Contacts of the helix formed by residues 113 - 127 (chain C) in PDB entry 2RHM
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 SER 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA* 1.3 76.2 - - - +
114C GLY* 1.3 65.2 + - - +
115C ASP* 4.0 7.6 + - - +
116C VAL* 3.0 28.4 + - - +
117C LEU* 3.0 19.2 + - - +
167C THR* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA 3.7 1.8 + - - -
113C SER* 1.3 71.8 - - - +
115C ASP* 1.3 62.7 + - - +
117C LEU* 3.3 8.2 + - - +
118C VAL* 3.0 28.9 + - - +
146C VAL 4.0 6.3 - - - -
147C ARG* 3.5 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER* 3.2 7.8 - - - +
114C GLY* 1.3 75.5 - - - +
116C VAL* 1.3 64.7 + - + +
118C VAL* 3.4 2.3 + - - +
119C GLU* 3.1 24.1 + - - +
147C ARG* 3.7 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA* 4.8 2.0 - - + -
113C SER* 3.0 24.5 + - - +
115C ASP* 1.3 78.5 - - + +
117C LEU* 1.3 57.5 + - - +
119C GLU* 3.6 6.6 - - + +
120C ARG* 2.9 68.4 + - + +
167C THR* 3.9 26.5 - - + +
168C PHE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS* 4.9 11.0 - - + -
13C PRO 3.8 9.6 - - - +
14C ALA* 3.3 36.1 - - + +
15C THR* 3.7 22.4 - - + +
112C ALA* 3.8 27.8 - - + +
113C SER 3.0 15.7 + - - +
114C GLY* 3.3 4.7 + - - +
116C VAL* 1.3 74.2 - - - +
118C VAL* 1.3 60.1 + - - +
120C ARG* 3.4 4.5 + - - +
121C ILE* 2.9 36.1 + - - +
146C VAL* 3.7 28.7 - - + +
149C ARG* 6.0 0.9 - - - +
150C GLY 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLY 3.0 20.7 + - - +
115C ASP 3.9 3.8 - - - +
117C LEU* 1.3 74.8 - - - +
119C GLU* 1.3 55.6 + - - +
121C ILE* 3.1 7.7 + - + +
122C LEU* 2.8 55.9 + - + +
143C LEU* 3.5 39.5 - - + +
146C VAL* 4.1 10.5 - - + -
147C ARG* 3.9 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP 3.1 17.5 + - - +
116C VAL* 3.6 8.7 - - - +
118C VAL* 1.3 77.7 - - - +
120C ARG* 1.3 57.9 + - + +
122C LEU* 3.9 6.8 - - - +
123C SER* 2.8 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.0 37.2 + - + -
15C THR 3.9 4.0 - - - -
16C GLY* 4.3 1.8 - - - +
112C ALA* 4.0 8.7 - - - +
116C VAL* 2.9 41.3 + - + +
117C LEU* 3.7 4.7 - - - +
118C VAL 3.2 0.2 - - - -
119C GLU* 1.3 73.4 - - + +
121C ILE* 1.3 56.8 + - - +
123C SER* 3.2 5.8 + - - -
124C ARG* 2.8 57.4 + - - +
166C THR* 2.7 47.1 + - - -
167C THR 3.9 3.8 + - - -
169C PRO* 4.0 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 4.5 18.6 - - + +
14C ALA* 4.0 13.2 - - + -
117C LEU 2.9 22.1 + - - +
118C VAL* 3.5 6.5 - - + +
120C ARG* 1.3 74.8 - - - +
122C LEU* 1.3 68.1 + - + +
124C ARG* 3.4 6.1 + - - +
125C ILE* 3.1 25.5 + - + +
136C ASP* 6.0 6.3 - - + -
137C ASP 5.2 9.9 - - - +
138C ARG* 5.7 7.2 - - + -
143C LEU* 6.4 1.8 - - + -
146C VAL* 3.8 35.9 - - + -
149C ARG* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 2.8 41.2 + - + +
119C GLU* 3.9 5.2 - - - +
121C ILE* 1.3 78.3 - - + +
123C SER* 1.3 62.2 + - - +
125C ILE* 3.6 6.2 + - + +
126C ALA* 3.1 25.5 + - - +
138C ARG* 5.6 10.3 - - + +
143C LEU* 6.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLU 2.8 21.0 + - - -
120C ARG* 3.5 7.4 - - - -
122C LEU* 1.3 77.2 - - - +
124C ARG* 1.3 59.2 + - - +
126C ALA* 3.3 6.0 + - - +
127C GLN* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.6 29.0 + - - +
16C GLY* 4.8 4.6 - - - +
18C THR* 5.2 2.4 + - - -
19C THR* 5.5 4.0 + - - -
120C ARG* 2.8 40.5 + - - +
121C ILE* 3.9 6.1 - - - +
123C SER* 1.3 73.1 - - - +
125C ILE* 1.3 64.7 + - - +
127C GLN* 3.5 13.4 + - - +
128C GLY* 3.6 6.8 + - - -
129C ALA* 4.0 8.9 + - - +
130C ARG* 4.4 23.4 + - + +
193C CL 3.6 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 3.1 18.6 + - + +
122C LEU* 4.0 6.3 - - + +
124C ARG* 1.3 77.7 - - - +
126C ALA* 1.3 61.6 + - - +
128C GLY* 3.4 12.9 + - - -
130C ARG* 5.4 5.8 - - - -
138C ARG* 6.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU 3.1 19.6 + - - +
123C SER* 3.7 6.3 - - - +
124C ARG 3.3 0.4 - - - -
125C ILE* 1.3 74.0 - - - +
127C GLN* 1.3 60.5 - - - +
128C GLY* 3.2 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C SER* 3.1 16.6 + - - +
124C ARG* 3.5 8.5 + - - +
125C ILE 3.3 0.4 - - - -
126C ALA* 1.3 76.3 - - - +
128C GLY* 1.3 64.7 + - - +
129C ALA* 3.4 11.6 + - + +
----------------------------------------------------------
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