Contacts of the helix formed by residues 1483 - 1499 (chain D) in PDB entry 5TWV
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 SER1483 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481D ASN 4.1 0.6 + - - -
1482D PHE* 1.3 78.0 - - - +
1484D GLN* 1.3 57.1 + - - +
1485D GLY* 3.3 5.0 + - - -
1486D GLN* 2.9 28.1 + - - +
1487D ARG* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427D GLN 4.5 8.7 - - - +
1483D SER* 1.3 73.2 - - - +
1485D GLY* 1.3 57.9 + - - +
1487D ARG* 3.5 6.5 + - - +
1488D GLN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483D SER* 3.2 5.6 + - - -
1484D GLN* 1.3 77.8 - - - +
1486D GLN* 1.3 59.1 + - - +
1488D GLN* 3.1 8.6 + - - +
1489D LEU* 2.9 27.9 + - - +
1512D ILE* 5.8 9.2 - - - +
1516D THR* 6.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463D VAL* 5.0 17.3 - - + -
1482D PHE* 4.2 9.6 - - + -
1483D SER* 2.9 28.0 + - - +
1485D GLY* 1.3 76.5 - - - +
1487D ARG* 1.3 57.1 + - - +
1489D LEU* 3.4 7.9 + - - +
1490D PHE* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429D PRO* 3.3 33.8 - - + +
1479D GLY 5.3 5.4 - - - +
1482D PHE* 4.4 8.6 - - + +
1483D SER 2.9 19.0 + - - +
1484D GLN* 3.6 7.4 - - - +
1486D GLN* 1.3 76.8 - - - +
1488D GLN* 1.3 57.6 + - - +
1490D PHE* 3.3 7.8 + - - +
1491D CYS 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425D ILE* 5.3 0.9 - - - +
1426D LEU 4.9 4.9 - - - +
1427D GLN* 4.6 13.7 - - - +
1429D PRO* 4.4 1.3 - - - +
1484D GLN 2.9 15.5 + - - +
1485D GLY* 3.1 12.8 + - - +
1487D ARG* 1.3 73.3 - - - +
1489D LEU* 1.3 60.3 + - - +
1491D CYS* 3.4 8.0 + - - +
1492D LEU* 2.9 27.7 + - - +
1520D LEU* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1458D ALA 4.5 5.7 - - - +
1459D GLN 5.0 3.6 - - - +
1460D LEU* 4.3 22.3 - - + +
1485D GLY 2.9 13.1 + - - +
1486D GLN* 3.6 10.8 - - - +
1488D GLN* 1.3 71.8 - - - +
1490D PHE* 1.3 61.1 + - - +
1492D LEU* 3.2 8.4 + - - +
1493D ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1490 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429D PRO* 6.0 0.2 - - + -
1440D LEU* 5.9 2.1 - - + +
1460D LEU* 4.9 3.7 - - - +
1486D GLN 2.9 18.1 + - - +
1487D ARG* 3.5 10.1 - - - +
1488D GLN 3.3 0.2 - - - -
1489D LEU* 1.3 75.0 - - - +
1491D CYS* 1.3 58.4 + - - +
1493D ALA* 3.4 7.2 + - - +
1494D ARG* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424D ILE 4.7 3.2 - - - +
1425D ILE* 3.5 29.0 - - + +
1426D LEU 4.4 6.3 - - - +
1429D PRO* 3.9 22.0 - - + +
1487D ARG 2.9 17.6 + - - +
1488D GLN 3.6 5.6 - - - +
1490D PHE* 1.3 76.5 - - - +
1492D LEU* 1.3 57.7 + - - +
1494D ARG* 3.3 9.6 + - - +
1495D ALA 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425D ILE* 4.1 9.3 - - + +
1458D ALA* 4.6 7.0 - - + +
1488D GLN 2.9 14.9 + - - +
1489D LEU* 3.5 12.6 - - - +
1491D CYS* 1.3 76.6 - - - +
1493D ALA* 1.3 56.3 + - - +
1495D ALA* 3.2 6.6 + - - +
1496D PHE* 2.9 26.9 + - - +
1523D VAL* 5.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1493 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451D LEU 5.7 0.7 - - - +
1454D ALA* 4.6 3.0 - - + +
1455D LEU* 4.2 22.7 - - + +
1458D ALA* 3.8 23.6 - - + +
1460D LEU* 4.6 3.8 - - + -
1489D LEU 2.9 17.1 + - - +
1490D PHE* 3.7 6.7 - - - +
1492D LEU* 1.3 74.8 - - - +
1494D ARG* 1.3 53.6 + - - +
1496D PHE* 3.1 3.5 + - - +
1497D VAL* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423D SER* 4.8 0.7 - - - -
1424D ILE 5.8 2.5 - - - +
1439D ASN 6.0 0.2 - - - +
1440D LEU* 5.6 12.7 - - + +
1442D PRO* 5.1 18.8 - - + +
1490D PHE 2.9 18.3 + - - +
1491D CYS* 3.4 10.8 - - - +
1493D ALA* 1.3 75.7 - - - +
1495D ALA* 1.3 59.6 + - - +
1497D VAL* 3.8 6.9 + - - +
1498D ARG* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423D SER* 3.7 26.0 - - - -
1424D ILE 5.1 2.3 + - - +
1425D ILE* 4.5 11.4 - - + +
1491D CYS 2.9 13.2 + - - +
1492D LEU* 3.4 11.7 - - - +
1494D ARG* 1.3 73.9 - - - +
1496D PHE* 1.3 63.3 + - - +
1498D ARG* 3.2 11.6 + - - +
1499D LYS 3.4 8.1 + - - -
1500D THR* 4.0 9.7 + - - -
1503D PHE* 6.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1454D ALA* 3.7 30.5 - - + -
1457D ILE* 3.6 29.2 - - + -
1458D ALA* 4.3 10.5 - - + -
1492D LEU 2.9 14.5 + - - +
1493D ALA* 3.1 11.6 + - - +
1495D ALA* 1.3 75.4 - - - +
1497D VAL* 1.3 61.9 + - - +
1499D LYS* 3.2 16.4 + - - +
1531D ARG* 4.2 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1497 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1440D LEU 5.5 6.1 - - - +
1443D GLU* 5.2 10.0 - - + +
1451D LEU* 5.4 8.3 - - + -
1454D ALA* 4.4 17.3 - - + -
1493D ALA 2.7 20.8 + - - +
1494D ARG* 4.1 7.9 - - - +
1496D PHE* 1.3 73.9 - - - +
1498D ARG* 1.3 60.3 + - - +
1499D LYS* 3.5 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1498 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1420D SER 5.7 5.6 - - - +
1421D ARG 5.6 2.2 - - - +
1422D LEU 5.9 0.9 - - - -
1423D SER* 4.1 16.8 - - - -
1443D GLU* 5.3 11.9 - - + +
1494D ARG 3.4 14.6 + - - +
1495D ALA 3.2 6.3 + - - +
1496D PHE 3.2 0.8 - - - -
1497D VAL* 1.3 76.4 - - - +
1499D LYS* 1.3 70.3 + - - +
1500D THR* 3.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1499 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495D ALA 3.4 2.0 + - - -
1496D PHE* 3.2 16.3 + - - +
1497D VAL 3.2 3.8 - - - +
1498D ARG* 1.3 79.6 - - - +
1500D THR* 1.3 67.0 + - - +
1501D SER 3.8 0.5 + - - -
1531D ARG* 4.5 12.3 - - - +
----------------------------------------------------------
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