Contacts of the helix formed by residues 1087 - 1098 (chain B) in PDB entry 5FLM
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 GLY1087 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A MET 4.1 2.8 - - - +
356A GLY* 4.1 11.0 - - - -
1085B ARG* 3.9 17.9 + - - +
1086B PHE* 1.3 78.1 - - - +
1088B GLU* 1.3 63.4 + - - +
1090B GLU* 3.1 25.7 + - - +
1091B ARG* 3.5 16.5 + - - +
17T G 5.5 0.4 - - - -
18T C 4.3 8.3 - - - -
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Residues in contact with GLU1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A ARG* 3.2 37.2 + - + +
355A MET* 4.1 27.6 - - + +
356A GLY 5.0 0.7 - - - +
862A ARG* 3.3 33.9 + - - +
866A LYS* 5.4 7.3 + - - +
1431A SER 5.0 1.0 - - - +
1085B ARG* 5.6 2.0 - - - +
1087B GLY* 1.3 70.2 - - - -
1089B MET* 1.3 71.7 + - + +
1090B GLU* 3.0 2.4 + - - -
1091B ARG* 2.8 26.7 + - + +
1092B ASP* 2.9 19.9 + - - +
17T G 5.1 8.3 + - - -
18T C 5.1 1.6 + - - -
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Residues in contact with MET1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A PRO* 3.8 28.5 - - + -
463A THR* 3.1 36.5 + - - +
464A LEU* 5.4 5.2 - - + -
858A GLY* 4.6 25.4 - - - +
861A GLN* 5.5 9.4 - - + -
862A ARG* 5.9 3.8 - - + -
865A ILE* 5.8 4.7 - - + -
1088B GLU* 1.3 77.5 - - + +
1090B GLU* 1.3 61.0 + - - +
1092B ASP* 3.3 14.5 + - - +
1093B CYS* 3.0 26.7 + - - -
16T A 5.2 6.7 - - - +
17T G 3.8 38.6 - - - +
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Residues in contact with GLU1090 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ASN* 3.1 27.0 + - - +
461A GLN* 3.2 35.6 + - - +
463A THR* 4.0 5.5 + - + +
469A MET* 3.7 13.0 - - - +
1085B ARG 4.7 0.2 - - - +
1086B PHE* 3.4 35.0 - - + -
1087B GLY* 3.1 31.5 + - - +
1088B GLU 2.9 0.8 + - - -
1089B MET* 1.3 77.3 + - - +
1091B ARG* 1.3 64.4 + - - +
1093B CYS* 3.0 6.8 + - - +
1094B GLN* 2.9 20.3 + - - +
17T G 5.5 2.4 - - - +
18T C 4.7 4.7 - - - +
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Residues in contact with ARG1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A MET* 3.0 55.2 + - - +
866A LYS* 4.7 4.0 - - - +
869A GLU* 4.1 5.5 + - - -
1455A SER* 3.2 28.7 + - - +
1458A ILE* 3.3 39.0 - - - +
1086B PHE* 3.8 3.3 - - + -
1087B GLY 3.5 6.5 + - - +
1088B GLU* 2.8 30.0 + - - +
1090B GLU* 1.3 76.5 - - - +
1092B ASP* 1.3 71.6 + - - +
1094B GLN 3.7 1.4 - - - +
1095B ILE* 2.9 50.4 + - - +
1103B LEU* 3.7 28.6 - - + +
1107B LEU* 4.7 2.2 - - + -
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Residues in contact with ASP1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A ARG* 5.7 3.3 - - - +
865A ILE* 3.4 51.4 - - + +
866A LYS* 5.8 3.0 - - - +
1089A ALA* 4.0 5.2 - - + +
1093A GLN* 3.6 9.7 + - - +
1088B GLU* 2.9 24.7 + - - +
1089B MET* 3.3 17.8 + - - +
1091B ARG* 1.3 94.8 + - - +
1093B CYS* 1.3 66.0 + - - +
1095B ILE* 3.1 10.3 + - - +
1096B ALA* 2.9 18.4 + - - +
