Contacts of the helix formed by residues 1002 - 1018 (chain E) in PDB entry 5ZCS
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 PRO1002 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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959E CYS* 6.3 2.9 - - + -
997E ARG* 5.4 4.9 - - + -
998E LYS 3.5 26.9 - - - +
999E HIS* 4.3 3.1 - - - +
1000E LEU 3.3 0.4 - - - -
1001E TRP* 1.3 77.3 - - - +
1003E VAL* 1.3 57.8 + - - -
1004E VAL 3.3 1.6 - - - -
1005E PRO* 3.7 11.6 - - + +
1006E ASP* 2.9 30.7 + - - +
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Residues in contact with VAL1003 (chain E).
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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999E HIS 4.0 13.1 + - - +
1000E LEU* 3.6 13.7 + - - +
1001E TRP 3.3 1.8 - - - -
1002E PRO* 1.3 75.9 - - - +
1004E VAL* 1.3 64.4 + - - +
1006E ASP* 3.6 12.9 + - - +
1007E ASP* 3.6 12.5 + - - +
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Residues in contact with VAL1004 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E LEU 4.7 1.6 + - - +
1001E TRP 4.0 9.2 + - - +
1003E VAL* 1.3 79.0 - - - +
1005E PRO* 1.3 60.9 - - - +
1006E ASP 3.6 0.3 + - - -
1007E ASP* 3.6 14.6 + - - +
1008E VAL* 4.0 7.3 + - - +
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Residues in contact with PRO1005 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959E CYS 5.5 0.7 - - - +
960E GLU* 5.6 5.4 - - - +
963E SER* 3.9 28.0 - - - -
1001E TRP 4.4 2.4 - - - +
1002E PRO* 3.3 18.6 - - + +
1003E VAL 3.3 0.2 - - - -
1004E VAL* 1.3 77.7 - - - +
1006E ASP* 1.3 59.9 + - - +
1007E ASP 3.3 0.2 - - - -
1008E VAL* 3.3 5.7 + - + +
1009E GLU* 2.9 32.5 + - + +
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Residues in contact with ASP1006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E PRO 2.9 18.4 + - - +
1003E VAL* 3.9 8.1 - - - +
1004E VAL 3.3 0.6 - - - -
1005E PRO* 1.3 77.0 - - - +
1007E ASP* 1.3 59.4 + - - +
1008E VAL 3.2 0.6 + - - -
1009E GLU* 4.5 5.8 - - - +
1010E GLN* 3.6 22.2 + - - +
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Residues in contact with ASP1007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A ASP* 5.4 7.6 - - - +
1214A CYS* 5.7 3.5 - - - +
1003E VAL 3.6 10.5 + - - +
1004E VAL* 4.0 10.5 - - - +
1005E PRO 3.3 0.8 - - - -
1006E ASP* 1.3 77.8 - - - +
1008E VAL* 1.3 58.5 + - - +
1010E GLN* 4.5 8.1 + - - +
1011E LEU* 5.2 1.7 + - - +
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Residues in contact with VAL1008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218A LYS* 4.1 25.0 + - - +
967E THR* 5.0 10.8 - - - -
1004E VAL 4.0 7.1 + - - +
1005E PRO* 3.3 8.1 + - + +
1006E ASP 3.2 0.2 - - - -
1007E ASP* 1.3 79.5 - - - +
1009E GLU* 1.3 62.5 + - - +
1010E GLN 3.3 2.8 + - - -
1011E LEU* 3.9 12.6 + - - +
1012E CYS* 4.1 6.9 + - - +
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Residues in contact with GLU1009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963E SER* 6.0 3.4 - - - +
967E THR* 5.2 8.3 - - - -
1005E PRO* 2.9 19.3 + - + +
1006E ASP* 3.8 5.1 + - - -
1007E ASP 3.7 0.2 - - - -
1008E VAL* 1.3 74.9 - - - +
1010E GLN* 1.3 58.8 + - - +
1011E LEU 3.3 0.4 - - - -
1012E CYS* 3.3 10.7 + - + +
1013E ASN* 2.9 28.9 + - - +
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Residues in contact with GLN1010 (chain E).
