Contacts of the helix formed by residues 367 - 372 (chain 1) in PDB entry 1O1F
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 PRO 367 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 GLU* 3.6 43.2 - - + +
1201 THR* 4.6 4.0 - - + -
1211 GLN* 4.7 6.1 - - + -
3621 TYR* 3.3 32.5 - - + +
3661 GLY* 1.3 81.1 - - - +
3681 SER* 1.3 62.5 - - - +
3691 ILE* 3.2 2.0 + - - -
3701 VAL* 3.3 22.9 - - - +
3711 HIS* 3.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 GLU* 3.9 20.1 + - - -
3651 ALA 4.0 13.9 - - - -
3661 GLY 4.4 0.4 - - - -
3671 PRO* 1.3 78.6 - - - +
3691 ILE* 1.3 62.6 + - - +
3711 HIS* 3.0 20.6 + - - +
3721 ARG 3.7 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3571 ILE* 3.9 28.5 - - + +
3611 GLU* 3.6 35.9 - - + -
3621 TYR* 4.1 20.4 - - + -
3651 ALA* 3.5 23.8 + - + +
3661 GLY 3.0 20.2 + - - +
3671 PRO* 4.2 2.2 - - + +
3681 SER* 1.3 76.5 - - - +
3701 VAL* 1.3 68.3 + - + +
3721 ARG* 3.9 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 ARG* 3.5 19.6 + - + +
1201 THR* 3.2 35.0 - - + +
1321 MET* 4.3 14.1 - - - -
1331 TYR* 4.7 2.0 - - - -
1341 VAL* 4.6 20.6 - - + +
3571 ILE* 3.6 37.0 - - + -
3671 PRO 3.3 13.7 - - - +
3691 ILE* 1.3 75.2 - - + +
3711 HIS* 1.3 70.9 + - - +
3721 ARG* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 371 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 LYS* 3.2 60.5 + - + +
1161 ARG* 3.7 27.5 + - - +
1171 GLU* 3.7 36.8 - - + +
3671 PRO 3.4 1.1 + - - +
3681 SER* 3.0 15.1 + - - +
3701 VAL* 1.3 83.7 - - + +
3721 ARG* 1.3 75.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 ARG* 3.6 29.8 - - - +
1331 TYR* 2.9 50.2 + - - -
1341 VAL 4.5 4.9 + - - +
1351 ALA* 5.9 0.2 - - - +
3551 MET 5.3 0.4 + - - -
3571 ILE* 5.8 3.8 - - - +
3681 SER 3.7 6.1 + - - -
3691 ILE 3.9 6.5 + - - -
3701 VAL* 3.1 14.4 + - - +
3711 HIS* 1.3 96.7 + - - +
----------------------------------------------------------
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