Contacts of the helix formed by residues 1493 - 1508 (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 PRO1493 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636C GLU* 4.3 1.3 - - - +
1438C GLY* 4.7 15.0 - - - +
1439C PRO* 5.1 4.3 - - + -
1489C LYS* 4.1 22.9 - - + +
1491C ILE 4.6 0.2 - - - +
1492C ALA* 1.3 84.8 - - + +
1494C GLY* 1.3 53.2 - - - +
1495C ASP* 3.4 19.3 - - + +
1496C GLU* 2.6 28.1 + - + +
1497C ARG* 2.2 38.2 + - - +
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Residues in contact with GLY1494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C PHE* 6.5 0.2 - - - -
636C GLU* 3.1 26.1 + - - -
640C GLU* 4.7 2.7 - - - +
1492C ALA 3.6 1.8 + - - -
1493C PRO* 1.3 70.4 - - - +
1495C ASP* 1.3 61.4 + - - +
1497C ARG* 3.3 17.3 - - - +
1498C GLN* 2.9 27.9 + - - +
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Residues in contact with ASP1495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636C GLU* 2.4 40.6 + - - +
640C GLU* 4.4 13.2 - - - +
1439C PRO* 5.7 5.0 - - - +
1441C ALA* 4.8 5.3 + - + +
1445C ARG* 3.1 32.9 + - - +
1493C PRO* 3.4 14.9 - - + +
1494C GLY* 1.3 67.5 - - - +
1496C GLU* 1.3 58.9 + - - +
1498C GLN* 2.8 23.5 + - - +
1499C CYS* 2.9 12.0 + - - -
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Residues in contact with GLU1496 (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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1434C VAL* 3.9 20.3 - - - +
1435C ASN* 5.0 6.2 - - - +
1438C GLY* 4.7 6.5 + - - +
1441C ALA* 4.3 6.1 - - - +
1486C LEU* 5.0 7.2 - - + -
1492C ALA* 3.6 16.6 - - + -
1493C PRO* 2.6 32.3 + - + +
1495C ASP* 1.3 78.6 - - - +
1497C ARG* 1.3 57.7 + - - +
1499C CYS* 2.8 48.3 + - - +
1500C LEU* 3.0 34.4 + - + +
1503C LEU* 5.1 5.5 - - - +
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Residues in contact with ARG1497 (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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1486C LEU* 5.0 4.9 - - - +
1490C GLY 5.2 0.2 + - - -
1491C ILE* 3.5 21.6 - - - +
1492C ALA* 3.1 39.1 + - - +
1493C PRO 2.2 35.9 + - - +
1494C GLY* 3.3 19.3 - - - +
1496C GLU* 1.3 68.2 - - - +
1498C GLN* 1.3 67.1 + - - +
1500C LEU* 3.9 19.7 + - - +
1501C PRO* 3.3 17.5 - - - +
1557C GLU* 4.7 0.6 + - - -
1565C GLU* 2.6 41.7 + - - +
1566C THR* 4.8 6.5 - - - +
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Residues in contact with GLN1498 (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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640C GLU* 4.2 19.3 - - - +
1445C ARG* 4.9 9.0 - - + +
1494C GLY 2.9 14.0 + - - +
1495C ASP* 2.8 10.6 + - - +
1497C ARG* 1.3 84.3 - - - +
1499C CYS* 1.3 65.5 + - - +
1500C LEU 3.3 0.9 - - - -
1501C PRO* 3.2 23.6 - - - +
1502C SER* 4.6 5.0 + - - -
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Residues in contact with CYS1499 (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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1434C VAL* 3.6 18.6 - - + -
1441C ALA* 3.9 5.8 - - - -
1445C ARG* 3.3 38.4 - - + -
1448C LEU* 4.3 4.3 - - + +
1495C ASP 2.9 4.9 + - - -
1496C GLU* 2.8 58.3 + - - +
1498C GLN* 1.3 72.9 - - - +
1500C LEU* 1.3 61.8 + - + +
1502C SER* 3.2 23.5 + - - -
1503C LEU* 3.6 9.9 + - + +
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Residues in contact with LEU1500 (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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1483C LEU* 5.2 14.4 - - + +
1486C LEU* 5.5 6.7 - - + -
1492C ALA* 5.4 3.4 - - + -
1496C GLU* 3.0 36.9 + - + +
1497C ARG* 4.2 23.1 - - - +
1499C CYS* 1.3 77.0 - - - +
1501C PRO* 1.4 70.1 - - + +
1502C SER 3.0 0.5 + - - -
1503C LEU* 3.1 10.1 + - + +
1504C ASP* 3.0 42.8 + - - +
1566C THR* 3.9 28.5 - - + -
1569C THR* 5.6 1.3 - - + -
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Residues in contact with PRO1501 (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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1497C ARG 3.3 16.2 - - - +
