Contacts of the helix formed by residues 1394 - 1406 (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 HIS1394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339C VAL* 6.4 1.6 - - + -
1343C GLU* 4.9 15.3 + - - -
1390C GLN* 2.9 34.1 + - - +
1391C VAL* 2.7 18.4 + - - +
1393C ALA* 1.3 75.3 - - - +
1395C LEU* 1.3 66.0 + - - +
1396C PRO* 3.3 0.4 - - - -
1397C ASP* 2.4 60.8 + - + +
1398C VAL* 3.6 9.7 + - + +
1401C ASN* 5.3 2.8 + - - -
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Residues in contact with LEU1395 (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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1338C VAL* 6.2 1.1 - - + -
1339C VAL* 5.7 8.7 - - + -
1372C LEU* 4.9 11.7 - - + -
1375C THR* 3.4 26.9 - - - +
1378C GLU* 4.0 21.5 - - - +
1391C VAL 3.2 5.6 + - - -
1392C MET* 2.9 54.6 + - + +
1394C HIS* 1.3 74.7 - - - +
1396C PRO* 1.3 67.7 - - + +
1398C VAL* 3.0 37.1 + - + +
1399C CYS* 3.8 3.2 + - - -
1457C GLN* 4.1 6.1 + - - +
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Residues in contact with PRO1396 (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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1392C MET 3.3 8.5 - - - +
1393C ALA* 3.1 17.7 - - - +
1394C HIS 3.4 0.9 - - - -
1395C LEU* 1.3 92.0 - - + +
1397C ASP* 1.3 64.6 + - - +
1398C VAL 2.8 2.1 + - - -
1399C CYS* 3.0 14.2 + - - +
1400C VAL* 3.6 11.1 + - - +
1453C SER* 5.8 1.8 - - - -
1456C LYS* 3.9 22.7 - - - +
1457C GLN* 3.2 19.5 + - + +
1460C ARG* 3.6 33.0 - - - +
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Residues in contact with ASP1397 (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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1390C GLN* 5.0 0.5 - - - +
1393C ALA 4.2 3.3 - - - +
1394C HIS* 2.4 70.7 + - + +
1396C PRO* 1.3 75.0 - - - +
1398C VAL* 1.3 60.4 + - - +
1400C VAL* 4.6 2.6 - - - +
1401C ASN* 2.6 41.0 + - - +
1460C ARG* 4.7 6.7 + - - +
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Residues in contact with VAL1398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338C VAL* 5.9 0.9 - - + -
1339C VAL* 4.9 22.9 - - + +
1342C MET* 3.8 34.3 - - + -
1343C GLU* 5.2 5.6 - - - +
1346C THR* 5.6 0.9 - - - +
1372C LEU* 4.8 7.0 - - + -
1394C HIS* 4.2 12.3 - - + +
1395C LEU* 3.2 27.6 - - + +
1396C PRO 2.8 0.8 + - - -
1397C ASP* 1.3 75.0 - - - +
1399C CYS* 1.3 56.9 + - - +
1401C ASN* 2.9 6.3 + - - +
1402C LEU* 2.3 49.0 + - + +
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Residues in contact with CYS1399 (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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1372C LEU* 3.4 47.8 - - + -
1375C THR* 5.9 2.5 - - - -
1395C LEU* 4.4 6.7 - - - -
1396C PRO 3.0 5.6 + - - +
1398C VAL* 1.3 74.1 - - - +
1400C VAL* 1.3 55.4 + - - +
1402C LEU* 4.0 0.9 - - - -
1403C MET* 2.2 48.7 + - + +
1457C GLN* 2.9 49.4 - - + +
1461C ALA* 6.3 0.2 - - + -
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Residues in contact with VAL1400 (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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1396C PRO 3.6 7.2 + - - +
1397C ASP* 4.6 2.5 - - - +
1398C VAL 3.4 0.2 - - - -
1399C CYS* 1.3 73.0 - - - +
1401C ASN* 1.3 71.3 + - - +
