Contacts of the helix formed by residues 1437 - 1449 (chain P) in PDB entry 5IJO
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 GLU1437 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1436P ASP* 1.3 77.8 - - - +
1438P PRO* 1.3 66.8 - - - +
1439P ASP* 2.8 7.8 + - + +
1440P THR* 2.9 16.7 + - - +
1441P LEU* 3.8 2.6 + - - +
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Residues in contact with PRO1438 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437P GLU* 1.3 73.5 - - - +
1439P ASP* 1.3 61.8 + - - +
1440P THR 3.2 0.2 - - - -
1441P LEU* 3.2 10.9 + - + +
1442P GLU* 3.0 22.5 + - - +
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Residues in contact with ASP1439 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437P GLU* 2.8 4.9 + - + +
1438P PRO* 1.3 76.6 - - - +
1440P THR* 1.3 63.2 + - - +
1442P GLU* 3.2 7.7 + - - +
1443P ALA* 3.0 22.6 + - - +
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Residues in contact with THR1440 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436P ASP* 3.9 23.1 - - - -
1437P GLU 2.9 12.0 + - - +
1439P ASP* 1.3 78.4 - - - +
1441P LEU* 1.3 62.1 + - - +
1443P ALA* 3.2 7.9 + - - +
1444P ALA* 3.1 21.5 + - - +
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Residues in contact with LEU1441 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437P GLU 3.8 2.5 + - - +
1438P PRO* 3.2 15.0 + - + +
1440P THR* 1.3 78.8 - - - +
1442P GLU* 1.3 63.1 + - - +
1444P ALA* 3.2 7.8 + - - +
1445P LYS* 3.1 22.0 + - - +
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Residues in contact with GLU1442 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1438P PRO 3.0 13.5 + - - +
1439P ASP* 3.2 9.8 + - - +
1441P LEU* 1.3 76.8 - - - +
1443P ALA* 1.3 62.3 + - - +
1445P LYS* 3.2 6.6 + - - +
1446P LYS* 3.0 22.2 + - - +
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Residues in contact with ALA1443 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439P ASP 3.0 12.9 + - - +
1440P THR* 3.2 11.0 + - - +
1442P GLU* 1.3 77.1 - - - +
1444P ALA* 1.3 62.3 + - - +
1446P LYS* 3.2 8.1 + - - +
1447P THR* 3.2 20.8 + - - -
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Residues in contact with ALA1444 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440P THR 3.1 13.7 + - - +
1441P LEU* 3.2 10.7 + - - +
1443P ALA* 1.3 77.5 - - - +
1445P LYS* 1.4 61.0 + - - +
1447P THR* 3.2 9.0 + - - -
1448P MET* 3.0 19.9 + - - +
1456P GLU 4.4 15.0 - - - +
1457P ASP* 5.4 6.6 - - + +
1460P SER* 6.1 5.2 - - - -
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Residues in contact with LYS1445 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441P LEU 3.1 13.3 + - - +
1442P GLU* 3.7 10.1 - - - +
1444P ALA* 1.4 73.1 - - - +
1446P LYS* 1.3 69.1 + - - +
1448P MET* 3.1 22.4 + - - +
1449P TRP* 3.3 6.2 + - - +
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Residues in contact with LYS1446 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1442P GLU 3.0 12.9 + - - +
1443P ALA* 3.6 10.5 - - - +
1444P ALA 3.2 0.2 - - - -
1445P LYS* 1.3 78.2 - - - +
1447P THR* 1.4 52.8 - - - +
1449P TRP* 2.7 41.3 + - + +
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Residues in contact with THR1447 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654O SER 4.8 1.3 - - - -
655O ALA* 2.4 56.4 - - - +
656O PRO* 5.3 1.1 - - - -
1443P ALA 3.2 9.6 + - - -
1444P ALA* 3.5 11.2 - - - -
1445P LYS 3.2 0.6 - - - -
1446P LYS* 1.4 71.5 - - - +
1448P MET* 1.3 74.6 + - - +
1449P TRP 2.9 4.7 + - - -
1455P PRO* 3.5 5.0 - - - +
1456P GLU* 4.8 7.0 - - - -
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Residues in contact with MET1448 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444P ALA 3.0 11.8 + - - +
1445P LYS* 3.2 14.8 - - - +
1447P THR* 1.3 83.3 - - - +
1449P TRP* 1.5 49.5 - - - +
1450P GLU* 3.0 4.9 - - - -
1451P ARG* 2.4 31.6 + - - +
1455P PRO* 3.8 13.4 - - + +
1456P GLU 5.3 1.3 + - - +
1457P ASP* 5.9 6.3 - - + -
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Residues in contact with TRP1449 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655O ALA* 5.5 0.4 - - - -
1445P LYS 3.3 4.7 + - - +
1446P LYS* 2.7 25.0 + - - +
1447P THR* 3.9 4.3 - - - -
1448P MET* 1.5 71.1 - - - +
1450P GLU* 1.1 118.4 + - + +
1452P LEU* 3.5 15.6 + - - +
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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
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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