Contacts of the helix formed by residues 1292 - 1296 (chain A) in PDB entry 5IMX
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 PRO1292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248A ARG 4.7 3.4 - - - +
1249A ASP* 3.4 24.7 - - - +
1253A ARG* 3.5 25.8 - - - +
1273A MET* 4.2 17.9 - - - -
1290A MET 4.3 3.1 - - - +
1291A LEU* 1.3 85.3 - - + +
1293A VAL* 1.3 52.1 + - - +
1294A LYS 3.1 3.1 - - - -
1295A TRP* 2.7 40.7 + - + +
1296A MET* 3.5 19.8 - - + +
1335A ASN* 5.9 0.2 - - - +
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Residues in contact with VAL1293 (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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1288A CYS 5.4 3.4 - - - +
1289A ALA* 6.4 0.9 - - - -
1291A LEU* 2.8 27.2 + - + +
1292A PRO* 1.3 71.3 - - - +
1294A LYS* 1.3 57.4 + - - +
1295A TRP 3.1 0.2 - - - -
1296A MET* 3.0 32.9 + - - +
1301A PHE* 4.5 24.7 - - + -
1335A ASN* 3.9 43.7 - - + +
1338A VAL* 4.3 14.6 - - + +
1339A LEU* 4.6 16.2 - - + +
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Residues in contact with LYS1294 (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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1292A PRO 2.9 1.4 + - - -
1293A VAL* 1.3 77.6 - - + +
1295A TRP* 1.3 76.0 + - + +
1296A MET 5.1 0.4 - - - -
1313A TRP* 4.9 1.0 + - - -
1317A VAL* 3.7 13.7 - - - +
1328A MET* 3.8 25.9 - - - +
1329A PRO* 2.6 33.4 + - + +
1330A TYR* 3.0 47.5 + - + -
1331A PRO 4.7 2.4 + - - -
1333A LYS 3.1 21.5 + - - -
1334A SER 4.5 0.2 - - - -
1335A ASN* 3.7 23.8 + - - +
1338A VAL* 4.0 22.0 - - + -
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Residues in contact with TRP1295 (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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1249A ASP* 5.2 3.4 - - - +
1250A ILE 3.3 26.0 - - - +
1251A ALA* 3.2 15.2 - - + +
1253A ARG* 3.8 26.0 - - - +
1292A PRO* 2.7 25.0 + - + +
1294A LYS* 1.3 100.0 - - + +
1296A MET* 1.3 58.1 + - + -
1313A TRP* 3.4 14.0 - - - -
1314A SER* 2.8 31.0 + - - +
1317A VAL* 3.5 22.6 - - + +
1318A LEU 4.6 0.2 - - - -
1321A GLU* 2.9 40.1 + - - -
1328A MET* 4.0 19.1 - - + -
1329A PRO* 3.6 23.8 - - + -
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Residues in contact with MET1296 (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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1248A ARG 5.5 4.3 - - - +
1273A MET* 5.9 0.2 - - - +
1291A LEU* 3.9 19.3 - - + -
1292A PRO* 3.5 43.7 - - + +
1293A VAL* 3.0 19.8 + - - +
1294A LYS 3.4 0.9 - - - -
1295A TRP* 1.3 82.1 - - + +
1297A PRO* 1.3 73.2 - - + +
1300A ALA* 3.6 16.6 - - + +
1301A PHE* 3.6 41.3 - - + +
1306A PHE* 3.8 22.0 - - + -
1313A TRP* 3.4 14.0 + - - -
1314A SER* 5.5 1.1 - - - +
1342A VAL* 5.0 1.2 - - - +
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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