Contacts of the helix formed by residues 1208 - 1221 (chain B) in PDB entry 5J67
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 GLY1208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203B SER 3.8 0.2 + - - -
1204B GLU* 3.0 20.3 + - - -
1205B ASP 4.6 1.0 + - - -
1206B GLU 3.8 1.0 - - - -
1207B LEU* 1.3 80.2 - - - +
1209B PRO* 1.4 76.4 - - - +
1210B ARG 3.3 2.7 + - - -
1211B LYS 3.6 0.9 + - - -
1212B ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B GLU* 3.9 25.3 - - + +
1208B GLY* 1.4 82.8 - - - +
1210B ARG* 1.3 60.8 + - + +
1212B ALA* 3.7 1.0 + - - +
1213B HIS* 2.7 39.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208B GLY 3.4 0.4 - - - -
1209B PRO* 1.3 81.6 - - + +
1211B LYS* 1.3 62.7 + - + +
1213B HIS* 3.1 8.2 + - + +
1214B LEU* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167B GLN* 5.3 4.3 - - + +
1168B GLN* 3.8 21.8 + - - +
1171B TYR* 3.7 58.0 - - + -
1207B LEU* 3.7 36.1 - - + +
1208B GLY 3.6 1.2 + - - -
1210B ARG* 1.3 76.0 - - + +
1212B ALA* 1.3 58.3 + - - +
1214B LEU* 3.3 8.5 + - + +
1215B ILE* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200B VAL* 4.5 9.4 - - + +
1203B SER* 4.1 4.7 - - - -
1204B GLU* 3.5 44.0 - - + +
1207B LEU* 5.1 0.6 - - - +
1208B GLY 3.3 9.1 + - - +
1209B PRO 3.8 4.3 - - - +
1210B ARG 3.2 0.4 - - - -
1211B LYS* 1.3 80.0 - - - +
1213B HIS* 1.3 58.5 + - - +
1215B ILE* 3.6 13.0 + - - +
1216B LEU* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B GLU* 3.7 24.2 - - - -
1209B PRO* 2.7 25.9 + - + +
1210B ARG* 3.1 10.6 + - - +
1212B ALA* 1.3 77.1 - - - +
1214B LEU* 1.3 61.0 + - - +
1216B LEU* 3.6 20.9 - - + +
1217B ARG* 3.0 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171B TYR* 3.1 31.2 - - + +
1175B MET* 3.9 15.4 - - - +
1210B ARG* 2.9 21.8 + - + +
1211B LYS* 3.3 11.2 + - + +
1213B HIS* 1.3 73.9 - - - +
1215B ILE* 1.3 64.1 + - - +
1217B ARG* 3.5 26.5 + - - +
1218B ARG* 3.3 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171B TYR* 4.4 9.4 - - + -
1174B LEU* 3.9 26.5 - - + -
1175B MET* 3.7 21.1 - - + -
1182B LEU* 3.5 15.8 - - + +
1199B PHE* 4.0 26.9 - - + -
1200B VAL* 5.8 3.6 - - + -
1203B SER* 4.4 9.4 - - - +
1207B LEU* 4.0 21.3 - - + -
1211B LYS 3.0 21.9 + - - +
1212B ALA* 3.6 11.7 - - - +
1214B LEU* 1.3 72.0 - - - +
1216B LEU* 1.3 66.3 + - - +
1218B ARG* 3.1 16.1 + - - +
1219B LEU* 3.3 12.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186B GLN* 5.6 0.4 - - - +
1200B VAL* 3.6 46.9 - - + -
1212B ALA* 3.0 17.5 + - + +
1213B HIS* 3.6 26.7 - - + +
1215B ILE* 1.3 75.9 - - - +
1217B ARG* 1.3 62.7 + - + +
1219B LEU* 3.1 26.0 + - + +
1220B GLU* 3.2 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213B HIS* 3.0 32.1 + - + +
1214B LEU* 3.7 26.1 - - + +
1215B ILE 3.3 0.4 - - - -
1216B LEU* 1.3 73.5 - - + +
1218B ARG* 1.3 65.9 + - - +
1220B GLU* 3.1 26.4 + - + +
1221B ARG* 3.6 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174B LEU 4.1 1.8 + - - -
1175B MET* 2.9 66.2 + - + +
1177B VAL 3.5 13.1 + - - -
1178B SER* 5.4 0.4 - - - +
1179B ALA* 3.5 26.2 - - + +
1182B LEU* 3.6 17.3 - - + -
1214B LEU 3.3 8.0 + - - +
1215B ILE 3.1 11.0 + - - +
1217B ARG* 1.3 77.7 - - - +
1219B LEU* 1.3 63.0 + - - +
1221B ARG* 3.1 52.0 + - - +
1222B VAL 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B ALA 4.4 0.4 - - - +
1182B LEU* 3.6 20.0 - - + +
1183B PHE* 3.4 50.8 - - + +
1186B GLN* 3.7 32.5 - - - +
1199B PHE* 4.7 3.6 - - + -
1200B VAL* 4.7 6.1 - - + -
1215B ILE* 3.7 22.0 - - + +
1216B LEU* 3.1 20.3 + - + +
1218B ARG* 1.3 76.0 - - - +
1220B GLU* 1.3 62.3 + - - +
1222B VAL* 3.4 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216B LEU* 3.2 20.5 + - - +
1217B ARG* 3.1 19.9 + - + +
1219B LEU* 1.3 77.1 - - - +
1221B ARG* 1.3 61.7 + - + +
1222B VAL 3.2 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111B ASP* 5.6 1.2 - - - +
1179B ALA* 4.3 11.7 - - + +
1217B ARG 3.8 12.6 - - - +
1218B ARG* 3.1 39.3 + - - +
1220B GLU* 1.3 75.4 - - + +
1222B VAL* 1.3 61.9 + - - +
1223B SER 3.8 1.0 + - - -
----------------------------------------------------------
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