Contacts of the helix formed by residues 1342 - 1349 (chain A) in PDB entry 5IYB
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 SER1342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1139A LEU* 4.2 1.1 - - - +
1302A GLU* 3.3 38.6 - - - +
1303A GLN* 4.1 5.6 + - - -
1304A ILE* 3.4 27.0 - - - +
1341A VAL* 1.3 75.7 - - - +
1343A LEU* 1.3 64.4 + - - +
1344A MET* 3.1 4.8 + - - +
1345A ARG* 3.3 2.8 + - - +
1346A VAL* 3.2 26.0 + - - +
1364A GLU* 5.2 2.2 - - - -
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Residues in contact with LEU1343 (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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1139A LEU* 4.0 25.1 - - + -
1341A VAL 2.4 25.9 + - - +
1342A SER* 1.3 66.9 - - - +
1344A MET* 1.3 62.6 + - - +
1346A VAL* 3.6 1.4 + - + +
1347A LEU* 3.2 36.2 + - + +
1357A THR* 3.9 33.0 - - + +
1358A THR 4.7 6.1 - - - +
1359A SER* 4.6 5.2 - - - +
1364A GLU* 4.7 7.5 + - + +
1365A ILE* 3.8 33.4 - - + +
1368A VAL* 4.5 24.5 - - + -
1369A LEU* 4.9 5.2 - - + -
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Residues in contact with MET1344 (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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1342A SER* 3.1 1.7 - - - -
1343A LEU* 1.3 80.6 - - - +
1345A ARG* 1.3 60.1 + - - +
1347A LEU* 3.6 1.4 + - + -
1348A SER* 3.0 27.5 + - - +
1364A GLU* 5.3 1.7 + - - +
1368A VAL* 3.9 34.1 - - + +
133E GLN* 3.1 48.9 - - + +
134E GLU* 4.6 16.2 - - + -
137E ILE* 3.7 31.2 - - + -
139E ILE* 6.0 0.9 - - + -
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Residues in contact with ARG1345 (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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1161A LEU* 6.4 1.1 - - + -
1301A ILE* 3.3 52.2 - - + +
1302A GLU* 2.9 40.9 + - - +
1342A SER* 3.3 7.9 + - - +
1344A MET* 1.3 76.5 - - - +
1346A VAL* 1.3 61.5 + - + +
1348A SER* 2.9 24.4 + - - -
1349A GLU* 3.2 15.0 + - + +
133E GLN* 4.1 27.2 + - - +
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Residues in contact with VAL1346 (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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1139A LEU* 3.6 19.7 - - + -
1141A VAL* 3.6 39.7 - - + -
1161A LEU* 3.7 33.2 - - + -
1304A ILE* 4.9 3.4 - - + -
1338A THR* 5.8 0.7 - - + +
1342A SER* 3.2 25.0 + - - +
1343A LEU* 4.0 4.7 - - + +
1345A ARG* 1.3 76.6 - - + +
1347A LEU* 1.3 59.9 + - - +
1349A GLU* 3.6 8.0 + - - +
1352A VAL* 3.2 23.6 - - + +
1357A THR* 4.8 4.3 - - + -
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Residues in contact with LEU1347 (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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1343A LEU* 3.2 40.0 + - + +
1344A MET 3.7 5.8 - - - +
1345A ARG 3.2 0.4 - - - -
1346A VAL* 1.3 78.5 - - - +
1348A SER* 1.3 61.1 + - - +
1349A GLU 3.3 7.4 + - - +
1352A VAL* 4.4 8.8 - - + +
1353A ASP 4.1 1.1 - - - +
1354A PRO* 3.5 38.0 - - + +
1357A THR* 3.9 23.1 - - + +
1368A VAL* 4.5 11.9 - - + -
1369A LEU* 5.0 0.7 - - + -
137E ILE* 3.4 39.5 - - + +
142E HIS* 4.5 14.8 - - + -
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Residues in contact with SER1348 (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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1344A MET* 3.0 24.6 + - - +
1345A ARG* 2.9 14.9 + - - -
1347A LEU* 1.3 75.5 - - - +
1349A GLU* 1.3 64.2 + - - +
1350A LYS 3.8 0.5 + - - -
8E TYR* 5.7 4.2 - - - -
133E GLN* 4.0 4.8 + - - +
136E LEU* 3.6 41.8 - - - +
137E ILE* 4.1 8.0 - - - +
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Residues in contact with GLU1349 (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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1157A ILE* 4.8 12.3 - - + +
1160A ARG* 3.3 37.2 - - + -
1161A LEU* 5.7 9.9 - - + +
1301A ILE* 4.9 11.5 - - - +
1345A ARG* 3.2 12.4 + - + +
1346A VAL* 3.8 14.6 - - - +
1347A LEU 3.2 9.0 - - - +
1348A SER* 1.3 80.9 - - - +
1350A LYS* 1.3 83.6 + - - +
1351A ASP 3.8 0.2 + - - -
1352A VAL* 3.8 16.9 + - + +
5E GLU* 5.7 2.9 - - - +
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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