Contacts of the helix formed by residues 1423 - 1430 (chain I) in PDB entry 3AOH
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 GLY1423 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1263I PHE 3.5 8.3 - - - -
1264I GLU* 2.8 18.4 - - - -
1265I ALA* 3.6 19.7 - - - +
1375I MET* 5.1 0.2 - - - -
1422I MET* 1.3 76.6 - - - +
1424I VAL* 1.3 65.6 + - - -
1425I THR 3.2 0.6 + - - -
1426I LYS* 3.3 9.1 + - - +
1427I SER* 2.9 21.4 + - - -
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Residues in contact with VAL1424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097I LYS* 4.0 22.9 - - + +
1098I LEU* 4.9 0.4 - - + -
1100I ASP* 5.4 0.9 - - + -
1101I VAL* 2.5 58.9 - - + +
1263I PHE* 2.9 52.2 + - + +
1264I GLU* 2.6 17.7 + - - +
1371I VAL* 5.0 0.7 - - + -
1375I MET* 4.3 13.1 - - + +
1422I MET 3.8 0.2 + - - -
1423I GLY* 1.3 71.0 - - - -
1425I THR* 1.3 69.0 + - - +
1427I SER* 3.3 1.9 + - - -
1428I ALA* 3.3 4.0 + - - +
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Residues in contact with THR1425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097I LYS* 4.3 27.3 + - - +
1100I ASP* 6.4 0.7 - - - -
1264I GLU* 2.3 32.6 + - + +
1266I ARG* 5.1 2.1 + - - +
1424I VAL* 1.3 85.5 - - - +
1426I LYS* 1.3 58.2 + - + +
1428I ALA* 3.1 4.5 + - - +
1429I LEU* 2.7 54.4 + - + +
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Residues in contact with LYS1426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264I GLU* 4.2 0.2 + - - -
1420I LEU* 6.2 1.8 - - - +
1422I MET* 3.0 40.4 - - + +
1423I GLY* 3.3 14.0 + - - +
1425I THR* 1.3 78.4 - - + +
1427I SER* 1.3 64.8 + - - +
1429I LEU* 3.4 24.5 - - + -
1430I SER* 3.0 20.4 + - - +
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Residues in contact with SER1427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101I VAL* 4.2 8.8 + - - +
1104I GLU* 5.7 1.2 + - - -
1374I GLN* 3.4 32.0 + - - +
1375I MET* 4.8 3.6 - - - -
1378I TYR* 3.1 26.3 + - - -
1422I MET* 3.2 16.6 - - - +
1423I GLY 2.9 16.6 + - - -
1424I VAL* 3.7 7.9 - - - -
1425I THR 3.1 0.4 + - - -
1426I LYS* 1.3 75.5 - - - +
1428I ALA* 1.3 68.3 + - - +
1430I SER 3.5 6.4 - - - +
1431I THR* 3.7 1.0 + - - -
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Residues in contact with ALA1428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100I ASP* 3.6 41.7 - - - +
1101I VAL* 3.6 13.9 - - + +
1103I HIS* 5.5 2.5 - - + -
1424I VAL 3.3 1.8 + - - +
1425I THR* 3.1 9.8 + - - +
1427I SER* 1.3 77.6 + - - +
1429I LEU* 1.3 71.3 + - + +
1431I THR* 2.8 30.7 + - - +
1440I PHE* 4.0 7.4 - - + -
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Residues in contact with LEU1429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097I LYS* 5.4 5.8 - - - +
1100I ASP* 6.6 0.2 - - - -
1425I THR* 2.7 46.1 + - + +
1426I LYS* 3.4 32.8 - - + +
1428I ALA* 1.3 82.2 - - + +
1430I SER* 1.3 59.2 + - - +
1431I THR* 3.2 4.7 + - - +
1437I ALA* 5.5 1.6 - - - +
1440I PHE* 4.0 21.0 - - + -
1441I GLN* 4.2 22.3 - - - +
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Residues in contact with SER1430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378I TYR* 3.3 22.1 + - - -
1422I MET* 3.3 18.4 - - - +
1426I LYS* 3.0 21.0 + - - +
1427I SER 3.5 3.6 - - - -
1428I ALA 3.2 0.8 - - - -
1429I LEU* 1.3 77.5 - - - +
1431I THR* 1.3 62.5 + - - +
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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