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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1207A GLN* 5.0 19.1 + - - +
1210A ASP* 4.7 19.5 - - + +
1211A VAL* 5.4 0.2 - - - -
1006E ASP 3.6 16.0 + - - +
1007E ASP* 4.7 7.4 - - - +
1008E VAL 3.3 1.4 - - - -
1009E GLU* 1.3 74.5 - - - +
1011E LEU* 1.3 59.5 + - - +
1013E ASN* 3.4 6.4 + - - +
1014E GLU* 2.9 28.9 + - - +
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Residues in contact with LEU1011 (chain E).
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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1210A ASP* 4.4 7.6 + - - +
1211A VAL* 3.8 40.9 - - + +
1214A CYS* 5.5 8.7 - - + -
1007E ASP 5.2 0.8 + - - -
1008E VAL* 3.9 9.5 + - - +
1009E GLU 3.3 0.4 - - - -
1010E GLN* 1.3 78.0 - - - +
1012E CYS* 1.3 58.2 + - - +
1014E GLU* 3.4 1.7 + - - +
1015E LEU* 2.9 29.6 + - - +
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Residues in contact with CYS1012 (chain E).
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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967E THR* 4.8 13.5 - - - +
970E TYR* 3.7 31.0 - - + +
971E VAL* 5.3 1.1 - - + +
1008E VAL 4.1 3.6 + - - +
1009E GLU* 3.3 16.4 + - + +
1010E GLN 3.3 0.6 - - - -
1011E LEU* 1.3 78.4 - - - +
1013E ASN* 1.3 56.8 + - - +
1015E LEU* 3.4 6.6 + - - +
1016E SER* 2.9 29.6 + - - -
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Residues in contact with ASN1013 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A GLN* 6.2 2.2 - - - +
1009E GLU 2.9 17.2 + - - +
1010E GLN* 3.8 7.2 - - - +
1011E LEU 3.3 0.2 - - - -
1012E CYS* 1.3 76.5 - - - +
1014E GLU* 1.3 57.2 + - - +
1016E SER* 3.4 5.9 + - - +
1017E SER* 2.9 31.4 + - - -
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Residues in contact with GLU1014 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A GLN* 4.2 30.5 - - + +
1208A ARG* 5.2 2.5 - - + -
1211A VAL* 4.3 10.3 - - + -
1010E GLN 2.9 17.4 + - - +
1011E LEU 3.8 4.5 - - - +
1013E ASN* 1.3 76.2 - - - +
1015E LEU* 1.3 58.8 + - - +
1017E SER* 4.3 3.9 - - - -
1018E ILE* 3.0 31.0 + - - +
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Residues in contact with LEU1015 (chain E).
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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974E LEU* 3.9 28.8 - - + +
1011E LEU 2.9 17.6 + - - +
1012E CYS* 3.8 7.0 - - - +
1013E ASN 3.3 0.2 - - - -
1014E GLU* 1.3 77.3 - - - +
1016E SER* 1.3 57.6 + - - +
1018E ILE 3.1 21.6 - - - +
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Residues in contact with SER1016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970E TYR* 6.0 4.0 - - - -
974E LEU* 5.4 0.9 - - - +
980E GLN* 5.9 2.1 - - - -
982E CYS* 3.8 33.6 - - - +
983E ASP* 3.7 21.1 + - - +
986E LYS* 6.5 0.7 - - - -
1012E CYS 2.9 17.9 + - - -
1013E ASN* 3.9 6.1 - - - -
1015E LEU* 1.3 77.5 - - - +
1017E SER* 1.3 61.5 + - - +
1018E ILE 4.3 2.1 - - - +
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Residues in contact with SER1017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983E ASP* 5.0 10.8 - - - +
1013E ASN 2.9 18.6 + - - -
1014E GLU* 4.3 4.0 - - - -
1016E SER* 1.3 80.9 - - - +
1018E ILE* 1.3 60.3 + - - +
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Residues in contact with ILE1018 (chain E).
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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1014E GLU 3.0 16.1 + - - +
1015E LEU* 3.1 20.3 - - - +
1016E SER 4.3 2.3 - - - +
1017E SER* 1.3 80.9 - - - +
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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