Contacts of the helix formed by residues 1005 - 1020 (chain A) in PDB entry 5IYB
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 HIS1005 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938A LEU* 3.5 28.5 - - + -
941A ASP* 6.3 0.2 - - + -
942A VAL* 3.5 18.4 - - + +
948A ILE* 4.1 11.3 - - + +
1003A ASP 3.6 1.4 + - - +
1004A LEU* 1.3 80.9 - - - +
1006A PRO* 1.3 71.6 - - + +
1007A ILE* 3.2 49.3 + - + +
1008A LYS* 3.2 31.4 + - + +
1009A VAL* 3.3 10.7 + - - +
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Residues in contact with PRO1006 (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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922A PHE* 4.9 17.9 - - + -
938A LEU* 4.0 10.8 - - + -
939A VAL* 6.5 1.6 - - + -
942A VAL* 5.2 6.5 - - + -
948A ILE* 5.0 5.2 - - + -
952A LEU* 4.6 16.6 - - + -
1004A LEU* 4.0 5.8 - - + +
1005A HIS* 1.3 95.4 - - + +
1007A ILE* 1.3 62.9 + - + +
1009A VAL* 3.1 12.0 + - + +
1010A VAL* 2.9 30.5 + - - +
1051A SER* 3.5 24.3 + - - +
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Residues in contact with ILE1007 (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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947A HIS* 6.3 1.3 - - + -
948A ILE* 3.6 44.4 - - + +
951A GLU* 4.3 22.9 - - + -
952A LEU* 4.7 9.6 - - + -
1005A HIS* 3.2 25.7 + - + +
1006A PRO* 1.3 75.1 - - - +
1008A LYS* 1.3 60.3 + - - +
1010A VAL* 4.2 5.6 - - + -
1011A GLU* 2.8 37.7 + - + +
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Residues in contact with LYS1008 (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* 5.0 11.4 - - + -
1005A HIS* 3.2 27.0 + - + +
1006A PRO 3.2 0.4 - - - -
1007A ILE* 1.3 79.3 - - - +
1009A VAL* 1.3 53.6 + - + +
1011A GLU* 4.9 2.0 - - - -
1012A GLY* 2.8 31.5 + - - -
1062A GLY* 4.7 14.8 - - - +
1065A PHE* 4.4 10.9 - - + -
1066A ASP* 4.4 17.6 + - - -
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Residues in contact with VAL1009 (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* 4.0 28.9 - - + -
1005A HIS 3.5 13.9 - - - +
1006A PRO* 3.1 12.2 + - + +
1008A LYS* 1.3 75.1 - - - +
1010A VAL* 1.3 56.8 + - + +
1012A GLY 3.3 0.3 + - - -
1013A VAL* 2.7 41.4 + - + +
1049A LEU 3.6 23.8 - - - +
1051A SER* 4.3 13.0 - - - +
1054A MET* 4.7 10.8 - - + -
1065A PHE* 3.8 32.0 - - + -
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Residues in contact with VAL1010 (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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951A GLU* 4.6 14.1 - - + +
952A LEU* 3.7 12.8 - - + -
955A GLU* 3.3 37.5 - - + +
1006A PRO 2.9 18.1 + - - +
1007A ILE* 3.7 12.3 - - + +
1009A VAL* 1.3 76.2 - - + +
1011A GLU* 1.3 57.7 + - - +
1013A VAL* 3.3 7.8 + - - +
1014A LYS* 3.0 51.4 + - - +
1051A SER* 3.6 10.1 - - - +
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Residues in contact with GLU1011 (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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1007A ILE* 2.8 25.7 + - + +
1008A LYS* 4.4 2.5 - - - +
1010A VAL* 1.3 74.0 - - - +
1012A GLY* 1.3 56.1 + - - +
1014A LYS* 3.2 23.6 + - - +
1015A GLU* 2.7 47.8 + - - +
1018A LYS* 5.4 6.1 + - - -
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Residues in contact with GLY1012 (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 LYS 2.8 21.9 + - - -
1009A VAL 3.5 0.9 - - - -
1011A GLU* 1.3 77.4 - - - +
1013A VAL* 1.3 51.6 + - - +
1015A GLU* 3.3 7.6 + - - +
1016A LEU* 2.7 35.9 + - - +
1065A PHE* 4.7 0.7 - - - -
1069A LEU* 4.2 23.2 - - - +
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Residues in contact with VAL1013 (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 VAL* 2.7 27.3 + - + +
