109A SER 2.9 8.7 + - - +
1110A ASP* 2.8 19.6 + - - +
1112A VAL* 1.3 77.5 - - - +
1114A ARG* 1.3 63.5 + - - +
1116A LEU* 3.5 3.9 + - - +
1117A VAL* 3.2 20.6 + - - +
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Residues in contact with ARG1114 (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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1110A ASP* 3.0 32.3 + - - +
1111A GLU* 3.5 39.7 + - - +
1113A GLU* 1.3 74.8 - - + +
1115A ARG* 1.3 64.7 + - + +
1116A LEU 2.9 4.7 + - - -
1117A VAL* 2.8 33.3 - - + +
1118A LYS* 3.4 9.5 + - - +
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Residues in contact with ARG1115 (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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1111A GLU* 3.0 18.6 + - + +
1112A VAL* 4.5 3.1 - - - +
1114A ARG* 1.3 75.1 - - + +
1116A LEU* 1.3 55.6 + - - +
1117A VAL 3.5 0.2 - - - -
1118A LYS* 3.2 44.0 + - - +
1119A VAL* 3.0 52.8 + - - +
2090B ILE* 3.0 36.7 + - + +
2091B GLY* 3.1 31.3 + - - -
2092B LEU* 4.5 11.7 - - + +
2093B ASP 5.5 0.4 - - - +
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Residues in contact with LEU1116 (chain A).
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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1081A LEU* 3.8 28.4 - - + +
1082A ALA* 5.2 0.4 - - - -
1085A LEU* 3.2 38.1 - - + -
1108A MET* 4.2 20.0 - - - -
1112A VAL* 3.1 22.3 + - + +
1113A GLU* 3.6 5.2 - - - +
1114A ARG 2.9 0.6 - - - -
1115A ARG* 1.3 77.6 - - - +
1117A VAL* 1.3 64.7 + - - +
1118A LYS 3.1 1.8 - - - -
1119A VAL* 3.2 25.4 - - + +
1120A LEU* 3.3 23.6 + - + +
2090B ILE* 3.5 25.6 - - + -
2104B TRP* 5.8 2.0 - - + -
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Residues in contact with VAL1117 (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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1081A LEU* 4.0 16.5 - - + +
1084A ARG* 5.7 3.4 + - - +
1113A GLU 3.2 11.5 + - - +
1114A ARG* 2.8 32.0 + - + +
1116A LEU* 1.3 77.0 - - - +
1118A LYS* 1.3 71.7 + - + +
1120A LEU* 3.6 12.2 - - - +
1121A LYS* 5.2 0.5 - - - +
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Residues in contact with LYS1118 (chain A).
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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1114A ARG* 3.4 7.8 + - - +
1115A ARG* 3.2 56.0 - - - +
1116A LEU 3.1 0.2 - - - -
1117A VAL* 1.3 83.4 - - + +
1119A VAL* 1.3 69.4 + - - +
1120A LEU 2.7 3.8 + - - -
1121A LYS* 2.8 25.2 - - - +
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Residues in contact with VAL1119 (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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1085A LEU* 5.3 1.1 - - + -
1089A ILE* 5.9 3.6 - - + +
1115A ARG* 3.0 30.5 - - - +
1116A LEU* 3.2 34.8 - - + +
1118A LYS* 1.3 76.7 - - - +
1120A LEU* 1.3 69.3 + - + +
1121A LYS* 3.5 16.0 + - - +
2089B ILE* 3.8 16.6 - - + +
2090B ILE* 3.6 21.5 - - + +
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Residues in contact with LEU1120 (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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1081A LEU* 4.3 3.6 - - + +
1084A ARG* 3.5 53.5 + - + +
1085A LEU* 4.0 12.6 - - - +
1088A ASP* 4.1 20.0 - - + +
1089A ILE* 3.7 31.0 - - + -
1116A LEU* 3.3 32.0 + - + +
1117A VAL* 3.6 10.1 - - - +
1118A LYS 2.7 8.9 + - - +
1119A VAL* 1.3 84.3 - - + +
1121A LYS* 1.3 70.4 + - - +
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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