Contacts of the helix formed by residues 1006 - 1021 (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 ASP1006 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A LEU 2.5 16.5 + - - +
1005A VAL* 1.3 75.9 - - + +
1007A THR* 1.3 67.9 + - - +
1008A THR* 3.0 17.4 + - - -
1009A GLU* 2.8 37.2 + - + +
1010A MET* 3.4 16.3 + - - +
1106A HIS* 3.9 17.2 - - + +
418F G 5.1 2.3 + - - -
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Residues in contact with THR1007 (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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1002A LYS* 5.0 5.2 - - - +
1004A LEU* 3.9 13.3 - - + +
1005A VAL 4.1 1.4 + - - -
1006A ASP* 1.3 76.5 + - - +
1008A THR* 1.3 64.2 + - - +
1010A MET* 3.2 3.8 + - - +
1011A TYR* 3.0 44.7 + - + -
1044A THR* 4.1 17.5 - - + +
418F G 3.8 31.7 + - - +
419F G 3.1 34.1 + - - +
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Residues in contact with THR1008 (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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1006A ASP* 3.0 8.4 + - - -
1007A THR* 1.3 79.1 - - - +
1009A GLU* 1.3 65.3 - - + +
1011A TYR* 3.1 6.5 + - - +
1012A LEU* 2.9 29.0 + - + +
1044A THR* 5.7 1.6 - - - +
1048A MET* 4.0 21.3 - - + +
1053A LEU* 3.5 32.3 - - + -
1071A LEU* 5.4 2.0 - - + -
418F G 4.8 11.2 + - - -
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Residues in contact with GLU1009 (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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1006A ASP* 2.8 29.5 + - - +
1007A THR 3.4 0.4 - - - -
1008A THR* 1.3 78.8 - - + +
1010A MET* 1.3 57.3 + - - +
1012A LEU* 3.4 9.3 + - + +
1013A ARG* 2.9 28.1 + - - +
1071A LEU* 6.1 2.4 - - + +
1075A VAL* 3.7 28.8 - - + +
1078A LYS* 6.2 0.2 - - - -
1105A GLU 3.9 4.6 - - - +
1106A HIS* 3.0 47.8 + - - +
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Residues in contact with MET1010 (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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251A NI 2.1 39.9 - - + -
1004A LEU* 3.6 24.0 - - + +
1006A ASP 3.4 13.4 + - - +
1007A THR 3.2 4.3 + - - +
1008A THR 3.2 0.6 - - - -
1009A GLU* 1.3 74.3 - - - +
1011A TYR* 1.3 62.3 + - - +
1013A ARG* 3.7 24.9 - - - +
1014A THR* 3.0 35.1 + - - +
1034A LEU* 4.2 19.0 - - + +
1102A ASP* 3.3 17.0 - - - +
1105A GLU* 2.4 6.3 - - - +
1106A HIS* 2.7 16.8 - - + +
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Residues in contact with TYR1011 (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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1004A LEU* 4.6 1.1 - - + -
1007A THR* 3.0 34.1 + - + +
1008A THR 3.1 6.9 + - - +
1010A MET* 1.3 76.3 - - - +
1012A LEU* 1.3 64.0 + - - +
1014A THR* 3.4 4.7 + - - -
1015A ILE* 3.1 29.2 + - + +
1030A ILE* 3.8 24.9 - - + +
1034A LEU* 3.5 22.9 - - + -
1036A GLN* 2.7 29.4 + - - -
1040A THR 4.2 0.2 + - - -
1041A VAL* 3.3 43.6 + - + +
1044A THR* 3.6 30.1 + - + -
1045A VAL* 4.0 6.1 - - + -
1048A MET* 3.7 22.9 - - + -
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Residues in contact with LEU1012 (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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1008A THR* 2.9 26.8 + - + +
1009A GLU* 3.6 9.4 - - + +
1011A TYR* 1.3 74.5 - - - +
1013A ARG* 1.3 67.9 + - - +
1015A ILE* 3.0 9.0 + - + +
1016A TYR* 2.9 23.0 + - - +
1048A MET* 3.6 22.7 - - + -
1053A LEU* 4.4 8.7 - - + +
1054A VAL* 5.6 0.4 - - + -
1064A MET* 4.4 11.7 - - + +
1068A GLY* 3.7 26.7 - - - +
1071A LEU* 3.4 44.6 - - + -
1072A ALA* 4.0 14.8 - - + +
1075A VAL* 5.6 0.7 - - + -
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Residues in contact with ARG1013 (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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1009A GLU 2.9 18.1 + - - +
1010A MET* 3.7 19.3 - - + +
1012A LEU* 1.3 75.4 - - - +
1014A THR* 1.3 58.5 + - - +
1016A TYR* 3.8 4.9 - - - +
1017A GLU* 2.6 64.9 + - - +
1072A ALA* 4.9 5.1 - - - +
1075A VAL* 4.3 14.8 - - + -
1076A MET* 3.6 27.1 - - + +