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Residues in contact with CYS1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A THR* 3.4 24.2 - - - -
465A HIS 3.3 23.8 - - - -
466A LYS* 4.0 9.0 - - - +
469A MET* 3.8 17.0 - - + -
1093A GLN* 3.3 22.4 - - - +
1089B MET 3.0 19.0 + - - -
1090B GLU 3.5 6.5 - - - +
1092B ASP* 1.3 74.6 - - - +
1094B GLN* 1.3 57.3 + - - +
1096B ALA* 3.1 7.2 + - - +
1097B HIS* 2.9 33.3 + - - +
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Residues in contact with GLN1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ILE* 3.4 16.0 - - - +
469A MET* 3.2 30.4 - - + +
1086B PHE* 3.3 17.6 - - - -
1090B GLU 2.9 13.8 + - - +
1091B ARG 3.7 3.1 - - - +
1093B CYS* 1.3 73.7 - - - +
1095B ILE* 1.3 63.6 + - - +
1096B ALA 3.3 0.2 - - - -
1097B HIS* 3.6 21.9 - - + -
1098B GLY 3.6 0.7 + - - -
1099B ALA* 3.6 33.9 + - + +
1102B PHE* 3.0 42.4 - - - -
1103B LEU* 3.7 20.3 - - + +
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Residues in contact with ILE1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865A ILE* 6.3 1.1 - - + -
869A GLU* 4.5 14.1 - - + +
1086A MET* 3.2 45.8 - - + +
1089A ALA* 3.9 15.0 - - + -
1454A VAL* 3.7 19.3 - - + -
1466A ALA* 5.3 3.4 - - + -
1091B ARG* 2.9 63.1 + - - +
1092B ASP* 3.5 9.9 - - - +
1094B GLN* 1.3 74.3 - - - +
1096B ALA* 1.3 64.6 + - - +
1097B HIS 3.3 0.4 - - - -
1098B GLY* 3.3 6.7 + - - -
1103B LEU* 4.0 13.0 - - + -
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Residues in contact with ALA1096 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LYS* 4.0 24.5 + - + -
1086A MET* 4.7 12.0 + - - +
1089A ALA* 4.0 12.5 - - + +
1090A LEU* 4.4 10.4 - - + +
1093A GLN* 3.4 26.0 - - - +
1092B ASP 2.9 8.5 + - - +
1093B CYS 3.1 10.3 + - - +
1095B ILE* 1.3 76.3 - - - +
1097B HIS* 1.3 64.3 + - - +
1098B GLY* 3.3 1.0 + - - -
60F TYR* 4.4 6.2 + - - -
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Residues in contact with HIS1097 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 6.4 0.4 - - + -
466A LYS* 3.1 38.5 + - + +
469A MET* 3.1 29.5 + - + +
518A LEU* 4.4 14.4 + - + +
519A ALA* 4.4 18.3 - - + +
524A MET* 3.3 21.3 - - + +
1093B CYS* 2.9 32.9 + - + +
1094B GLN* 3.6 23.3 - - + +
1095B ILE 3.3 0.4 - - - -
1096B ALA* 1.3 76.4 - - - +
1098B GLY* 1.3 60.2 - - - +
1099B ALA* 4.3 10.5 - - + +
60F TYR* 3.4 17.0 + - - -
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Residues in contact with GLY1098 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LEU* 3.9 2.4 - - - +
1086A MET* 4.9 3.1 - - - -
1466A ALA* 4.9 2.9 - - - -
1467A GLY* 2.8 37.5 - - - +
1468A THR* 3.5 6.8 + - - -
1094B GLN 3.6 1.9 + - - -
1095B ILE 3.3 12.3 + - - -
1096B ALA 3.2 4.6 - - - -
1097B HIS* 1.3 79.2 - - - +
1099B ALA* 1.3 59.3 + - - +
60F TYR* 3.8 16.9 - - - -
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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