Contacts of the helix formed by residues 1041 - 1055 (chain A) in PDB entry 1FO4
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 GLY1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A HIS* 3.8 16.2 - - - -
1037A GLU* 3.0 13.3 + - - -
1039A GLY 3.2 3.4 + - - -
1040A GLN* 1.3 78.8 - - - +
1042A LEU* 1.3 59.5 + - - +
1043A HIS 3.5 2.0 - - - -
1044A THR* 3.4 11.4 + - - -
1045A LYS* 3.0 34.0 + - - +
1190A ILE* 4.4 9.6 - - - +
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Residues in contact with LEU1042 (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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1033A HIS* 3.8 23.8 - - + -
1035A GLY* 3.8 10.8 - - - -
1036A THR 3.6 21.1 - - - +
1037A GLU* 3.0 5.4 + - - +
1040A GLN* 3.5 21.9 + - + +
1041A GLY* 1.3 74.1 - - - +
1043A HIS* 1.3 62.9 + - - +
1045A LYS* 3.1 6.2 + - - +
1046A MET* 2.8 46.2 + - + +
1077A THR* 4.3 0.4 - - + -
1082A SER* 3.7 24.2 - - - +
1083A THR* 3.8 38.1 - - - +
1086A TYR* 4.4 1.3 - - + -
3003A MTE 4.3 0.4 - - - +
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Residues in contact with HIS1043 (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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579A HIS* 6.4 1.1 - - + -
580A LEU* 4.3 7.4 - - + -
792A LYS 4.3 9.5 + - - -
1033A HIS* 2.9 39.4 + + - -
1035A GLY 3.7 12.3 - - - -
1036A THR 4.7 0.9 - - - -
1037A GLU* 3.3 41.7 + - + +
1042A LEU* 1.3 77.3 - - + +
1044A THR* 1.3 58.3 + - - +
1046A MET* 3.2 1.0 + - - -
1047A VAL* 2.9 34.7 + - - +
1063A ILE* 3.3 41.4 - - + +
1064A SER 5.8 1.1 - - - -
1065A GLU* 4.9 6.2 - - - -
1066A THR* 4.0 9.9 + - - -
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Residues in contact with THR1044 (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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577A LEU* 4.0 14.8 - - + +
578A PRO 4.0 11.0 - - - +
579A HIS* 3.6 15.0 + - - -
580A LEU* 2.9 46.3 + - + +
1037A GLU* 4.7 0.2 + - - -
1041A GLY* 3.5 14.5 - - - +
1043A HIS* 1.3 80.0 - - - +
1045A LYS* 1.3 63.3 + - - +
1047A VAL* 3.3 3.1 + - - +
1048A GLN* 3.0 39.3 + - - +
1187A ASN* 4.2 8.1 - - - +
1190A ILE* 4.9 3.4 - - + -
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Residues in contact with LYS1045 (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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1040A GLN 5.1 1.7 + - - +
1041A GLY 3.0 17.4 + - - +
1042A LEU* 3.1 8.5 + - - +
1044A THR* 1.3 75.8 - - - +
1046A MET* 1.3 67.7 + - + +
1048A GLN* 3.1 20.6 + - - +
1049A VAL* 2.9 31.9 + - - +
1083A THR* 3.6 32.3 + - + +
1186A LEU* 4.5 18.0 - - + +
1187A ASN* 4.5 7.6 - - + -
1190A ILE* 3.8 23.7 - - + +
1191A ASP* 2.6 35.5 + - - -
1194A GLN* 5.5 0.2 - - - +
1257A LYS 5.4 3.0 + - - -
1259A VAL* 4.0 12.3 - - - +
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Residues in contact with MET1046 (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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1031A VAL* 5.5 1.5 - - + +
1033A HIS* 3.5 21.8 - - + +
1042A LEU* 2.8 31.5 + - + +
1043A HIS 3.2 4.9 + - - +
1045A LYS* 1.3 79.6 - - - +
1047A VAL* 1.3 58.0 + - - +
1049A VAL* 3.4 8.4 + - + +
1050A ALA* 2.9 28.6 + - - +
1063A ILE* 3.7 14.8 - - + -
1083A THR* 3.7 28.7 - - + +
1086A TYR* 3.4 15.7 - - - +
1087A GLY* 3.3 42.4 - - - +
1090A VAL* 4.0 15.3 - - + +
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Residues in contact with VAL1047 (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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577A LEU* 6.0 0.4 - - + -
580A LEU* 3.7 26.5 - - + -
1031A VAL* 6.2 0.2 - - - -
1043A HIS 2.9 19.1 + - - +
1044A THR 3.7 4.5 - - - +
1046A MET* 1.3 74.7 - - - +
1048A GLN* 1.3 61.6 + - + +
1050A ALA* 3.3 5.8 + - - +
1051A SER* 2.9 28.9 + - - -
1058A ILE* 3.8 35.2 - - + +
1061A ILE* 4.0 22.8 - - + +
1063A ILE* 3.8 28.0 - - + +
