Contacts of the helix formed by residues 140 - 153 (chain C) in PDB entry 2CNW
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 ALA 140 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ARG 3.4 0.8 + - - -
139C PRO* 1.3 73.5 - - - +
141C ALA* 1.3 58.6 + - - +
142C ARG 3.4 2.7 - - - -
143C GLU* 3.6 9.1 + - - +
144C GLN* 2.9 30.9 + - - +
144F ALA* 3.7 13.7 - - + +
147F THR* 3.6 31.9 - - + +
148F GLN* 4.0 9.9 - - + +
151F GLU* 4.7 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 4.8 5.5 + - - +
133C ALA* 4.9 1.8 - - - +
135C ASP* 3.5 40.6 - - + +
138C ARG* 3.1 26.0 + - + +
139C PRO 3.2 1.7 - - - -
140C ALA* 1.3 77.4 - - - +
142C ARG* 1.3 62.2 + - - +
144C GLN* 3.4 15.2 - - - +
145C LEU* 3.1 21.5 + - - +
187C ASP* 5.3 1.2 - - - +
1007C ALF 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ALA* 3.7 31.6 - - + +
135C ASP 3.9 13.3 + - - +
136C THR* 3.9 19.8 + - - +
140C ALA 3.4 0.4 - - - -
141C ALA* 1.3 75.9 - - - +
143C GLU* 1.3 54.8 + - - +
145C LEU* 3.2 4.2 + - - +
146C ARG* 2.7 34.7 + - - +
158C GLU* 3.7 33.9 - - + +
159C VAL 2.7 37.9 + - - -
160C MET* 3.9 1.4 - - - +
161C ASP* 3.1 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ALA* 3.6 12.2 + - - +
141C ALA 3.4 0.2 - - - -
142C ARG* 1.3 74.9 - - - +
144C GLN* 1.3 56.9 + - - +
146C ARG* 3.4 37.3 + - - +
147C LEU* 2.7 54.5 + - + +
144F ALA* 4.6 2.0 - - + -
147F THR* 3.3 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 3.8 22.7 + - + +
113C THR* 4.4 4.8 + - - -
138C ARG* 3.4 23.2 + - - +
140C ALA 2.9 18.5 + - - +
141C ALA* 3.4 11.6 - - - +
143C GLU* 1.3 77.1 - - - +
145C LEU* 1.3 56.9 + - - +
147C LEU* 3.5 2.1 + - - +
148C LEU* 3.1 35.6 + - + +
1001C GDP 3.1 25.4 + - - -
1007C ALF 5.3 0.5 - - - -
142F ARG* 3.5 28.8 + - - +
143F ALA* 3.6 18.8 - - + +
144F ALA* 3.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 4.0 29.6 - - + +
115C ALA* 4.5 0.7 - - + -
116C ALA 4.7 1.1 - - - +
131C LEU* 4.0 34.1 - - + -
132C VAL 3.8 17.5 - - - +
133C ALA* 3.8 16.2 - - + -
141C ALA 3.1 13.3 + - - +
142C ARG 3.8 5.6 - - - +
144C GLN* 1.3 73.9 - - - +
146C ARG* 1.3 60.2 + - - +
148C LEU* 3.5 7.1 + - + +
149C GLY 3.0 23.9 + - - -
156C VAL* 3.4 17.7 - - + +
187C ASP* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ARG* 2.7 22.0 + - - +
143C GLU* 3.4 42.3 + - - +
145C LEU* 1.3 69.7 - - - +
147C LEU* 1.3 66.9 + - + +
149C GLY* 3.4 2.3 + - - -
150C GLU* 3.2 21.6 + - + +
156C VAL* 4.0 14.2 - - + +
158C GLU* 2.7 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLU* 2.7 45.8 + - + +
144C GLN 3.9 3.4 - - - +
146C ARG* 1.3 73.2 - - + +
148C LEU* 1.3 64.7 + - - +
150C GLU* 3.2 19.4 + - - +
151C LYS* 3.2 22.2 + - - +
143F ALA* 4.2 10.5 - - + -
144F ALA* 3.7 27.4 - - + +
165F GLU* 4.6 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 3.7 29.4 - - + +
113C THR* 4.2 13.9 - - + +
116C ALA* 3.7 30.3 - - + -
144C GLN* 3.1 26.2 + - + +
145C LEU* 3.9 7.2 - - + +
147C LEU* 1.3 76.0 - - - +
149C GLY* 1.3 56.7 + - - +
151C LYS* 3.2 24.8 - - + +
152C VAL* 3.0 32.5 + - - +
274C GLU 5.7 4.5 - - - +
276C PRO* 4.9 8.5 - - + -
143F ALA* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 4.0 10.9 - - - +
145C LEU 3.0 16.2 + - - -
146C ARG 3.8 4.0 - - - -
147C LEU 3.3 0.2 - - - -
148C LEU* 1.3 73.9 - - - +
150C GLU* 1.3 57.9 + - - +
152C VAL* 3.4 3.8 + - - -
153C GLY 2.9 23.7 + - - -
154C VAL 2.9 29.3 + - - +
156C VAL* 3.8 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ARG* 3.2 12.8 + - + +
147C LEU* 3.7 22.2 - - - +
149C GLY* 1.3 75.5 - - - +
151C LYS* 1.3 63.5 + - - +
153C GLY* 3.3 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU 3.2 9.5 + - - +
148C LEU* 3.2 24.9 - - + +
150C GLU* 1.3 80.3 - - - +
152C VAL* 1.3 60.5 + - + +
275C LYS* 4.9 9.2 - - - +
276C PRO* 3.7 37.9 - - + +
277C GLU* 5.0 4.0 + - - -
165F GLU* 5.6 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 4.2 16.6 - - + +
119C ALA* 4.5 3.4 - - + -
120C LEU* 4.0 30.6 - - + +
123C LYS* 3.5 20.3 + - - +
131C LEU* 4.8 2.2 - - + -
148C LEU 3.0 20.3 + - - +
149C GLY* 3.9 7.6 - - - +
151C LYS* 1.3 79.3 - - + +
153C GLY* 1.3 61.3 + - - +
154C VAL* 3.9 22.2 - - + -
276C PRO* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LYS* 2.7 27.6 + - - -
149C GLY 2.9 6.2 + - - -
150C GLU* 3.3 10.2 + - - -
151C LYS 3.5 0.2 - - - -
152C VAL* 1.3 76.8 - - - +
154C VAL* 1.3 60.5 + - - +
155C PRO* 4.3 4.0 - - - +
181C ARG* 5.1 2.9 + - - -
----------------------------------------------------------
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