Contacts of the helix formed by residues 1197 - 1210 (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 GLN1197 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193D ASP 4.4 4.2 + - - +
1194D ASP 4.0 10.0 + - - +
1195D THR 3.3 2.4 - - - -
1196D THR* 1.3 79.1 - - - +
1198D LEU* 1.3 65.1 + - - +
1200D LEU* 3.2 23.0 + - - +
1201D VAL* 3.8 3.9 + - - +
1234D ASN* 4.2 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195D THR 4.4 4.1 + - - +
1197D GLN* 1.3 77.8 - - - +
1199D PRO* 1.4 67.7 - - + +
1201D VAL* 3.3 10.4 + - - +
1202D SER* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195D THR 4.2 6.3 - - - +
1196D THR 3.7 13.5 - - - +
1197D GLN 3.6 4.3 - - - -
1198D LEU* 1.4 91.6 - - + +
1200D LEU* 1.3 56.3 + - - +
1202D SER* 3.2 10.9 + - - -
1203D HIS* 3.0 34.1 + - - +
1230D TYR* 4.8 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196D THR 4.8 1.2 + - - +
1197D GLN 3.2 13.8 + - - +
1198D LEU 3.2 0.4 - - - -
1199D PRO* 1.3 79.1 - - - +
1201D VAL* 1.3 58.4 + - - +
1203D HIS* 3.3 17.9 + - - +
1204D PHE* 2.9 48.5 + - + -
1230D TYR* 5.2 5.4 - - + -
1231D THR* 6.1 0.4 - - - +
1234D ASN* 3.7 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D ALA* 5.8 5.6 - - + -
1197D GLN 3.8 3.9 + - - +
1198D LEU* 3.3 11.4 + - - +
1200D LEU* 1.3 75.8 - - - +
1202D SER* 1.3 60.0 + - - +
1204D PHE* 3.4 16.3 - - + +
1205D ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781D ASN* 4.8 17.9 - - - +
1198D LEU 3.0 13.5 + - - -
1199D PRO* 3.3 15.3 - - - -
1201D VAL* 1.3 77.0 - - - +
1203D HIS* 1.3 58.2 + - - +
1205D ALA* 3.2 8.5 + - - +
1206D GLU* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781D ASN* 6.2 0.2 - - - -
1199D PRO 3.0 29.9 + - - +
1200D LEU* 3.3 13.3 - - + -
1202D SER* 1.3 72.8 - - - +
1204D PHE* 1.3 88.4 + + - +
1206D GLU* 3.7 11.8 - - + -
1207D THR* 2.9 25.8 + - - -
1223D PHE* 3.2 30.5 - + + -
1227D LEU* 3.5 15.7 - - + -
1230D TYR* 3.2 51.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D GLN* 5.8 3.1 - - + -
396D TYR* 3.2 54.9 - + + +
418D CYS* 4.8 14.4 - - + +
422D ALA* 4.9 15.7 - - + -
1200D LEU* 2.9 33.9 + - + -
1201D VAL* 3.4 18.2 - - + +
1202D SER 3.1 0.2 - - - -
1203D HIS* 1.3 101.6 - + - +
1205D ALA* 1.3 59.7 + - - +
1207D THR* 3.1 5.5 + - - -
1208D VAL* 2.9 28.4 + - - +
1227D LEU* 3.6 12.3 - - + -
1231D THR* 6.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D CYS* 6.0 0.9 - - - -
825D GLU* 5.7 9.9 - - + -
1201D VAL 2.9 13.3 + - - +
1202D SER* 3.6 9.6 - - - +
1204D PHE* 1.3 73.9 - - - +
1206D GLU* 1.3 58.4 + - - +
1208D VAL* 3.3 6.5 + - - +
1209D GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780D LEU* 4.8 10.8 - - + +
781D ASN* 4.5 21.5 - - + +
1202D SER 3.0 15.6 + - - +
1203D HIS* 3.8 12.3 - - + +
1205D ALA* 1.3 76.3 - - - +
1207D THR* 1.3 60.3 + - - +
1209D GLU* 4.0 5.6 - - - +
1210D GLY* 3.1 21.8 + - - -
1223D PHE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D TYR* 4.8 13.0 - - - -
1203D HIS 2.9 21.2 + - - -
1204D PHE* 3.1 10.3 + - - -
1206D GLU* 1.3 79.4 - - - +
1208D VAL* 1.3 59.9 + - - +
1210D GLY 4.4 1.3 - - - +
1211D LEU* 4.2 16.1 + - - +
1223D PHE* 3.7 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ALA* 5.0 5.4 - - + +
415D GLY* 4.7 15.5 - - - +
418D CYS* 4.7 16.2 - - + -
1204D PHE 2.9 15.0 + - - +
1205D ALA* 3.9 7.0 - - - +
1207D THR* 1.3 78.2 - - - +
1209D GLU* 1.3 64.8 + - - +
1211D LEU* 4.1 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778D TRP* 5.0 18.0 - - + +
779D LEU 5.0 11.0 - - - +
1205D ALA 2.9 17.3 + - - +
1206D GLU* 4.0 6.3 - - - +
1207D THR 3.3 0.2 - - - -
1208D VAL* 1.3 79.8 - - - +
1210D GLY* 1.3 57.2 + - - +
1211D LEU* 3.1 6.9 + - - +
1212D THR 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778D TRP* 5.8 3.6 - - - -
1206D GLU 3.1 12.6 + - - -
1207D THR* 4.4 4.4 - - - +
1209D GLU* 1.3 76.7 - - - +
1211D LEU* 1.3 52.5 + - - +
1212D THR 3.4 2.2 - - - -
1213D THR* 3.2 19.2 + - - -
1214D ILE* 2.7 32.4 + - - +
----------------------------------------------------------
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