Contacts of the helix formed by residues 114 - 128 (chain F) 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 GLY 114 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F GLY 3.4 0.8 + - - -
113F VAL* 1.3 79.0 - - - +
115F LYS* 1.3 55.0 + - - +
117F THR* 3.3 1.0 + - - -
118F THR* 2.6 44.2 + - - -
227F VAL* 4.2 2.0 - - - -
1001F GDP 3.0 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F VAL* 4.0 10.2 - - + +
108F VAL* 3.6 31.4 - - - -
109F GLY* 3.6 7.9 - - - +
110F VAL 2.9 21.8 + - - -
113F VAL* 3.8 3.1 - - + -
114F GLY* 1.3 71.2 - - - +
116F THR* 1.3 57.6 + - - +
118F THR* 3.2 1.9 + - - -
119F ILE* 3.0 34.1 + - - +
191F ASP* 3.7 10.8 - - - +
192F THR* 3.1 29.8 - - - +
193F ALA 4.0 0.7 - - - -
194F GLY* 3.4 7.5 - - - +
227F VAL* 3.7 30.7 - - + -
1001F GDP 2.8 26.5 + - - +
1007F ALF 2.5 25.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LYS* 1.3 76.3 - - - +
117F THR* 1.3 63.4 + - - +
119F ILE* 3.4 5.0 + - - +
120F ALA* 3.3 18.5 + - - +
145F GLY 4.7 2.3 + - - +
148F GLN* 3.8 33.0 - - + +
149F LEU* 3.7 27.8 - - + +
152F TRP* 4.2 4.0 - - + -
191F ASP* 2.4 27.9 + - - +
1001F GDP 3.1 7.8 + - - -
1002F MG 2.1 30.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLY 3.8 0.2 - - - -
116F THR* 1.3 75.4 - - - +
118F THR* 1.3 61.7 + - - +
120F ALA* 3.3 5.9 - - - +
121F LYS* 3.2 39.3 + - + +
148F GLN* 4.2 7.4 + - - -
152F TRP* 4.3 20.0 + - + +
284F GLU* 4.3 14.4 - - - +
1001F GDP 2.9 66.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F VAL* 5.7 1.3 - - + -
114F GLY 2.6 27.6 + - - -
115F LYS* 3.6 6.5 - - - -
117F THR* 1.3 71.7 - - - +
119F ILE* 1.3 60.1 + - + +
121F LYS* 3.2 13.2 + - - +
122F LEU* 2.9 33.3 + - + +
227F VAL* 4.4 7.7 - - + +
253F ILE* 3.8 39.0 - - + -
255F THR* 3.3 22.9 - - - +
289F LEU* 4.9 7.4 - - + -
1001F GDP 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F VAL* 4.0 23.8 - - + -
115F LYS 3.0 18.4 + - - +
116F THR 3.4 5.4 + - - +
118F THR* 1.3 72.7 - - - +
120F ALA* 1.3 60.9 + - - +
122F LEU* 3.4 10.4 + - + +
123F GLY 2.9 23.4 + - - -
135F PHE* 3.1 37.1 - - + -
149F LEU* 4.1 7.9 - - + -
189F PHE* 3.5 14.8 - - + +
190F VAL 4.0 4.3 - - - -
191F ASP* 3.4 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F THR 3.3 7.0 + - - +
117F THR 3.3 10.8 - - - +
118F THR 3.3 0.6 - - - -
119F ILE* 1.3 76.0 - - - +
121F LYS* 1.3 64.4 + - + +
123F GLY 3.3 1.2 + - - -
124F ARG* 3.0 20.4 + - - +
135F PHE* 3.9 11.4 - - - -
149F LEU* 4.6 0.4 - - - +
152F TRP* 3.4 49.8 - - + -
156F LEU* 3.2 13.9 - - + +
286F PRO* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F THR* 3.4 25.4 - - + +
118F THR* 3.2 16.8 + - - +
