Contacts of the helix formed by residues 1044 - 1062 (chain A) in PDB entry 3I7H
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 SER1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.3 15.9 - - - -
1043A LEU* 1.3 77.1 - - - +
1045A GLU* 1.3 81.4 + - - +
1047A TRP* 3.7 28.3 + - - -
1048A TYR* 3.2 17.8 + - - +
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Residues in contact with GLU1045 (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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3A TYR* 3.6 26.2 - - + +
1044A SER* 1.3 85.9 - - - +
1046A SER* 1.3 92.9 + - - +
1048A TYR* 4.0 0.5 - - - +
1049A ASN* 3.1 34.6 + - - +
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Residues in contact with SER1046 (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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1044A SER* 3.5 0.6 - - - -
1045A GLU* 1.3 96.7 + - - +
1047A TRP* 1.3 72.2 + - - +
1049A ASN* 3.4 4.5 + - - +
1050A LEU* 2.6 40.9 + - - +
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Residues in contact with TRP1047 (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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1023A PRO* 4.4 28.9 - - + -
1043A LEU* 3.9 24.0 - - + -
1044A SER* 3.7 26.8 + - - +
1045A GLU 3.3 0.4 - - - -
1046A SER* 1.3 88.4 + - - +
1048A TYR* 1.3 60.6 + - - +
1049A ASN 2.8 1.7 + - - -
1050A LEU* 3.0 13.9 + - + -
1051A LEU* 2.5 53.5 + - + +
1132A VAL* 3.7 35.9 - - + -
1135A GLU* 4.7 13.7 - - + -
1136A LEU* 5.2 10.5 - - + -
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Residues in contact with TYR1048 (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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3A TYR* 3.3 57.2 - + + -
4A ASN 4.4 1.1 - - - -
1043A LEU* 3.9 4.6 - - + +
1044A SER 3.2 9.5 + - - +
1045A GLU 4.1 0.7 - - - +
1047A TRP* 1.3 77.7 - - - +
1049A ASN* 1.3 70.1 + - - +
1052A LEU* 2.9 64.2 + - + +
1086A THR* 4.8 3.8 - - - +
1087A GLY* 3.5 40.8 + - - -
1088A PHE 3.7 9.6 + - - -
1089A ILE* 3.8 22.1 - - + +
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Residues in contact with ASN1049 (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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3A TYR* 5.2 6.7 + - - -
1045A GLU* 3.1 29.4 + - - +
1046A SER* 3.7 4.0 - - - +
1047A TRP 2.8 1.8 + - - -
1048A TYR* 1.3 93.5 - - - +
1050A LEU* 1.3 65.8 + - - +
1052A LEU* 3.7 7.8 - - - +
1053A ASP* 2.9 24.1 + - - +
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Residues in contact with LEU1050 (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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1046A SER* 2.6 24.8 + - - +
1047A TRP* 3.5 17.0 - - + +
1049A ASN* 1.3 71.7 - - - +
1051A LEU* 1.3 57.0 + - + +
1053A ASP* 2.8 12.8 - - + +
1054A MET* 2.7 47.8 + - + +
1122A ARG* 6.3 4.7 - - + -
1129A LEU* 4.4 18.8 - - + -
1132A VAL* 5.0 19.3 - - + -
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Residues in contact with LEU1051 (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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5A TYR* 4.1 13.0 - - + -
1043A LEU* 4.0 31.2 - - + -
1047A TRP* 2.5 35.8 + - + +
1050A LEU* 1.3 76.7 - - + +
1052A LEU* 1.3 58.9 + - - +
1054A MET* 3.2 17.4 + - + +
1055A GLN* 2.8 34.8 + - - +
1089A ILE* 3.6 9.9 - - + -
1094A ILE* 3.4 37.9 - - + +
1132A VAL* 5.0 13.0 - - + -
1133A VAL* 5.8 0.2 - - + -
1136A LEU* 4.7 10.5 - - + -
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Residues in contact with LEU1052 (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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1048A TYR* 2.9 58.8 + - + +
1049A ASN* 3.3 11.4 + - - +
1051A LEU* 1.3 73.9 - - - +
1053A ASP* 1.3 67.0 + - - +
1055A GLN* 3.3 17.4 - - - +
1056A ASN* 3.2 41.0 + - - +
1088A PHE 5.6 1.6 - - - +
1089A ILE* 4.3 4.6 - - + +
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Residues in contact with ASP1053 (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 ASN 2.9 13.5 + - - +
1050A LEU* 2.8 20.4 - - - +
1052A LEU* 1.3 71.3 - - - +
1054A MET* 1.3 68.6 + - - +
1056A ASN* 2.6 23.9 + - - +
1057A ARG* 2.8 53.5 + - - +
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Residues in contact with MET1054 (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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1050A LEU* 2.7 31.8 + - + +