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Residues in contact with GLN1048 (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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572A THR* 2.8 51.7 + - - +
573A VAL* 3.6 19.1 - - + +
575A ARG 3.8 3.4 + - - -
577A LEU* 3.5 17.2 - - + +
1044A THR* 3.0 21.5 + - - +
1045A LYS* 3.3 16.8 - - - +
1047A VAL* 1.3 77.1 - - - +
1049A VAL* 1.3 61.8 + - + +
1051A SER* 3.7 2.1 - - - -
1052A LYS* 3.1 18.0 + - - +
1058A ILE* 4.3 3.4 - - - -
1186A LEU* 3.2 17.6 + - + +
1187A ASN* 3.0 36.1 + - - +
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Residues in contact with VAL1049 (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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573A VAL* 4.5 1.8 - - + -
1045A LYS 2.9 18.5 + - - +
1046A MET* 3.7 18.6 - - + +
1047A VAL 3.3 0.2 - - - -
1048A GLN* 1.3 76.4 - - + +
1050A ALA* 1.3 56.4 - - - +
1052A LYS* 3.4 2.6 + - - +
1053A ALA* 3.0 27.5 + - - +
1087A GLY* 3.7 21.5 - - - +
1090A VAL* 4.5 8.7 - - + -
1091A TYR* 4.5 8.1 - - + -
1186A LEU* 4.0 24.9 - - + -
1253A ILE* 4.2 16.4 - - + -
1254A TYR* 3.8 24.0 + - + +
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Residues in contact with ALA1050 (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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1031A VAL* 4.5 7.9 - - + -
1046A MET 2.9 17.7 + - - +
1047A VAL* 3.7 1.6 - - - +
1049A VAL* 1.3 78.0 - - - +
1051A SER* 1.3 57.4 + - - +
1053A ALA* 3.3 0.3 + - - +
1054A LEU* 2.9 37.5 + - + +
1061A ILE* 3.5 27.1 - - + -
1090A VAL* 4.0 14.1 - - + +
1094A CYS* 3.9 17.7 - - - -
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Residues in contact with SER1051 (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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570A GLU 3.2 19.8 + - - +
572A THR* 5.0 1.3 + - - -
1047A VAL 2.9 10.9 + - - -
1048A GLN 3.7 3.4 - - - -
1050A ALA* 1.3 77.0 - - - +
1052A LYS* 1.3 56.0 + - - +
1055A LYS* 2.8 24.3 + - - -
1056A ILE* 2.6 35.1 + - - -
1058A ILE* 3.3 36.8 + - - +
1061A ILE* 3.2 8.0 - - - +
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Residues in contact with LYS1052 (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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567A GLN* 5.3 1.0 + - - -
571A ASP* 2.5 51.6 + - - +
573A VAL* 3.6 13.5 - - + -
1048A GLN 3.1 16.7 + - - +
1049A VAL 3.8 3.1 - - - +
1051A SER* 1.3 74.2 + - - +
1053A ALA* 1.3 68.6 + - - +
1055A LYS* 3.2 23.4 + - - +
1254A TYR* 3.4 44.0 - - + +
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Residues in contact with ALA1053 (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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1049A VAL 3.0 18.6 + - - +
1050A ALA 3.8 3.6 - - - +
1052A LYS* 1.3 78.2 - - - +
1054A LEU* 1.3 59.4 + - - +
1055A LYS* 4.3 9.8 + - - +
1091A TYR* 4.2 9.2 - - + -
1094A CYS* 3.8 22.4 - - + -
1095A GLN* 4.1 14.7 + - - +
1098A LEU* 3.2 22.1 - - - +
1254A TYR* 3.6 14.7 + - - +
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Residues in contact with LEU1054 (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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1021A ILE* 5.8 2.0 - - + -
1023A VAL* 5.7 0.9 - - + -
1029A VAL* 4.4 16.6 - - + -
1050A ALA* 2.9 19.6 + - + +
1053A ALA* 1.3 74.2 - - - +
1055A LYS* 1.3 72.2 + - - +
1056A ILE* 3.6 37.4 - - + +
1061A ILE* 4.5 6.3 - - + -
1094A CYS* 3.6 46.9 - - + +
1097A ILE* 4.1 9.9 - - + -
1098A LEU* 3.9 21.4 - - + +
1113A TRP* 4.1 25.1 - - + -
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Residues in contact with LYS1055 (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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570A GLU* 4.5 8.7 - - - +
1051A SER 2.8 12.5 + - - -
1052A LYS* 3.2 14.1 + - - +
1053A ALA* 4.3 10.0 + - - +
1054A LEU* 1.3 82.1 - - - +
1056A ILE* 1.3 59.2 + - - +
1098A LEU* 5.7 2.4 - - - +
1105A LYS* 5.9 4.7 - - - +
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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