Contacts of the helix formed by residues 1382 - 1386 (chain A) in PDB entry 3F2B
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 PRO1382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362A ILE* 4.3 7.0 - - - +
1368A GLN 3.1 20.0 - - - +
1369A ALA 3.4 11.9 - - - +
1370A THR 3.7 14.4 - - - +
1371A GLU 3.6 15.5 - - - +
1372A PHE* 3.5 35.0 - - + -
1380A ILE 3.7 0.2 - - - -
1381A PRO* 1.3 86.9 - - + +
1383A PHE* 1.3 67.9 + - - +
1384A ASN* 3.2 17.0 - - - +
1385A ALA* 3.1 22.2 + - + +
1386A ILE 4.2 0.7 + - - -
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Residues in contact with PHE1383 (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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1362A ILE* 3.9 28.9 - - + -
1363A ASP 4.1 1.3 - - - -
1364A LEU* 3.9 22.2 - - + -
1367A SER* 3.6 25.1 - - - -
1368A GLN 3.0 26.5 + - - -
1381A PRO 4.1 0.2 + - - -
1382A PRO* 1.3 71.6 - - - +
1384A ASN* 1.3 58.2 + - - +
1385A ALA 3.0 0.2 - - - -
1386A ILE* 2.9 38.9 + - + +
1389A LEU* 3.6 19.2 - - + +
1394A ALA* 4.1 18.4 - - + -
1397A ILE* 3.7 39.9 - - + -
1398A VAL* 4.1 9.4 - - + -
1401A ARG* 3.6 17.9 - - - -
1426A LEU* 5.2 5.6 - - + -
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Residues in contact with ASN1384 (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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1309A PHE* 5.6 0.7 - - - -
1369A ALA 3.1 20.8 + - - +
1370A THR* 3.3 24.1 + - - +
1382A PRO* 3.2 18.2 - - - +
1383A PHE* 1.3 77.0 - - - +
1385A ALA* 1.3 61.6 + - - +
1386A ILE 3.1 2.4 - - - +
1389A LEU 3.2 23.1 - - - +
1391A THR* 4.1 18.1 + - - +
1394A ALA* 3.9 13.2 - - + +
10P G 5.1 2.3 + - - -
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Residues in contact with ALA1385 (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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1309A PHE* 4.1 33.4 - - + +
1311A LEU* 3.6 32.0 - - + +
1372A PHE* 4.4 3.8 - - + -
1381A PRO* 4.6 1.6 - - + -
1382A PRO* 3.1 30.8 + - + +
1383A PHE 2.9 1.0 + - - -
1384A ASN* 1.3 80.8 + - - +
1386A ILE* 1.3 63.7 + - - +
1387A PRO* 3.4 4.2 - - - +
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Residues in contact with ILE1386 (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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1311A LEU* 4.3 1.1 - - - -
1362A ILE* 3.6 26.2 - - + -
1383A PHE* 2.9 16.7 + - + +
1384A ASN 3.8 1.0 - - - +
1385A ALA* 1.3 77.2 - - - +
1387A PRO* 1.3 89.6 - - + +
1388A GLY 3.2 0.3 + - - -
1389A LEU* 2.9 40.9 + - + +
1422A LEU* 4.2 12.3 - - + +
1425A TYR* 3.6 36.6 - - + +
1426A LEU* 3.7 31.0 - - + -
10P G 4.1 1.6 + - - -
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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