Contacts of the helix formed by residues 1413 - 1420 (chain E) 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 PRO1413 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1325E TYR 3.3 13.2 - - - +
1326E GLU* 4.8 2.7 - - - -
1327E GLY* 3.5 14.6 - - - +
1329E LEU 4.6 10.1 - - - +
1331E PRO* 5.9 6.5 - - + -
1334E ILE* 4.7 6.7 - - + -
1411E LYS 3.8 5.2 - - - +
1412E LEU* 1.3 88.8 - - + +
1414E LEU* 1.3 54.6 + - - +
1415E HIS* 3.1 3.6 - - + +
1416E THR* 2.4 55.7 + - + +
1417E LEU* 2.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1414 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323E GLU 3.7 13.7 - - - +
1324E SER* 3.3 26.2 - - - +
1325E TYR* 3.1 21.3 + - + +
1392E PHE 4.7 3.6 - - - +
1393E ARG* 3.6 55.2 - - + +
1412E LEU 3.3 1.2 + - - +
1413E PRO* 1.3 71.6 - - - +
1415E HIS* 1.3 56.8 + - - +
1417E LEU* 3.1 14.7 - - + +
1418E ARG* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1415 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513E ALA* 4.1 31.6 + - + +
516E ASN* 5.1 16.9 + - + +
1325E TYR* 4.7 10.8 + - + +
1413E PRO* 3.1 3.3 - - + +
1414E LEU* 1.3 76.1 - - - +
1416E THR* 1.3 62.6 + - + +
1418E ARG* 3.4 0.5 + - - -
1419E SER* 2.2 53.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1416 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331E PRO* 6.1 4.9 - - + -
1334E ILE* 5.4 4.0 - - + +
1412E LEU* 4.3 6.3 - - - +
1413E PRO* 2.4 58.3 + - + +
1415E HIS* 1.3 81.7 - - + +
1417E LEU* 1.3 64.7 + - - +
1419E SER* 3.4 7.6 + - - -
1420E ARG* 3.3 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1417 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391E PHE 3.8 4.0 - - - +
1392E PHE* 3.6 37.2 - - + -
1393E ARG* 3.7 32.8 - - + -
1409E ILE* 3.8 19.7 - - + -
1412E LEU* 4.4 24.0 - - + -
1413E PRO 2.5 16.2 + - - +
1414E LEU* 3.1 23.3 - - + +
1415E HIS 3.1 0.2 - - - -
1416E THR* 1.3 77.6 + - - +
1418E ARG* 1.3 68.7 + - + +
1419E SER 3.4 0.2 + - - -
1420E ARG* 3.6 1.2 + - - +
1421E LEU* 3.3 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1418 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510E LYS* 2.6 51.6 + - - +
511E LEU* 3.1 25.5 - - - +
512E TYR 4.5 1.2 - - - +
513E ALA* 4.5 9.4 - - + -
1392E PHE* 2.5 51.9 + - + +
1393E ARG* 3.7 3.8 + - - +
1394E MET* 3.1 43.1 - - - +
1414E LEU* 2.9 28.3 + - - +
1417E LEU* 1.3 86.6 - - + +
1419E SER* 1.3 63.3 + - - +
1420E ARG 3.3 0.6 + - - -
1421E LEU 3.6 6.7 - - - +
1497E ARG* 3.5 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1419 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512E TYR 5.2 1.3 - - - -
513E ALA* 3.9 8.8 - - - +
1415E HIS* 2.2 49.0 + - - -
1416E THR* 3.7 7.4 - - - -
1417E LEU 3.2 0.4 - - - -
1418E ARG* 1.3 80.6 - - - +
1420E ARG* 1.3 70.5 + - - +
1421E LEU 3.7 1.4 + - - +
1497E ARG* 4.1 14.7 + - - +
1499E THR* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1420 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1334E ILE* 4.5 20.2 - - - +
1335E PRO 5.1 2.2 + - - -
1336E LYS* 4.6 20.5 + - - +
1338E TRP* 5.3 5.8 - - + +
1339E PRO* 3.9 32.2 - - + +
1416E THR* 3.3 39.5 + - - +
1417E LEU 3.6 0.2 + - - -
1418E ARG 3.3 0.4 - - - -
1419E SER* 1.3 88.7 - - - +
1421E LEU* 1.3 72.8 + - + +
1499E THR* 3.8 17.5 - - - +
1501E ILE* 4.7 2.3 - - - +
----------------------------------------------------------
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