Contacts of the strand formed by residues 1378 - 1381 (chain I) in PDB entry 3AOI
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 TYR1378 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104I GLU* 4.7 0.3 + - - -
1374I GLN 4.0 2.7 - - - -
1375I MET 5.5 0.7 - - - -
1376I MET* 3.2 3.0 - - - +
1377I LYS* 1.3 123.1 + - + +
1379I VAL* 1.3 69.4 + - - +
1392I GLY 5.3 4.9 - - - -
1393I GLN* 3.5 11.9 - - - +
1394I VAL* 4.1 22.0 - - + -
1395I LEU 3.9 0.2 - - - +
1420I LEU* 3.2 27.9 + - + +
1422I MET* 3.4 34.1 - - + -
1427I SER* 2.7 49.3 + - - -
1430I SER* 3.3 21.4 + - - -
1431I THR* 3.5 8.8 - - - -
1432I LYS 5.0 1.6 - - - -
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Residues in contact with VAL1379 (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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1376I MET 5.2 1.6 - - - +
1378I TYR* 1.3 81.6 - - - +
1380I GLU* 1.3 62.5 + - - +
1391I GLU 3.9 0.2 - - - +
1392I GLY* 3.6 0.3 - - - -
1393I GLN 3.0 26.4 + - - +
1395I LEU* 3.6 29.2 - - + +
1398I TRP* 3.4 32.5 + - + -
1417I TRP* 3.8 28.0 - - + +
1418I LYS 3.5 7.2 - - - +
1419I PRO* 3.5 24.9 - - + -
1420I LEU* 3.8 6.7 - - - -
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Residues in contact with GLU1380 (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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1379I VAL* 1.3 73.8 - - - +
1381I VAL* 1.3 80.1 + - - +
1389I LEU 4.8 1.1 - - - +
1390I LEU* 4.2 24.4 - - - +
1391I GLU 3.3 13.9 - - - +
1392I GLY* 5.2 0.2 - - - -
1417I TRP* 3.0 12.1 - - - +
1418I LYS* 3.0 53.8 + - + +
1420I LEU* 3.3 28.5 - - + +
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Residues in contact with VAL1381 (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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1380I GLU* 1.3 88.1 - - - +
1382I THR* 1.3 64.1 + - - +
1383I ASP 4.0 19.7 - - - +
1384I PRO* 4.3 5.6 - - + -
1387I SER 5.0 2.2 - - - +
1388I ARG 4.4 4.0 - - - +
1389I LEU* 2.3 51.0 - - - +
1391I GLU* 3.2 25.0 + - + +
1398I TRP* 3.9 35.9 - - + +
1415I VAL* 5.7 4.5 - - + -
1416I ALA 3.9 6.7 - - - +
1417I TRP* 4.4 2.0 - - + +
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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