Contacts of the helix formed by residues 1433 - 1439 (chain N) in PDB entry 5D4C
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 SER1433 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103N HIS* 6.0 0.2 - - - -
1431N THR* 3.3 17.4 + - - +
1432N LYS* 1.3 77.3 - - - +
1434N TRP* 1.3 59.6 + - - +
1436N SER* 3.0 24.5 + - - -
1437N ALA* 3.4 15.2 + - - +
1457N ASP* 3.1 24.5 + - - +
1464N GLU* 3.1 27.4 - - - +
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Residues in contact with TRP1434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 6.3 0.2 - - + -
1092M LEU* 4.9 7.4 - - + -
1099M VAL* 4.2 14.8 - - + -
8N VAL* 3.1 46.4 + - + -
9N ARG 4.7 0.2 - - - -
10N ILE* 3.5 33.7 - - + -
614N PHE* 5.4 1.3 - + - -
1431N THR 5.3 1.1 - - - -
1432N LYS 3.4 4.4 + - - -
1433N SER* 1.3 70.4 - - - +
1435N LEU* 1.3 88.8 + - + +
1437N ALA* 4.6 1.1 - - - +
1438N ALA* 2.9 32.9 + - + +
1446N VAL* 3.7 10.4 - - + +
1447N LEU* 3.7 29.6 - - + -
1450N ALA* 3.8 20.4 - - + -
1455N LYS* 3.7 31.1 + - + +
1456N LYS 4.1 3.1 - - - -
1457N ASP* 3.5 17.7 + - + +
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Residues in contact with LEU1435 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085M PHE* 5.3 2.5 - - + -
1088M LEU* 4.8 7.0 - - + -
8N VAL* 4.4 16.2 - - + -
614N PHE* 4.1 24.2 - - + -
1433N SER* 3.3 0.4 - - - +
1434N TRP* 1.3 105.3 - - + +
1436N SER* 1.3 59.4 + - - +
1438N ALA* 3.8 1.8 - - - +
1439N SER* 2.8 31.9 + - - -
1457N ASP* 3.2 19.1 + - - +
1459N LEU* 4.4 11.0 - - + -
1464N GLU* 4.3 8.7 - - + +
1467N ILE* 4.0 19.8 - - + +
1468N LEU* 3.8 28.3 - - + -
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Residues in contact with SER1436 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100N ASP* 3.5 12.6 + - - -
1103N HIS* 2.9 29.4 + - - -
1431N THR* 4.2 9.2 - - - +
1433N SER* 3.0 25.6 + - - -
1435N LEU* 1.3 77.8 - - - +
1437N ALA* 1.3 56.3 + - - +
1439N SER* 2.9 19.2 + - - -
1440N PHE* 3.0 16.3 + - - +
1463N LYS* 3.2 16.1 + - - +
1464N GLU* 4.2 6.9 - - - +
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Residues in contact with ALA1437 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428N ALA 4.2 11.0 - - - +
1429N LEU* 3.8 21.6 - - - +
1431N THR* 4.3 5.6 - - + +
1433N SER 3.4 13.2 + - - +
1434N TRP* 4.6 1.1 - - - -
1436N SER* 1.3 78.7 + - - +
1438N ALA* 1.3 62.1 + - - +
1440N PHE* 3.1 18.7 + - - +
1441N GLN 3.3 17.3 - - - +
1446N VAL* 3.7 26.8 - - + +
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Residues in contact with ALA1438 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614N PHE* 3.8 17.1 - - + +
1434N TRP* 2.9 21.0 + - + +
1435N LEU* 3.8 5.6 - - - +
1437N ALA* 1.3 78.5 - - - +
1439N SER* 1.3 59.1 + - - +
1440N PHE 3.6 0.3 + - - -
1441N GLN 4.5 0.3 + - - -
1443N THR* 3.2 30.9 + - + +
1446N VAL* 3.5 11.6 - - + +
1447N LEU* 3.7 31.4 - - + -
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Residues in contact with SER1439 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614N PHE* 3.7 29.6 - - - -
615N ARG* 4.2 8.5 - - - +
619N LEU* 3.8 24.2 - - - +
1096N ARG* 4.0 6.2 + - - -
1435N LEU 2.8 21.7 + - - -
1436N SER* 2.9 11.3 + - - -
1438N ALA* 1.3 75.6 - - - +
1440N PHE* 1.3 63.5 + - - +
1463N LYS* 3.0 22.3 + - - -
1467N ILE* 3.9 7.3 - - - +
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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