Contacts of the helix formed by residues 1376 - 1382 (chain C) in PDB entry 5Y3R
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 LEU1376 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1373C VAL 4.8 5.2 - - - +
1374C GLN* 3.2 22.1 - - + +
1375C THR* 1.3 80.1 - - + +
1377C CYS* 1.3 101.8 + - - +
1378C GLU 3.1 1.1 - - - -
1379C PRO* 3.2 11.8 - - - +
1380C ALA* 3.9 8.8 + - - +
1426C GLN* 4.9 13.7 - - - +
1447C ARG* 5.1 24.7 - - + +
1450C ALA* 5.2 8.5 - - + -
1451C VAL* 6.4 2.0 - - + -
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Residues in contact with CYS1377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306C ILE* 6.2 2.7 - - + -
1374C GLN* 2.8 45.8 - - - +
1376C LEU* 1.3 93.4 - - - +
1378C GLU* 1.3 52.3 + - - +
1380C ALA* 3.0 9.2 + - - -
1381C SER* 2.8 45.9 + - - +
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Residues in contact with GLU1378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335C CYS* 5.4 0.9 - - - -
1338C VAL* 4.1 17.2 - - - +
1371C VAL* 4.3 9.9 - - + +
1372C LEU* 4.7 7.9 - - - +
1374C GLN* 2.7 27.8 + - + +
1375C THR* 3.5 12.4 + - - -
1377C CYS* 1.3 76.8 - - - +
1379C PRO* 1.3 66.3 - - + +
1381C SER* 4.8 0.9 - - - -
1382C ILE* 2.7 64.8 + - + +
1383C GLY 4.1 0.7 - - - +
1392C MET* 4.3 11.7 - - + +
1395C LEU* 4.0 23.2 - - - +
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Residues in contact with PRO1379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375C THR* 3.0 30.1 - - - +
1376C LEU 3.2 9.6 - - - +
1378C GLU* 1.3 84.4 - - + +
1380C ALA* 1.3 57.2 + - - +
1381C SER* 2.9 11.2 + - - +
1382C ILE 3.0 10.9 - - - +
1384C PHE* 3.3 51.5 + - + +
1392C MET* 4.0 12.6 - - + -
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Residues in contact with ALA1380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376C LEU 3.9 7.6 + - - +
1377C CYS* 3.0 11.9 + - - +
1379C PRO* 1.3 79.5 - - - +
1381C SER* 1.3 60.3 + - - +
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Residues in contact with SER1381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306C ILE* 4.5 21.9 - - - +
1331C ASN* 3.6 16.2 + - - +
1377C CYS* 2.8 24.4 + - - +
1378C GLU* 4.3 1.3 - - - -
1379C PRO 2.9 2.2 + - - +
1380C ALA* 1.3 82.8 + - - +
1382C ILE* 1.3 67.1 + - - +
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Residues in contact with ILE1382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306C ILE* 3.5 35.0 - - + -
1330C TYR* 6.5 0.4 - - + -
1331C ASN* 4.1 8.5 - - - +
1334C LYS* 3.5 29.2 - - + +
1335C CYS* 3.4 31.6 - - - +
1338C VAL* 4.4 6.3 - - + -
1371C VAL* 5.7 4.5 - - + -
1378C GLU* 2.7 53.3 + - + +
1379C PRO 3.0 11.3 - - - +
1381C SER* 1.3 82.2 - - - +
1383C GLY* 1.3 69.0 + - - +
1384C PHE 3.2 0.3 + - - -
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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