1051A LEU* 3.2 26.0 - - - +
1053A ASP* 1.3 76.3 + - - +
1055A GLN* 1.3 51.9 + - - +
1057A ARG* 3.4 7.0 + - - +
1058A LEU* 2.7 67.0 + - + +
1094A ILE* 4.7 8.5 - - + +
1097A PHE* 3.8 33.2 - - + -
1108A VAL* 4.5 8.9 - - + +
1109A VAL* 6.0 0.7 - - + -
1129A LEU* 3.6 24.5 - - + -
1132A VAL* 6.2 1.3 - - - -
1133A VAL* 4.5 10.8 - - - -
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Residues in contact with GLN1055 (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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1051A LEU 2.8 17.7 + - - +
1052A LEU* 3.3 18.0 - - + +
1053A ASP 2.6 4.0 + - - -
1054A MET* 1.3 70.9 - - - +
1056A ASN* 1.3 59.7 + - - +
1058A LEU* 2.9 9.3 + - - +
1059A ASN* 2.8 36.9 + - - +
1070A HIS* 4.0 14.7 + - + +
1088A PHE 4.4 1.8 + - - +
1089A ILE* 3.2 52.3 - - - +
1090A ASP* 3.5 14.7 + - - +
1093A LEU* 3.8 16.3 - - + +
1094A ILE* 4.1 8.8 - - + +
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Residues in contact with ASN1056 (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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1052A LEU* 3.2 30.9 - - - +
1053A ASP* 2.6 14.8 + - - +
1055A GLN* 1.3 73.9 - - - +
1057A ARG* 1.3 66.2 + - + +
1059A ASN* 3.6 16.4 + - - +
1060A LYS* 3.4 19.8 + - - +
1071A SER* 5.7 2.8 + - - -
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Residues in contact with ARG1057 (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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1053A ASP* 2.8 39.7 + - - +
1054A MET* 3.6 7.0 - - - +
1056A ASN* 1.3 75.3 - - + +
1058A LEU* 1.3 63.0 + - - +
1060A LYS* 3.1 27.1 + - - +
1061A VAL* 3.4 9.0 + - - +
1107A GLU 5.1 0.6 + - - -
1108A VAL* 3.8 21.8 - - + +
1109A VAL* 4.0 14.9 - - - +
1110A ALA* 3.3 33.3 - - - +
1111A ASN* 2.9 40.1 + - - +
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Residues in contact with LEU1058 (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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1054A MET* 2.7 49.4 + - + +
1055A GLN* 3.2 8.7 - - - +
1057A ARG* 1.3 71.5 - - - +
1059A ASN* 1.3 58.4 + - - +
1061A VAL* 5.3 0.2 - - + -
1062A ILE* 3.0 62.7 + - + +
1093A LEU* 3.3 42.0 - - + +
1094A ILE* 4.2 7.4 - - + +
1097A PHE* 4.6 8.3 - - + -
1100A ILE* 4.0 19.1 - - + -
1108A VAL* 4.0 12.6 - - + -
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Residues in contact with ASN1059 (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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58A TYR* 5.0 3.6 + - - -
1055A GLN* 2.8 33.5 + - - +
1056A ASN* 3.6 17.5 + - - +
1057A ARG 3.3 0.4 - - - -
1058A LEU* 1.3 69.8 - - - +
1060A LYS* 1.3 66.2 + - + +
1062A ILE* 3.4 19.6 - - - +
1069A GLU* 5.5 10.1 - - + +
1070A HIS* 3.2 45.7 + - - +
1071A SER* 5.7 4.5 - - - -
1093A LEU* 4.6 8.7 - - - +
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Residues in contact with LYS1060 (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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1056A ASN 3.4 17.5 - - - +
1057A ARG* 3.1 12.1 - - - +
1059A ASN* 1.3 78.3 - - + +
1061A VAL* 1.3 66.3 + - + +
1062A ILE 4.7 0.3 - - - +
1107A GLU* 5.2 7.4 - - - +
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Residues in contact with VAL1061 (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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1057A ARG 3.4 5.8 + - - +
1058A LEU 4.0 3.1 - - - +
1059A ASN 3.4 0.2 - - - -
1060A LYS* 1.3 80.7 - - + +
1062A ILE* 1.3 68.6 + - + +
1063A LYS* 3.4 3.5 + - - +
1100A ILE* 4.9 8.1 - - + -
1104A LYS* 3.4 63.5 + - + +
1107A GLU* 4.5 17.3 - - + +
1108A VAL* 3.1 42.8 - - + +
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Residues in contact with ILE1062 (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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58A TYR* 4.4 14.4 - - + +
1058A LEU* 3.0 48.8 + - + +
1059A ASN* 3.4 14.2 + - - +
1060A LYS 4.7 0.2 - - - +
1061A VAL* 1.3 77.9 - - - +
1063A LYS* 1.3 78.8 + - - +
1064A SER* 3.8 5.5 + - - -
1093A LEU* 3.8 14.4 - - + -
1096A SER* 3.6 26.5 - - - +
1100A ILE* 4.4 13.7 - - + -
1104A LYS* 5.6 1.8 - - - +
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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