Contacts of the helix formed by residues 1465 - 1480 (chain C) in PDB entry 5O9Z
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 PRO1465 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463C ASN* 3.9 2.5 - - - +
1464C GLY* 1.3 88.3 - - - +
1466C VAL* 1.3 56.6 + - - +
1468C GLU* 4.3 7.9 - - + -
1469C VAL* 2.9 32.6 + - - +
1727C HIS* 3.3 35.4 - - + +
1728C LEU* 4.6 8.5 - - + -
1730C HIS* 5.1 2.2 - - + -
1731C CYS* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429C PRO* 3.7 32.2 - - + +
1430C GLU* 4.8 2.0 - - - +
1433C ASP* 5.4 8.9 - - + +
1463C ASN* 3.6 17.2 + - + +
1464C GLY 3.0 1.4 + - - -
1465C PRO* 1.3 79.1 - - - +
1467C LEU* 1.3 58.1 + - - +
1469C VAL* 3.8 3.0 - - - +
1470C ILE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429C PRO* 4.0 19.0 - - + +
1459C ILE* 3.9 27.6 - - + -
1463C ASN 3.6 6.8 + - - +
1464C GLY 3.1 4.0 + - - +
1466C VAL* 1.3 77.5 - - - +
1468C GLU* 1.3 60.9 + - - +
1470C ILE* 3.8 4.1 - - - +
1471C CYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459C ILE* 5.5 1.5 - - + +
1464C GLY 2.9 16.4 + - - +
1465C PRO* 4.3 7.0 - - + +
1467C LEU* 1.3 76.0 - - - +
1469C VAL* 1.3 60.1 + - - +
1471C CYS* 3.8 5.7 - - - +
1472C SER* 2.9 30.1 + - - -
1727C HIS 6.1 1.3 - - - +
1728C LEU* 4.8 16.8 - - + +
1758C THR* 5.3 2.2 - - - -
1759C PHE* 5.6 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433C ASP* 6.3 3.8 - - + -
1465C PRO 2.9 22.4 + - - +
1466C VAL* 4.0 3.4 - - - +
1468C GLU* 1.3 75.7 - - - +
1470C ILE* 1.3 59.7 + - - +
1472C SER* 4.1 5.0 - - - -
1473C ARG* 2.9 30.8 + - - +
1735C HIS* 5.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429C PRO* 5.3 4.0 - - + +
1432C TRP* 4.4 29.4 - - + +
1433C ASP* 5.6 1.3 - - - +
1436C SER* 5.5 3.1 - - - -
1466C VAL 2.9 19.6 + - - +
1467C LEU* 3.8 6.5 - - - +
1468C GLU 3.3 0.2 - - - -
1469C VAL* 1.3 77.3 - - - +
1471C CYS* 1.3 56.5 + - - +
1473C ARG* 3.9 4.3 - - - +
1474C MET* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467C LEU 2.9 17.5 + - - +
1468C GLU* 3.9 5.8 - - - +
1470C ILE* 1.3 76.0 - - - +
1472C SER* 1.3 59.3 + - - +
1474C MET* 3.4 5.4 + - - +
1475C ARG* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1468C GLU 2.9 17.7 + - - -
1469C VAL* 4.1 4.9 - - - -
1471C CYS* 1.3 78.1 - - - +
1473C ARG* 1.3 58.4 + - - +
1475C ARG* 3.3 5.8 + - - +
1476C TYR* 2.9 30.9 + - - +
1754C TYR 5.1 3.6 - - - -
1757C TRP* 4.5 8.2 - - - +
1758C THR* 3.7 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436C SER* 4.6 20.9 - - - +
1469C VAL 2.9 20.9 + - - +
1470C ILE* 4.1 4.5 - - - +
1472C SER* 1.3 77.2 - - - +
1474C MET* 1.3 58.0 + - - +
1476C TYR* 4.2 4.2 - - - +
1477C ILE* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1470C ILE 2.9 21.4 + - - +
1471C CYS* 3.8 6.3 - - - +
1473C ARG* 1.3 75.2 - - - +
1475C ARG* 1.3 58.6 + - - +
1477C ILE* 4.2 4.0 - - - +
1478C SER* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471C CYS 2.9 18.1 + - - +
1472C SER* 3.8 6.1 - - - +
1474C MET* 1.3 76.7 - - - +
1476C TYR* 1.3 60.9 + - - +
1478C SER* 3.8 5.2 - - - -
1479C SER* 2.9 29.8 + - - -
1757C TRP* 4.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472C SER 2.9 17.8 + - - +
1473C ARG* 4.2 4.9 - - - +
1475C ARG* 1.3 75.6 - - - +
1477C ILE* 1.3 60.2 + - - +
1479C SER* 3.4 5.2 + - - -
1480C GLN* 2.9 30.3 + - - +
1754C TYR* 6.4 2.0 - - + -
1757C TRP* 5.2 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1477 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439C TRP* 5.7 9.2 - - + -
1445C VAL* 6.1 3.6 - - + +
1446C GLN* 6.0 5.6 - - + +
1473C ARG 2.9 21.5 + - - +
1474C MET* 4.2 4.0 - - - +
1476C TYR* 1.3 75.9 - - - +
1478C SER* 1.3 58.7 + - - +
1480C GLN* 3.9 5.8 - - - +
1481C ILE* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474C MET 2.9 20.6 + - - -
1475C ARG* 3.8 5.6 - - - -
1476C TYR 3.3 0.2 - - - -
1477C ILE* 1.3 78.7 - - - +
1479C SER* 1.3 60.8 + - - +
1481C ILE* 3.6 10.4 + - - +
1482C GLU 3.6 5.2 + - - -
1483C ARG 3.4 20.7 + - - +
1485C ILE* 3.9 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475C ARG 2.9 18.7 + - - -
1476C TYR* 3.9 5.6 - - - -
1478C SER* 1.3 75.0 - - - +
1480C GLN* 1.3 62.1 + - - +
1482C GLU* 3.4 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476C TYR 2.9 18.2 + - - +
1477C ILE* 4.0 6.7 - - - +
1478C SER 3.4 0.2 - - - -
1479C SER* 1.3 77.2 - - - +
1481C ILE* 1.3 60.6 + - - +
1482C GLU* 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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