Contacts of the helix formed by residues 1501 - 1515 (chain X) in PDB entry 2IWL
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 ALA1501 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432X TYR* 3.1 42.4 - - + +
1444X TYR* 5.2 2.5 - - - -
1498X ASP 3.1 15.0 + - - +
1499X VAL 2.7 9.0 + - - +
1500X ALA* 1.3 70.6 - - - +
1502X LYS* 1.3 57.7 + - - +
1503X ARG* 3.1 7.2 - - - +
1504X LYS* 3.4 21.7 + - - +
1505X ILE* 3.9 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1502 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499X VAL* 3.4 40.7 - - + +
1500X ALA* 3.0 4.9 - - - -
1501X ALA* 1.3 77.7 - - - +
1503X ARG* 1.3 59.5 + - - +
1504X LYS 3.1 0.9 - - - -
1505X ILE* 3.3 17.7 + - + +
1506X GLU* 2.8 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1503 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1444X TYR* 3.1 29.1 + - + +
1463X PHE* 3.6 54.3 - - + +
1487X ASN 4.9 6.3 + - - -
1500X ALA* 3.8 20.8 - - + +
1502X LYS* 1.3 79.7 - - - +
1504X LYS* 1.3 51.7 + - - +
1506X GLU* 4.2 12.1 + - - +
1507X LEU* 2.6 47.7 + - + +
2540X SO4 2.8 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1504 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429X VAL* 3.9 30.1 + - + +
1430X PHE 3.8 23.3 + - - -
1431X THR* 4.4 4.5 - - - +
1432X TYR* 4.0 31.4 - - + -
1444X TYR* 3.9 15.1 - - + -
1501X ALA 3.4 14.3 + - - +
1502X LYS 3.1 0.8 - - - -
1503X ARG* 1.3 78.0 - - - +
1505X ILE* 1.3 69.7 + - + +
1507X LEU* 4.0 0.2 - - - -
1508X ASN* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1505 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501X ALA 3.9 10.3 + - - +
1502X LYS* 3.3 20.6 + - + +
1504X LYS* 1.3 90.4 - - + +
1506X GLU* 1.3 61.3 + - + +
1508X ASN* 3.3 8.3 + - - +
1509X SER* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1506 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486X PRO* 3.4 38.3 - - + +
1502X LYS* 2.8 37.9 + - + +
1503X ARG* 4.0 11.1 - - - +
1505X ILE* 1.3 75.4 - - + +
1507X LEU* 1.3 64.2 + - - +
1509X SER* 3.3 7.1 + - - -
1510X TYR* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1507 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429X VAL* 3.8 13.9 - - + -
1444X TYR* 3.6 44.2 - - + -
1463X PHE* 4.0 27.8 - - + -
1466X PHE* 3.9 40.3 - - + -
1485X PHE* 4.4 10.1 - - + -
1486X PRO* 4.8 5.8 - - + -
1503X ARG* 2.6 30.3 + - - +
1506X GLU* 1.3 70.5 - - - +
1508X ASN* 1.3 60.6 + - - +
1510X TYR* 3.3 6.9 + - + +
1511X LEU* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1508 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428X SER* 3.1 19.2 - - - -
1429X VAL* 3.0 35.2 + - + +
1504X LYS* 3.0 22.1 + - + +
1505X ILE* 3.4 9.0 + - - +
1506X GLU 3.2 0.2 - - - -
1507X LEU* 1.3 76.9 - - - +
1509X SER* 1.3 65.0 + - - +
1511X LEU* 3.2 3.5 + - - +
1512X GLN* 3.0 39.6 + - - +
2541X SO4 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1509 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505X ILE* 3.0 18.1 + - - +
1506X GLU* 3.3 9.3 + - - -
1508X ASN* 1.3 73.6 + - - +
1510X TYR* 1.3 68.3 + - - +
1512X GLN* 3.2 8.7 + - - +
1513X SER* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1510 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466X PHE* 5.0 7.2 - + - -
1469X LEU* 4.8 8.5 - - + -
1470X HIS* 2.6 38.2 + + + +
1473X LEU* 4.1 12.1 - - - +
1482X LEU* 5.1 0.3 - - - +
1483X PRO* 3.5 34.7 - - + +
1484X GLY 3.1 23.6 - - - +
1485X PHE* 3.6 28.3 - + + -
1486X PRO* 4.8 5.2 - - + -
1506X GLU 3.0 11.7 + - - +
1507X LEU* 3.4 12.6 - - + +
1509X SER* 1.3 80.4 - - - +
1511X LEU* 1.3 70.0 + - + +
1513X SER* 3.3 5.3 + - - -
1514X LEU* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1511 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427X VAL* 4.4 11.2 - - + +
1428X SER* 4.4 7.2 - - - -
1429X VAL* 4.2 13.2 - - + -
1446X VAL* 4.0 25.4 - - + -
1466X PHE* 3.9 30.1 - - + -
1469X LEU* 5.5 1.1 - - + -
1507X LEU 2.8 21.1 + - - +
1508X ASN* 3.2 4.5 + - - +
1510X TYR* 1.3 83.4 - - + +
1512X GLN* 1.3 70.1 + - - +
1514X LEU* 3.2 16.1 + - + +
1515X MET* 3.1 26.4 + - - +
1530X PHE* 4.8 3.4 - - + -
1531X PHE* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1512 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427X VAL* 2.9 32.2 + - - +
1428X SER* 4.2 3.3 - - - -
1508X ASN* 3.0 36.2 + - - +
1509X SER* 3.5 11.0 - - - +
1511X LEU* 1.3 76.4 - - - +
1513X SER* 1.3 63.3 + - - +
1515X MET* 3.3 14.7 + - - +
1516X ASN* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1513 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483X PRO* 3.5 27.9 - - - +
1509X SER* 2.9 21.8 + - - -
1510X TYR 3.6 0.7 - - - -
1512X GLN* 1.3 69.4 - - - +
1514X LEU* 1.3 58.0 + - - +
1516X ASN* 2.6 33.5 + - - +
1517X ALA* 3.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1514 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1469X LEU* 4.2 18.8 - - + -
1473X LEU* 4.0 14.1 - - + -
1482X LEU* 5.0 0.2 - - + -
1483X PRO* 3.8 25.1 - - + +
1510X TYR* 2.9 26.9 + - + +
1511X LEU* 3.4 20.2 - - + +
1513X SER* 1.3 76.3 - - - +
1515X MET* 1.3 65.2 + - - +
1516X ASN 3.1 0.9 + - - -
1517X ALA* 3.2 16.7 + - + +
1521X VAL* 4.0 24.0 - - + -
1522X ALA* 3.5 11.3 - - - +
1527X VAL* 3.8 33.9 - - + -
1531X PHE* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1515 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1418X PHE* 5.8 0.4 - - + -
1424X ILE* 3.2 58.3 - - + +
1425X LYS 5.7 0.9 - - - -
1426X GLU* 6.4 0.2 - - - -
1427X VAL* 3.5 27.6 - - + -
1511X LEU* 3.1 15.2 + - - +
1512X GLN* 3.7 9.9 - - - +
1513X SER 3.1 0.6 - - - -
1514X LEU* 1.3 80.4 - - - +
1516X ASN* 1.3 63.2 + - - +
1517X ALA 3.4 3.0 + - - +
1522X ALA* 4.1 23.4 - - + +
1527X VAL* 5.4 2.5 - - - -
1531X PHE* 4.9 9.2 - - - -
----------------------------------------------------------
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