Contacts of the helix formed by residues 1235 - 1240 (chain O) in PDB entry 5Z3U
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 VAL1235 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926O PRO* 6.0 1.1 - - + -
927O LEU 5.6 0.2 - - - +
928O GLN 5.1 4.3 - - - +
929O ASN* 4.7 9.2 - - - +
931O LEU* 3.6 45.5 - - + -
959O PRO* 5.5 7.4 - - + -
980O ILE* 5.9 0.2 - - + -
1231O ILE* 3.2 18.6 - - + +
1232O ASP* 2.6 18.8 + - + +
1233O GLY 3.3 0.4 - - - -
1234O LYS* 1.3 76.8 - - + +
1236O ILE* 1.3 66.3 + - + +
1237O GLN 3.3 0.7 - - - -
1238O ALA* 3.0 4.8 + - - +
1239O GLY* 2.5 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1236 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925O THR* 4.2 7.0 - - - +
926O PRO* 3.8 38.9 - - + +
927O LEU 4.1 13.0 - - - +
928O GLN 5.8 0.7 - - - +
1188O HIS* 4.0 15.3 - - + +
1191O LEU* 5.2 8.5 - - + -
1229O LEU* 6.0 0.7 - - + -
1232O ASP* 2.5 47.1 + - + +
1235O VAL* 1.3 82.5 - - + +
1237O GLN* 1.3 66.1 + - + +
1238O ALA 3.2 0.2 - - - -
1239O GLY* 3.6 3.3 - - - +
1240O LYS* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1237 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229O LEU* 4.4 11.6 + - - +
1232O ASP* 2.9 6.9 + - - +
1233O GLY* 3.1 36.8 - - - +
1236O ILE* 1.3 81.7 - - + +
1238O ALA* 1.3 58.0 + - - +
1240O LYS* 3.6 33.1 - - + +
1241O PHE* 3.0 24.6 - - - -
1253O LEU* 4.3 5.1 - - + +
1257O LEU* 3.4 34.8 - - + +
1261O GLU* 3.4 6.6 - - - +
1264O ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1238 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980O ILE* 4.0 8.3 - - + -
984O HIS* 2.8 39.6 + - + +
987O LEU* 6.1 0.4 - - - -
1233O GLY 3.6 3.6 + - - +
1234O LYS* 3.2 25.8 - - - +
1235O VAL* 3.0 12.3 + - - +
1237O GLN* 1.3 78.9 - - - +
1239O GLY* 1.3 58.0 + - - +
1240O LYS 3.3 0.2 - - - -
1241O PHE* 3.0 17.9 - - - -
1242O ASP* 5.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1239 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791O ALA* 5.4 0.3 - - - +
926O PRO* 5.7 3.1 - - - -
984O HIS* 5.1 0.7 - - - -
987O LEU* 5.0 17.4 - - - +
991O LEU* 4.4 27.3 - - - +
1235O VAL 2.5 19.3 + - - -
1236O ILE* 3.5 4.4 + - - -
1238O ALA* 1.3 73.4 - - - +
1240O LYS* 1.3 63.1 + - - +
1241O PHE 3.5 0.4 + - - -
1242O ASP* 4.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1240 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791O ALA* 5.8 2.9 - - - -
926O PRO* 6.1 2.5 - - + -
993O ARG* 3.4 75.0 + - - +
995O LEU* 5.9 0.2 - - - +
1236O ILE* 2.9 28.7 + - - +
1237O GLN* 3.6 42.6 - - + +
1238O ALA 3.3 0.6 - - - -
1239O GLY* 1.3 79.5 - - - +
1241O PHE* 1.3 64.7 + - + +
1242O ASP 3.2 9.5 + - - +
1253O LEU* 5.5 5.4 - - + -
----------------------------------------------------------
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