1498C GLN* 3.2 29.8 - - - +
1500C LEU* 1.4 89.2 - - + +
1502C SER* 1.3 51.1 + - - +
1505C LEU* 2.3 51.8 + - + +
1569C THR* 4.6 16.6 - - + -
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Residues in contact with SER1502 (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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1445C ARG* 4.8 0.3 + - - +
1448C LEU* 3.5 26.9 - - - +
1449C ALA* 3.6 14.6 + - - +
1452C VAL* 3.8 25.7 - - - +
1498C GLN 4.6 4.2 + - - -
1499C CYS* 3.2 13.0 + - - -
1500C LEU 3.0 0.4 + - - -
1501C PRO* 1.3 78.4 - - - +
1503C LEU* 1.3 63.7 + - - -
1505C LEU* 4.5 0.9 - - - -
1506C SER* 2.8 33.7 + - - -
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Residues in contact with LEU1503 (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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1431C LEU* 5.5 7.2 - - + +
1434C VAL* 3.8 26.0 - - + -
1435C ASN* 5.8 1.1 - - + +
1448C LEU* 3.6 29.8 - - + -
1452C VAL* 5.8 1.8 - - + -
1479C VAL* 3.2 26.5 - - + +
1482C GLU* 4.4 15.9 - - + +
1496C GLU* 5.1 6.7 - - - +
1499C CYS 4.0 12.3 - - - +
1500C LEU* 3.1 11.8 + - + +
1502C SER* 1.3 77.7 - - - +
1504C ASP* 1.3 52.4 + - - +
1506C SER* 5.5 0.9 - - - -
1507C CYS* 2.4 37.9 + - - +
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Residues in contact with ASP1504 (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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1479C VAL* 3.1 19.6 - - - +
1483C LEU* 3.7 31.1 - - - +
1500C LEU* 3.0 28.3 + - - +
1503C LEU* 1.3 77.5 - - - +
1505C LEU* 1.3 67.3 + - - +
1507C CYS* 3.0 14.6 + - - +
1508C LYS* 3.0 28.2 + - + +
1566C THR* 4.7 5.9 - - - -
1569C THR* 3.6 29.5 + - + +
1570C GLU* 5.3 2.2 - - - +
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Residues in contact with LEU1505 (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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1452C VAL* 4.7 14.8 - - + -
1501C PRO* 2.3 43.4 + - + +
1502C SER* 3.5 0.9 - - - +
1504C ASP* 1.3 79.9 - - - +
1506C SER* 1.3 59.1 + - - +
1508C LYS* 3.6 5.8 + - - +
1509C GLN* 2.7 47.5 + - - +
1569C THR* 5.2 9.1 - - + -
1572C LEU* 6.6 0.2 - - + -
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Residues in contact with SER1506 (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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1452C VAL* 3.1 39.6 - - - +
1455C CYS* 4.0 18.7 - - - +
1459C HIS* 5.3 0.5 - - - -
1468C LEU* 5.5 0.2 - - - +
1476C HIS* 3.1 16.1 - - - -
1502C SER 2.8 14.5 + - - -
1503C LEU* 5.4 0.7 - - - -
1505C LEU* 1.3 73.1 - - - +
1507C CYS* 1.3 67.0 + - - +
1508C LYS 3.2 0.2 + - - -
1509C GLN* 3.2 21.5 + - - +
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Residues in contact with CYS1507 (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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1476C HIS* 2.2 71.1 + - - +
1479C VAL* 3.4 17.9 - - + -
1480C GLY 5.0 1.1 - - - -
1503C LEU 2.4 30.5 + - - +
1504C ASP* 3.0 13.0 + - - +
1506C SER* 1.3 77.0 - - - +
1508C LYS* 1.3 72.7 + - - +
1510C LEU 4.2 1.0 + - - -
1511C ALA* 4.5 1.9 + - - +
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Residues in contact with LYS1508 (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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1504C ASP* 3.0 25.3 + - + +
1505C LEU 3.6 2.9 + - - +
1506C SER 3.2 0.2 - - - -
1507C CYS* 1.3 88.5 - - - +
1509C GLN* 1.3 60.0 + - - +
1510C LEU 3.0 11.3 + - - -
1511C ALA* 3.7 7.9 - - - +
1512C SER 5.3 5.2 - - - +
1513C GLY* 5.5 0.4 - - - -
1515C LEU* 6.3 1.6 - - - -
1516C GLU* 3.2 43.1 + - - +
1569C THR* 5.2 2.4 + - - +
1570C GLU* 3.4 23.8 - - - +
1573C LYS* 3.5 54.0 - - + +
1577C LEU* 5.0 3.5 - - - +
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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