1010A VAL* 3.6 7.0 - - - +
1012A GLY* 1.3 71.0 - - - +
1014A LYS* 1.3 62.2 + - + +
1016A LEU* 3.8 7.3 - - + +
1017A SER* 2.9 35.6 + - - +
1045A LEU* 4.7 9.8 - - + +
1046A ARG* 3.5 38.1 - - + -
1049A LEU* 4.0 37.2 - - + +
1065A PHE* 4.5 6.3 - - + -
1069A LEU* 5.5 1.3 - - + -
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Residues in contact with LYS1014 (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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951A GLU* 2.6 30.7 + - - -
954A ARG* 6.0 0.4 - - - +
958A ARG* 6.3 1.1 - - - +
1010A VAL* 3.0 32.4 + - - +
1011A GLU* 3.6 26.1 + - - +
1013A VAL* 1.3 75.9 - - + +
1015A GLU* 1.3 63.7 + - - +
1017A SER* 3.3 7.6 + - - -
1018A LYS* 3.2 39.3 + - - +
1046A ARG* 6.4 2.2 - - - +
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Residues in contact with GLU1015 (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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1011A GLU* 2.7 34.2 + - - +
1012A GLY* 3.5 8.7 - - - +
1014A LYS* 1.3 73.5 - - - +
1016A LEU* 1.3 61.1 + - - +
1018A LYS* 3.3 15.0 + - + +
1019A LYS* 3.1 48.4 + - + +
1069A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU1016 (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 GLY 2.7 21.0 + - - +
1013A VAL* 3.8 7.0 - - - +
1015A GLU* 1.3 73.8 - - - +
1017A SER* 1.3 62.0 + - - +
1019A LYS* 3.2 14.6 + - + +
1020A LEU* 3.1 35.1 + - + +
1045A LEU* 3.9 25.8 - - + -
1049A LEU* 5.1 2.2 - - + -
1069A LEU* 3.5 47.3 - - + +
1072A ILE* 4.4 21.3 - - + -
1073A GLU* 4.2 16.8 - - + +
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Residues in contact with SER1017 (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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1013A VAL* 2.9 24.3 + - - +
1014A LYS* 3.3 7.9 + - - -
1016A LEU* 1.3 77.5 - - - +
1018A LYS* 1.3 62.6 + - - +
1020A LEU* 3.3 23.7 + - - +
1021A VAL* 4.4 1.7 + - - +
1034A GLN* 5.8 0.3 + - - -
1042A ASN* 3.0 30.7 + - - +
1045A LEU* 4.6 4.8 - - - +
1046A ARG* 5.0 3.1 - - - -
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Residues in contact with LYS1018 (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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1011A GLU* 5.4 6.1 + - - -
1014A LYS* 3.2 25.4 + - - +
1015A GLU* 3.5 14.3 - - + +
1017A SER* 1.3 77.3 - - - +
1019A LYS* 1.3 63.3 + - + +
1020A LEU 3.4 0.5 + - - -
1021A VAL* 3.4 24.2 - - - +
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Residues in contact with LYS1019 (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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1015A GLU* 3.1 41.7 + - + +
1016A LEU* 3.2 17.9 + - + +
1018A LYS* 1.3 79.2 - - + +
1020A LEU* 1.3 56.1 + - - +
1021A VAL* 3.0 14.6 + - - +
1069A LEU* 6.4 0.2 - - - +
1073A GLU* 3.5 41.2 + - + +
1077A ASN* 4.9 10.2 + - - -
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Residues in contact with LEU1020 (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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1016A LEU* 3.1 28.4 + - + +
1017A SER* 3.3 13.0 + - - +
1018A LYS 3.2 1.8 - - - -
1019A LYS* 1.3 75.0 - - - +
1021A VAL* 1.3 63.3 + - - +
1022A ILE* 3.4 4.7 + - - +
1034A GLN* 3.8 3.6 + - - -
1038A THR* 4.6 5.0 - - + +
1041A PHE* 3.4 36.6 - - + -
1042A ASN* 6.1 1.3 - - - +
1045A LEU* 4.6 14.1 - - + -
1072A ILE* 4.4 4.5 - - + +
1073A GLU* 4.2 22.4 - - + +
1076A PHE* 3.6 49.1 - - + -
1077A ASN* 5.3 0.9 - - + +
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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