120F ALA* 1.3 79.4 - - + +
122F LEU* 1.3 57.4 + - - +
124F ARG* 3.3 4.2 + - - +
125F TYR* 2.9 28.8 + - - +
281F GLY* 3.9 4.4 - - - -
283F GLY 2.6 29.0 + - - -
285F GLY 3.2 28.0 - - - +
286F PRO* 3.5 19.7 - - + +
288F ASP 3.1 27.0 + - - +
289F LEU* 3.8 24.0 - - + +
1001F GDP 3.3 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F VAL* 5.0 5.4 - - + -
118F THR* 2.9 35.2 + - + +
119F ILE* 3.7 12.3 - - + +
120F ALA 3.2 0.2 - - - -
121F LYS* 1.3 75.3 - - - +
123F GLY* 1.3 59.3 + - - +
125F TYR* 4.1 2.9 - - - -
126F TYR* 2.9 42.9 + - + +
189F PHE* 3.7 35.8 - - + -
225F TRP* 4.1 10.1 - - + -
253F ILE* 4.1 9.9 - - + -
279F PHE* 3.7 37.2 - - + -
289F LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE 2.9 16.1 + - - -
120F ALA 3.3 4.9 + - - -
122F LEU* 1.3 76.3 - - - +
124F ARG* 1.3 55.0 + - - +
127F GLN* 2.8 34.8 + - - +
133F VAL* 4.0 13.8 - - - +
135F PHE* 3.9 4.7 - - - -
158F ILE* 3.8 24.6 - - - +
189F PHE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F ALA 3.0 10.8 + - - +
121F LYS 3.3 7.8 + - - +
123F GLY* 1.3 75.5 - - - +
125F TYR* 1.3 61.3 - - - +
127F GLN* 3.1 24.6 + - - +
128F ASN* 3.2 37.9 + - - +
155F ARG 5.4 3.0 + - - -
156F LEU* 3.5 25.7 - - + +
286F PRO* 3.6 33.9 - - + +
287F ASP* 3.0 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PRO* 4.1 6.2 - - - +
98F VAL* 3.3 29.9 + - - +
121F LYS 2.9 16.5 + - - +
122F LEU* 3.6 8.1 - - - +
123F GLY 3.3 0.2 - - - -
124F ARG* 1.3 78.8 - - - +
126F TYR* 1.3 94.4 + + - +
128F ASN* 3.6 9.0 + - - +
129F LEU* 3.4 45.0 + - + +
279F PHE* 3.8 24.9 - + - -
289F LEU* 4.2 15.9 - - + -
291F PRO* 4.2 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL* 2.7 35.8 + - - +
99F GLU* 3.9 8.7 - - - -
100F PRO* 3.7 24.0 - - + +
122F LEU* 2.9 40.1 + - + +
125F TYR* 1.3 92.0 - + - +
127F GLN* 1.3 64.6 + - - +
128F ASN 3.2 0.4 - - - -
129F LEU* 3.0 22.3 + - + +
131F LYS* 3.0 27.6 + - + +
133F VAL* 3.9 10.3 - - + -
187F LEU* 3.8 24.5 - - + -
189F PHE* 3.7 24.5 - + - -
225F TRP* 4.1 4.5 - + - -
279F PHE* 3.5 14.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F GLY 2.8 22.4 + - - +
124F ARG* 3.1 35.1 + - - +
126F TYR* 1.3 71.3 - - - +
128F ASN* 1.3 65.4 + - - +
130F GLY* 2.9 20.4 + - - -
131F LYS 3.7 15.4 - - - +
133F VAL* 4.1 5.5 - - + +
156F LEU* 2.9 31.4 + - - +
157F SER 5.3 0.4 + - - -
158F ILE* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ARG* 3.2 41.0 + - - +
125F TYR* 3.6 9.0 - - - +
127F GLN* 1.3 81.0 - - - +
129F LEU* 1.3 60.7 + - + +
130F GLY 3.1 2.8 + - - -
287F ASP* 4.8 4.6 + - - -
----------------------------------------------------------
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