Contacts of the strand formed by residues 1548 - 1551 (chain H) in PDB entry 6C3P
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 VAL1548 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375H GLY 3.2 3.6 - - - -
1377H CYS* 4.2 5.6 - - - -
1542H ILE* 4.0 34.5 - - + +
1545H ALA 5.1 0.2 - - - +
1547H LEU* 1.3 75.4 - - - +
1549H ILE* 1.3 64.3 + - - +
1550H VAL* 4.1 19.6 + - + -
1559H PHE* 3.0 6.1 - - - +
1560H ASP 2.6 37.4 + - - +
1562H PRO* 3.6 36.6 - - + -
1565H LEU* 3.9 12.2 - - + +
1573H PHE* 4.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1549 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366H ALA* 5.4 5.8 - - + -
1368H ILE* 4.9 12.1 - - + -
1374H ILE* 3.8 23.3 - - + -
1375H GLY 2.4 17.7 + - - +
1376H ILE* 3.2 36.5 - - + +
1377H CYS* 2.8 33.1 + - - +
1387H PHE* 6.1 0.7 - - + -
1547H LEU* 5.1 4.7 - - + -
1548H VAL* 1.3 79.0 - - - +
1550H VAL* 1.3 62.4 + - - +
1551H LEU* 4.7 3.4 - - + -
1556H ILE* 3.7 34.5 - - + -
1559H PHE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1550 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377H CYS* 3.8 15.5 - - - +
1378H GLY* 5.2 0.7 - - - -
1548H VAL* 4.1 11.2 + - + +
1549H ILE* 1.3 77.9 - - - +
1551H LEU* 1.3 69.7 + - - +
1552H LYS* 4.9 2.9 - - + +
1556H ILE* 3.0 9.8 - - - +
1557H LEU* 2.8 50.8 + - + +
1558H GLU 5.4 0.2 - - - +
1559H PHE* 4.8 0.8 - - - +
1565H LEU* 5.0 4.9 - - + -
1571H SER* 4.4 10.5 - - - +
1572H VAL* 5.5 4.5 - - + +
1573H PHE* 4.0 27.6 - - + +
1576H PHE* 4.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1551 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361H LEU* 4.4 13.0 - - + -
1364H VAL* 5.5 1.6 - - + -
1376H ILE* 4.1 17.7 - - + -
1377H CYS 3.4 8.0 + - - +
1378H GLY* 4.1 7.8 - - - -
1379H ARG* 3.9 6.6 + - - -
1382H SER* 2.9 32.5 + - - +
1383H GLY 4.2 6.1 - - - +
1384H LYS* 3.7 38.1 - - + +
1387H PHE* 5.0 9.0 - - + -
1549H ILE* 4.7 2.0 - - + -
1550H VAL* 1.3 77.5 - - - +
1552H LYS* 1.3 60.0 + - - +
1555H ALA* 3.3 27.8 - - - +
1556H ILE* 3.6 19.3 - - + -
----------------------------------------------------------
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