Contacts of the helix formed by residues 115 - 120 (chain M) in PDB entry 2ZHX
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 LEU 115 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M LEU* 5.0 0.7 - - - -
80M SER 3.6 15.5 - - - +
81M PHE* 4.2 8.7 - - + -
82M SER* 2.7 36.6 + - - +
94M LEU* 4.1 9.2 - - + -
97M ILE* 6.2 0.7 - - + -
98M PHE* 3.7 28.3 - - + -
113M GLY 3.6 14.8 - - - +
114M ASP* 1.3 74.3 + - - +
116M THR* 1.3 67.1 + - - +
117M PRO* 3.1 4.5 - - - -
118M TRP* 2.8 47.2 + - + +
119M ALA* 3.4 3.6 + - - +
125M LEU* 3.6 19.2 - - + +
226M LEU* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M ARG* 3.0 31.2 + - - +
55M PHE* 4.4 10.5 - - + -
79M LEU* 4.5 11.3 - - - +
82M SER* 4.4 0.8 + - - -
114M ASP* 2.6 24.1 + - - -
115M LEU* 1.3 75.5 - - - +
117M PRO* 1.3 72.2 - - - +
119M ALA* 2.7 15.4 + - - +
120M GLN* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M ASP* 3.7 13.2 - - - +
115M LEU 3.2 4.5 - - - -
116M THR* 1.3 95.8 - - - +
118M TRP* 1.3 61.6 + - - +
120M GLN* 3.1 24.3 + - + +
121M ARG* 3.0 50.3 - - - +
226M LEU* 4.0 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M ILE* 4.4 14.6 - - + -
94M LEU* 6.1 0.2 - - + -
97M ILE* 4.5 9.6 - - + -
98M PHE* 4.4 15.3 - + - -
101M TYR* 4.2 17.3 - + - -
115M LEU* 2.8 43.1 + - + +
117M PRO* 1.3 74.3 - - - +
119M ALA* 1.3 61.9 + - - +
121M ARG* 3.0 18.3 + - - +
123M VAL* 3.0 34.0 + - + +
125M LEU* 4.6 6.3 - - + -
168M TRP* 5.6 1.8 - + - -
207M PHE* 3.6 31.2 - + - -
222M ILE* 5.3 0.4 - - + -
224M TRP* 3.4 55.0 - + - +
225M ARG 4.0 0.2 - - - +
226M LEU* 3.3 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M PHE* 3.7 34.8 - - + +
79M LEU* 3.9 29.4 - - + -
115M LEU 3.4 2.3 + - - +
116M THR 2.7 14.7 + - - +
118M TRP* 1.3 70.6 - - - +
120M GLN* 1.3 56.4 + - - +
121M ARG 2.9 9.7 + - - -
122M GLY* 3.5 8.5 + - - -
123M VAL 3.3 20.5 + - - +
125M LEU* 4.8 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M PHE* 3.5 27.3 - - + -
56M PRO* 6.3 0.4 - - - -
59M ASN* 5.2 3.6 - - - +
116M THR* 3.0 23.7 + - - +
117M PRO* 3.2 33.8 - - + +
119M ALA* 1.3 74.2 - - - +
121M ARG* 1.3 62.6 + - + +
122M GLY 3.7 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