1079A HIS* 3.6 15.6 + - - -
1098A HIS* 3.6 21.3 + - - -
1102A ASP* 3.8 17.8 + - - -
1105A GLU* 2.3 47.1 + - - -
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Residues in contact with THR1014 (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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1010A MET* 3.0 22.7 + - - +
1011A TYR* 3.6 6.3 - - - -
1012A LEU 3.2 0.2 - - - -
1013A ARG* 1.3 78.0 - - - +
1015A ILE* 1.3 58.2 + - - +
1017A GLU* 3.8 6.9 - - - +
1018A LEU* 2.8 46.9 + - + +
1030A ILE* 3.7 33.7 - - + -
1033A ARG* 4.1 18.8 + - + +
1034A LEU* 3.6 21.9 - - - +
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Residues in contact with ILE1015 (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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1011A TYR* 3.2 18.4 - - + +
1012A LEU* 3.0 12.0 + - + +
1014A THR* 1.3 76.7 - - - +
1016A TYR* 1.3 64.1 + - - +
1018A LEU* 3.0 9.4 + - - +
1019A GLU* 2.9 31.8 + - - +
1025A PRO* 4.0 19.1 - - + -
1030A ILE* 4.1 9.4 - - + -
1045A VAL* 6.3 0.4 - - + -
1048A MET* 5.1 4.9 - - + -
1054A VAL* 4.2 16.6 - - + -
1062A LEU* 3.7 40.8 - - + +
1064A MET* 3.9 28.7 - - + -
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Residues in contact with TYR1016 (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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1012A LEU 2.9 15.0 + - - +
1013A ARG* 3.8 4.9 - - - +
1015A ILE* 1.3 75.5 - - - +
1017A GLU* 1.3 67.0 - - - +
1019A GLU* 2.9 17.8 + - + +
1020A GLU* 3.0 45.3 + - + +
1064A MET* 4.0 18.1 - - + +
1069A ARG* 4.9 11.0 - - + -
1072A ALA* 4.0 25.6 - - + -
1073A THR* 4.6 25.5 - - + +
1076A MET* 3.6 34.8 - - + -
1080A ARG* 4.4 8.7 + - - -
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Residues in contact with GLU1017 (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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1013A ARG* 2.6 62.3 + - - +
1014A THR* 3.9 5.0 - - - +
1016A TYR* 1.3 75.4 - - + +
1018A LEU* 1.3 65.1 + - - +
1020A GLU* 3.0 19.3 + - - +
1021A GLU* 3.1 24.3 + - + +
1033A ARG* 4.4 14.5 + - - +
1076A MET* 3.6 29.0 - - + +
1079A HIS* 5.2 0.5 - - - -
1098A HIS* 5.0 4.7 + - - -
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Residues in contact with LEU1018 (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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1014A THR* 2.8 37.6 + - + +
1015A ILE* 3.0 7.8 + - - +
1017A GLU* 1.3 75.6 - - - +
1019A GLU* 1.3 64.9 + - - +
1021A GLU* 3.1 15.4 + - - +
1022A GLY 3.2 7.8 + - - -
1023A VAL* 3.2 43.6 + - + +
1025A PRO* 4.4 15.3 - - + -
1026A LEU 5.0 0.4 - - - +
1029A ARG* 3.5 31.6 - - + -
1030A ILE* 4.8 2.5 - - + +
1033A ARG* 3.1 38.3 - - - +
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Residues in contact with GLU1019 (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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1015A ILE* 2.9 22.7 + - + +
1016A TYR* 2.9 9.1 + - + +
1018A LEU* 1.3 76.7 - - - +
1020A GLU* 1.3 57.6 + - + +
1022A GLY* 2.7 21.8 + - - +
1023A VAL 4.5 4.9 - - - +
1025A PRO* 4.1 23.1 - - + +
1062A LEU 4.2 7.4 - - - +
1063A GLN* 5.1 5.0 + - - +
1064A MET* 3.4 15.4 + - - +
1069A ARG* 3.0 37.3 + - - -
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Residues in contact with GLU1020 (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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1016A TYR* 3.0 51.7 + - + +
1017A GLU* 3.0 11.2 + - - +
1019A GLU* 1.3 76.8 - - - +
1021A GLU* 1.3 60.9 + - + +
1022A GLY* 3.1 4.7 + - - -
1076A MET* 5.3 2.6 - - - +
1080A ARG* 3.7 19.1 + - - -
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Residues in contact with GLU1021 (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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1017A GLU* 3.1 19.4 + - + +
1018A LEU* 3.5 7.9 - - - +
1020A GLU* 1.3 76.8 - - + +
1022A GLY* 1.3 64.2 + - - +
1023A VAL* 3.7 15.4 - - + +
1033A ARG* 2.7 44.3 + - - -
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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