Contacts of the helix formed by residues 1309 - 1315 (chain B) in PDB entry 2IUK
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 SER1309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1307B PHE* 3.5 0.4 - - - +
1308B GLU* 1.3 83.3 - - - +
1310B PHE* 1.3 61.3 + - - +
1311B GLU* 3.9 10.0 + - - +
1312B ASP* 3.1 33.0 + - - +
1313B VAL* 3.2 6.8 + - - +
1757B GLN* 3.5 15.3 - - - -
1761B LEU* 3.5 16.3 - - - +
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Residues in contact with PHE1310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309B SER* 1.3 75.6 - - - +
1311B GLU* 1.3 58.4 + - - +
1313B VAL* 3.4 4.3 + - - +
1314B ARG* 2.9 48.1 + - - +
1364B VAL* 5.0 4.3 - - + -
1365B MET* 4.0 36.6 - - + -
1506B LEU* 4.7 11.9 - - + -
1731B LEU* 3.5 30.6 - - + +
1756B PRO 5.8 0.2 - - - -
1757B GLN* 3.3 42.8 + - + +
1760B TYR* 3.6 44.9 - + + -
1761B LEU* 4.3 5.8 - - + -
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Residues in contact with GLU1311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309B SER* 3.2 8.6 + - - +
1310B PHE* 1.3 75.4 - - - +
1312B ASP* 1.3 64.3 + - - +
1314B ARG* 2.9 36.3 + - - +
1315B SER* 3.1 23.4 + - - -
1318B GLU* 3.1 19.8 - - - +
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Residues in contact with ASP1312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306B GLU 4.3 1.4 - - - +
1307B PHE* 3.4 14.1 - - + -
1308B GLU* 2.8 27.7 + - + +
1309B SER* 3.1 29.3 + - - +
1311B GLU* 1.3 77.9 - - - +
1313B VAL* 1.3 58.6 + - - +
1315B SER* 2.8 23.5 + - - -
1316B LEU* 4.0 8.0 - - - +
1322B LYS* 4.0 12.9 + - - +
1767B LYS* 3.5 20.5 + - - -
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Residues in contact with VAL1313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1307B PHE* 3.4 40.6 - - + -
1309B SER 3.2 10.7 + - - +
1310B PHE 3.4 7.2 + - - +
1312B ASP* 1.3 74.7 - - - +
1314B ARG* 1.3 66.6 + - - +
1316B LEU* 3.3 22.8 + - + +
1317B TYR* 4.7 3.1 - - - -
1729B LEU* 4.8 5.4 - - + -
1730B ILE* 3.6 30.5 - - + +
1731B LEU* 4.0 18.2 - - + -
1761B LEU* 3.7 17.9 - - + -
1770B THR* 5.4 0.4 - - + -
1774B LEU* 6.5 0.4 - - + -
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Residues in contact with ARG1314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1310B PHE* 2.9 26.9 + - - +
1311B GLU* 2.9 58.7 + - - +
1312B ASP 3.5 0.2 - - - -
1313B VAL* 1.3 75.1 - - - +
1315B SER* 1.3 57.5 + - - +
1316B LEU 3.0 5.9 + - - -
1317B TYR* 2.9 55.8 + - - +
1318B GLU* 3.3 19.5 + - - +
1360B SER* 4.3 29.4 + - - +
1729B LEU* 3.9 16.4 - - + -
1731B LEU* 4.9 4.3 - - + +
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Residues in contact with SER1315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311B GLU* 3.1 25.7 + - - -
1312B ASP* 2.8 19.1 + - - -
1313B VAL 3.3 0.2 - - - -
1314B ARG* 1.3 74.4 - - - +
1316B LEU* 1.3 58.2 + - - +
1317B TYR 3.1 1.2 + - - -
1318B GLU* 3.6 13.2 + - - -
1319B GLY* 3.3 7.5 + - - -
1320B GLY* 2.7 29.9 + - - -
1322B LYS* 3.1 25.6 + - - -
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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