Contacts of the helix formed by residues 118 - 123 (chain A) in PDB entry 1JPM
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 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 1.3 88.0 - - + +
119A LEU* 1.3 66.8 + - - +
120A TYR* 3.5 25.6 - - + -
121A GLN* 2.9 47.4 + - - +
122A MET* 3.1 8.8 + - - +
309A HIS* 4.5 2.2 - - + -
347A PRO 4.0 5.2 - - - +
348A GLY* 3.0 29.6 - - - +
349A LYS 3.4 16.4 - - - +
350A PRO* 3.9 0.9 - - + -
351A GLY 3.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET 5.5 0.2 - - - +
108A TYR* 3.8 36.1 - - + +
111A TRP* 4.9 1.8 - - + -
112A ALA* 3.8 12.3 - - + -
117A LEU 3.3 1.8 + - - -
118A PRO* 1.3 70.9 - - - +
120A TYR* 1.3 63.7 + - - +
122A MET* 2.9 18.1 + - + +
123A LEU* 3.0 31.6 + - + +
275A ILE* 3.9 25.1 - - + -
306A ALA 4.6 0.2 - - - +
309A HIS* 3.5 22.8 + - + +
351A GLY* 2.8 23.5 + - - +
352A LEU* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 3.5 23.8 - - + -
119A LEU* 1.3 72.4 - - - +
121A GLN* 1.3 82.4 + - + +
123A LEU 3.8 0.4 - - - -
124A GLY 3.4 0.5 + - - -
125A GLY* 2.5 41.0 + - - -
127A ARG 3.3 28.7 - - - -
128A ASP* 3.5 20.8 + - + +
309A HIS* 2.9 59.0 + + - +
312A ALA* 4.1 6.3 - - + -
313A SER* 3.1 12.4 - - - +
346A MET* 3.6 27.7 + - + +
347A PRO 3.7 7.0 + - - -
348A GLY* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.5 22.4 - - + +
118A PRO* 2.9 36.9 + - + +
120A TYR* 1.3 110.3 + - + +
122A MET* 1.3 67.2 + - - +
123A LEU 3.1 2.0 - - - -
124A GLY* 3.2 11.4 + - - -
125A GLY* 3.6 7.8 + - - +
348A GLY* 6.2 0.2 - - - -
79B LEU 5.2 3.1 - - - +
80B ALA* 3.7 37.8 - - - +
82B TYR* 5.4 1.7 - - - +
111B TRP* 5.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TRP* 3.3 45.0 - - + -
112A ALA* 4.3 11.4 - - + -
115A CYS* 3.6 30.3 - - - -
117A LEU* 4.0 19.2 - - + +
118A PRO 3.1 9.8 + - - +
119A LEU* 2.9 15.0 + - + +
121A GLN* 1.3 79.3 - - - +
123A LEU* 1.3 59.5 + - - +
111B TRP* 3.5 51.7 - - + +
115B CYS* 4.1 15.7 - - - -
122B MET* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 4.2 11.4 - - + -
111A TRP* 4.1 23.6 - - + -
119A LEU* 3.0 36.5 + - + +
120A TYR 3.6 0.2 + - - -
121A GLN 3.1 0.4 - - - -
122A MET* 1.3 78.5 - - - +
124A GLY* 1.3 55.0 + - - +
275A ILE* 4.0 21.1 - - + -
279A GLU* 3.7 23.3 - - - +
309A HIS 4.6 0.9 - - - +
310A PHE* 4.1 23.3 - - + -
313A SER* 3.3 19.3 + - - +
314A LYS* 3.0 27.1 + - - +
83B GLU* 4.8 0.9 - - - +
111B TRP* 6.0 0.4 - - - -
----------------------------------------------------------
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