Contacts of the helix formed by residues 1199 - 1208 (chain B) in PDB entry 4DDI
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 THR1199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191B GLU* 5.6 3.6 - - - -
1194B ILE* 4.0 8.1 - - - +
1198B ARG* 1.3 81.7 - - - +
1200B VAL* 1.3 61.2 + - - +
1201B LYS* 3.0 7.0 + - - +
1202B GLU* 2.6 57.3 + - + +
1203B PHE* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B LEU* 3.4 42.6 - - + +
1184B GLN* 4.1 5.6 - - - +
1187B SER* 3.4 40.6 - - - +
1190B PHE* 4.3 9.0 - - + -
1191B GLU* 3.8 23.7 - - + +
1194B ILE* 4.9 5.8 - - + -
1199B THR* 1.3 75.2 - - - +
1201B LYS* 1.3 60.8 + - - +
1203B PHE* 3.3 7.4 + - + +
1204B CYS* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130B PHE* 6.3 1.8 - - - -
1184B GLN* 3.3 37.8 + - - +
1199B THR* 3.0 5.1 + - - +
1200B VAL* 1.3 77.7 - - - +
1202B GLU* 1.3 59.8 + - + +
1204B CYS* 3.0 4.6 + - + +
1205B GLN* 2.9 58.5 + - + +
1209B GLU* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197B GLY 4.3 2.3 - - - +
1198B ARG* 3.2 20.8 - - + +
1199B THR* 2.6 51.5 + - + +
1201B LYS* 1.3 72.4 - - + +
1203B PHE* 1.3 56.6 + - - +
1205B GLN* 3.5 10.6 + - - +
1206B GLN* 2.9 43.3 + - - +
92C GLN* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B LEU* 4.5 13.7 - - + -
1194B ILE* 4.0 33.2 - - + -
1195B GLU* 5.6 2.9 - - + -
1198B ARG* 3.5 39.6 - - - +
1199B THR 3.3 19.0 + - - +
1200B VAL* 3.3 7.4 + - + +
1202B GLU* 1.3 76.8 - - - +
1204B CYS* 1.3 61.1 + - - +
1206B GLN* 4.6 0.2 - - - -
1207B GLU* 2.8 37.4 + - + +
1208B VAL* 3.4 23.9 - - + +
1216B ASP* 5.9 2.0 - - + -
1218B ILE* 4.6 15.3 - - + -
1219B HIS* 3.7 25.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B SER* 3.2 48.9 - - - +
1183B LEU* 3.8 23.1 - - - -
1184B GLN* 4.4 10.5 - - - +
1200B VAL 2.9 17.6 + - - +
1201B LYS* 3.0 11.2 + - + +
1203B PHE* 1.3 74.1 - - - +
1205B GLN* 1.3 61.4 + - - +
1208B VAL* 2.9 16.7 + - - -
1209B GLU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201B LYS* 2.9 50.7 + - + +
1202B GLU* 4.0 10.4 - - - +
1204B CYS* 1.3 77.1 - - - +
1206B GLN* 1.3 58.4 + - - +
1209B GLU* 4.0 22.0 + - - +
1210B PRO* 3.1 23.5 - - - +
92C GLN* 3.8 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198B ARG* 3.2 46.7 + - - +
1202B GLU* 2.9 25.7 + - - +
1203B PHE 4.3 0.2 - - - +
1205B GLN* 1.3 77.5 - - - +
1207B GLU* 1.3 65.7 + - + +
1208B VAL 3.7 0.7 - - - -
1210B PRO* 3.4 15.6 - - - +
1213B LYS* 3.7 17.3 + - - +
91C SER 5.5 0.2 - - - +
92C GLN* 3.9 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176B ARG* 4.3 1.6 + - - -
1198B ARG* 3.2 33.3 + - - +
1203B PHE* 2.8 43.5 + - + +
1206B GLN* 1.3 83.6 - - - +
1208B VAL* 1.3 57.4 + - - +
1213B LYS* 4.2 24.7 + - - +
1214B GLU* 3.6 18.2 + - - +
1219B HIS* 2.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B TYR* 4.6 0.2 - - - +
1176B ARG* 3.1 39.7 + - - +
1179B THR* 3.2 26.9 - - - +
1180B SER* 3.6 20.0 - - - +
1183B LEU* 4.1 8.5 - - + -
1203B PHE* 3.4 35.9 - - + +
1204B CYS* 2.9 14.0 + - - +
1206B GLN 3.7 1.0 - - - -
1207B GLU* 1.3 81.2 - - - +
1209B GLU* 1.3 68.0 + - - +
1210B PRO* 3.4 2.0 - - - +
1219B HIS* 3.6 15.0 - - + +
----------------------------------------------------------
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