Contacts of the helix formed by residues 1050 - 1063 (chain A) in PDB entry 5EPG
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 GLY1050 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A HIS* 4.1 9.2 + - - -
1046A GLU* 2.5 27.4 + - - -
1048A GLY 3.2 3.0 + - - -
1049A GLN* 1.3 73.3 - - - +
1051A VAL* 1.3 62.5 + - - -
1052A HIS 3.3 2.2 - - - -
1053A THR* 3.3 16.0 - - - -
1054A LYS* 3.2 27.2 + - - +
1199A ILE* 4.4 7.8 - - - +
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Residues in contact with VAL1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A HIS* 4.2 14.4 - - + -
1045A ILE 3.7 14.8 - - - +
1046A GLU* 3.4 7.5 + - - -
1049A GLN* 3.5 29.5 - - + +
1050A GLY* 1.3 76.4 - - - +
1052A HIS* 1.3 82.2 + - + +
1054A LYS* 3.2 10.3 + - - +
1055A MET* 3.1 25.5 + - + +
1091A VAL* 4.0 14.8 - - + +
1092A ALA* 3.9 27.6 - - + +
1095A ASN* 5.2 0.2 - - + -
3003A MTE 4.8 1.6 - - - +
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Residues in contact with HIS1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU* 4.2 5.8 - - + -
800A VAL 5.3 0.2 - - - -
801A ARG 4.0 14.1 + - - -
1042A HIS* 3.1 27.0 + + - -
1044A GLY 3.3 21.0 + - - -
1046A GLU* 3.4 33.2 + - + +
1050A GLY 3.3 0.4 - - - -
1051A VAL* 1.3 83.8 - - + +
1053A THR* 1.3 62.7 + - - +
1055A MET* 3.3 6.7 + - - +
1056A ILE* 3.2 27.0 + - - +
1072A LEU* 3.1 37.9 - - + +
1073A ARG 5.6 0.2 + - - -
1074A GLY* 4.4 4.2 + - - -
1075A THR* 3.7 12.2 + - - -
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Residues in contact with THR1053 (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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584A ILE* 4.4 6.1 - - + +
585A MET 3.7 23.3 - - - +
586A HIS* 3.7 9.9 + - - -
587A LEU* 3.5 35.1 + - + +
1046A GLU* 4.0 1.5 + - - -
1050A GLY* 3.3 21.1 + - - -
1052A HIS* 1.3 77.2 - - - +
1054A LYS* 1.3 61.1 + - - +
1056A ILE* 3.5 3.8 + - - +
1057A GLN* 3.2 32.3 + - - +
1067A MET* 4.5 1.1 - - + +
1199A ILE* 3.8 20.0 - - + -
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Residues in contact with LYS1054 (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 GLN 5.1 2.3 + - - +
1050A GLY 3.2 14.1 + - - +
1051A VAL* 3.2 8.3 + - - +
1053A THR* 1.3 82.7 - - - +
1055A MET* 1.3 66.3 + - + +
1057A GLN* 3.3 16.7 - - - +
1058A VAL* 3.0 31.4 + - + +
1092A ALA* 3.9 24.7 - - + +
1195A ILE* 4.3 33.2 - - + +
1196A ASN* 4.4 7.0 - - + -
1199A ILE* 3.9 22.1 - - + +
1200A ASP* 3.2 34.7 + - - -
1203A GLN* 6.3 0.4 - - - +
3003A MTE 5.9 0.2 + - - -
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Residues in contact with MET1055 (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 VAL* 5.4 2.2 - - + -
1042A HIS* 3.5 31.9 - - + +
1051A VAL* 3.1 17.3 + - + +
1052A HIS* 3.3 7.1 + - - +
1054A LYS* 1.3 86.9 - - + +
1056A ILE* 1.3 58.7 + - - +
1058A VAL* 3.3 9.7 + - + +
1059A VAL* 2.8 33.4 + - - +
1072A LEU* 5.0 4.9 - - + -
1092A ALA* 3.5 20.2 - - + +
1095A ASN* 3.5 13.9 - - - +
1096A GLY* 3.3 40.6 - - - -
1099A VAL* 3.9 13.5 - - + +
1195A ILE* 6.1 0.4 - - + -
1262A LEU* 4.8 1.8 - - + -
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Residues in contact with ILE1056 (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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587A LEU* 3.7 19.1 - - + -
1040A VAL* 4.0 11.4 - - + -
1052A HIS 3.2 14.9 + - - +
1053A THR 3.8 6.5 - - - +
1055A MET* 1.3 73.9 - - + +
1057A GLN* 1.3 56.6 + - - +
1059A VAL* 3.7 4.6 - - - +
1060A SER* 2.8 31.5 + - - -
1067A MET* 3.6 39.7 - - + +
1070A VAL* 3.3 44.2 - - + +
1071A HIS* 4.0 9.6 - - - +