1404C LYS* 2.7 56.4 + - - +
1457C GLN* 3.2 36.1 - - + +
1460C ARG* 3.4 39.3 - - + +
1461C ALA* 4.1 8.9 - - - +
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Residues in contact with ASN1401 (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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1346C THR* 3.2 15.5 - - + +
1350C ASN* 5.7 6.0 + - - +
1394C HIS* 5.3 2.8 + - - -
1397C ASP* 2.6 36.2 + - - +
1398C VAL* 2.9 5.4 + - - +
1400C VAL* 1.3 79.7 - - - +
1402C LEU* 1.3 65.9 + - - +
1404C LYS* 5.3 1.6 - - - +
1405C ALA* 3.0 25.9 + - - +
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Residues in contact with LEU1402 (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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1342C MET* 3.7 35.2 - - + -
1345C THR* 4.2 12.1 - - + -
1346C THR* 3.2 25.0 + - - +
1349C LEU* 3.7 18.5 - - + +
1368C LEU* 5.9 3.4 - - + -
1369C MET* 4.7 6.1 - - + -
1372C LEU* 3.5 28.9 - - + -
1398C VAL* 2.3 37.0 + - + +
1399C CYS 3.2 2.0 - - - +
1401C ASN* 1.3 65.7 - - - +
1403C MET* 1.3 54.9 + - - +
1405C ALA* 2.9 5.2 + - - +
1406C LEU* 2.5 50.6 + - + +
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Residues in contact with MET1403 (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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1369C MET* 3.9 6.3 - - - +
1372C LEU* 3.6 24.0 - - + -
1399C CYS* 2.2 48.7 + - + +
1400C VAL* 4.0 3.6 - - - +
1402C LEU* 1.3 69.3 - - - +
1404C LYS* 1.3 52.1 + - - +
1406C LEU* 3.0 26.2 - - + +
1407C LYS* 2.7 31.6 + - - +
1415C LEU* 3.0 41.8 - - + +
1418C HIS* 3.5 29.2 - - + +
1419C LEU* 5.8 1.8 - - + -
1461C ALA* 4.8 11.9 - - + -
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Residues in contact with LYS1404 (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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1400C VAL* 2.7 34.7 + - - +
1401C ASN* 4.7 1.3 - - - +
1403C MET* 1.3 70.0 - - - +
1405C ALA* 1.3 56.5 + - - +
1406C LEU 3.0 4.3 - - - -
1407C LYS* 2.8 52.0 + - + +
1408C MET* 3.7 9.6 - - - +
1460C ARG* 2.3 33.0 + - - +
1461C ALA* 3.7 16.8 - - + +
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Residues in contact with ALA1405 (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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1346C THR* 3.6 9.4 - - + -
1349C LEU* 3.3 38.2 - - + +
1350C ASN* 3.6 22.4 - - + +
1401C ASN 3.0 20.9 + - - +
1402C LEU 2.9 4.1 + - - +
1404C LYS* 1.3 76.3 - - - +
1406C LEU* 1.3 55.4 + - - +
1407C LYS 3.7 1.8 - - - +
1408C MET* 4.9 4.2 - - - +
1410C PRO* 3.1 21.1 - - - +
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Residues in contact with LEU1406 (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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1349C LEU* 3.6 30.1 - - + -
1368C LEU* 5.7 7.0 - - + -
1369C MET* 3.7 8.5 - - + -
1402C LEU* 2.5 30.2 + - + +
1403C MET* 3.0 44.6 - - + +
1404C LYS 3.0 0.2 - - - -
1405C ALA* 1.3 71.7 - - - +
1407C LYS* 1.3 58.5 - - - +
1410C PRO* 2.7 34.8 - - + +
1411C TYR 4.3 0.7 - - - +
1414C ILE* 3.5 33.4 - - + -
1415C LEU* 3.5 13.6 - - + +
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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