1072A LEU* 4.4 9.4 - - + -
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Residues in contact with GLN1057 (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 PRO* 3.0 38.3 + - + +
580A ILE* 3.4 19.0 - - + +
582A HIS 4.0 1.6 + - - -
584A ILE* 3.8 7.5 - - - +
1053A THR* 3.2 21.0 + - - +
1054A LYS* 3.3 16.1 - - - +
1056A ILE* 1.3 74.4 - - - +
1058A VAL* 1.3 63.5 + - - +
1061A ARG 3.1 17.2 + - - -
1067A MET* 4.0 19.3 - - + -
1195A ILE* 2.9 28.5 + - + +
1196A ASN* 2.6 33.1 + - - +
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Residues in contact with VAL1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ILE* 4.0 9.4 - - + -
1054A LYS* 3.0 22.5 + - + +
1055A MET* 3.4 20.9 - - + +
1056A ILE 3.3 0.2 - - - -
1057A GLN* 1.3 72.8 - - - +
1059A VAL* 1.3 66.4 + - - +
1061A ARG* 3.2 2.9 + - - +
1062A GLU* 2.9 25.1 + - + +
1096A GLY 3.8 18.6 - - - +
1099A VAL* 4.4 5.2 - - + -
1100A LYS* 4.1 20.2 - - + +
1195A ILE* 5.1 4.3 - - + -
1262A LEU* 4.4 13.2 - - + -
1263A TYR* 4.1 27.8 - - + +
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Residues in contact with VAL1059 (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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1030A VAL* 5.7 1.1 - - + -
1038A VAL* 4.7 5.4 - - + -
1040A VAL* 4.1 21.1 - - + -
1055A MET 2.8 23.7 + - - +
1056A ILE 3.7 4.9 - - - +
1058A VAL* 1.3 71.4 - - - +
1060A SER* 1.3 62.7 + - - +
1063A LEU* 3.0 46.8 + - + +
1065A MET* 4.7 1.1 - - - +
1070A VAL* 3.5 33.0 - - + -
1099A VAL* 3.4 22.9 - - + -
1103A CYS* 4.0 14.8 - - - -
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Residues in contact with SER1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLU 4.3 4.9 + - - +
578A ASP* 5.7 0.2 - - - -
579A PRO* 3.5 18.7 - - - +
1056A ILE 2.8 22.1 + - - -
1058A VAL 3.2 0.2 - - - -
1059A VAL* 1.3 74.9 - - - +
1061A ARG* 1.3 55.6 + - - +
1064A ARG* 3.1 7.6 + - - -
1065A MET* 2.2 60.2 + - - +
1066A PRO* 3.6 1.4 - - - +
1067A MET* 3.4 28.9 + - - +
1070A VAL* 5.0 0.4 - - - -
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Residues in contact with ARG1061 (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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574A GLN* 3.5 22.8 + - - +
578A ASP* 2.5 52.0 + - - +
579A PRO* 4.0 4.2 - - + +
580A ILE* 3.7 19.3 - - + +
1057A GLN 3.1 13.5 + - - +
1058A VAL 3.2 5.8 + - - +
1060A SER* 1.3 76.8 - - - +
1062A GLU* 1.3 69.5 + - - +
1064A ARG* 3.3 18.1 + - - +
1263A TYR* 3.2 55.6 - - - +
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Residues in contact with GLU1062 (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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1058A VAL* 2.9 18.8 + - + +
1059A VAL 4.2 0.9 - - - +
1061A ARG* 1.3 83.3 - - - +
1063A LEU* 1.3 61.6 + - - +
1064A ARG* 3.7 5.2 + - - -
1100A LYS* 2.9 40.4 - - + -
1103A CYS* 3.8 21.3 - - + -
1104A GLN* 3.7 17.8 - - - +
1107A LEU* 3.6 24.3 - - - +
1263A TYR* 2.7 31.2 + - - +
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Residues in contact with LEU1063 (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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1030A VAL* 5.2 0.4 - - + -
1032A ILE* 4.3 18.6 - - + -
1038A VAL* 4.3 8.3 - - + -
1059A VAL* 3.0 29.2 + - + +
1062A GLU* 1.3 76.9 - - - +
1064A ARG* 1.3 77.6 + - - +
1065A MET* 3.6 28.5 - - + -
1103A CYS* 3.5 47.8 - - + +
1106A LEU* 4.9 7.0 - - + -
1107A LEU* 4.2 14.3 - - + +
1122A TRP* 3.1 24.6 + - + -
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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