Contacts of the helix formed by residues 116 - 130 (chain C) in PDB entry 2VZE
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 VAL 116 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TRP* 3.7 9.4 - - + +
113C LEU* 4.7 5.2 - - + -
114C PRO* 2.8 42.6 + - + +
115C ARG* 1.3 77.0 - - - +
117C PRO* 1.3 79.4 - - + +
118C GLU* 3.4 23.8 - - + +
119C TRP* 3.0 16.4 + - - +
120C TRP* 3.3 13.7 - - - -
183C VAL* 4.8 9.0 - - + -
287C LEU* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.4 10.2 - - + +
71C TRP* 3.7 30.5 - - + +
79C LEU* 3.7 28.3 - - + -
81C TRP* 3.7 26.2 - - + -
116C VAL* 1.3 90.4 - - + +
118C GLU* 1.3 71.6 + - - +
120C TRP* 2.9 24.9 + - + +
121C LEU* 3.2 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 6.0 1.2 - - - +
113C LEU* 3.9 3.8 - - + -
116C VAL* 3.0 24.6 + - + +
117C PRO* 1.3 82.7 - - - +
119C TRP* 1.3 56.9 + - - +
121C LEU* 4.1 13.9 - - + +
122C VAL* 2.8 35.4 + - + +
183C VAL* 3.8 32.2 - - + +
194C PHE* 4.0 22.0 - - + -
195C LYS* 2.2 38.9 + - + +
198C LEU* 5.5 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 3.7 27.4 + - + +
113C LEU* 3.6 25.8 - - + +
114C PRO 4.2 6.7 - - - +
116C VAL 3.0 14.7 + - - +
118C GLU* 1.3 77.8 - - - +
120C TRP* 1.3 89.2 + + + +
122C VAL* 3.8 1.5 - - - +
123C ILE* 3.0 55.4 + - + +
135C PRO* 4.3 13.0 - - + +
136C GLY 5.8 0.2 + - - -
219C TYR* 4.9 1.6 - - - -
263C THR* 3.3 44.4 + - + -
268C ASN* 3.1 34.3 - - + -
269C ILE* 4.3 17.7 - - + -
273C LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.0 16.4 - - + -
86C LEU* 5.4 0.9 - - + -
115C ARG* 4.4 10.3 - - + -
116C VAL 3.3 28.0 - - - -
117C PRO* 2.9 11.2 + - + +
119C TRP* 1.3 99.7 - + + +
121C LEU* 1.3 63.1 + - - +
123C ILE* 3.6 1.6 + - - +
124C LEU* 3.0 31.2 + - - +
263C THR* 4.8 1.3 - - + -
268C ASN* 3.7 22.9 - - - -
272C SER* 3.1 38.4 + - - -
273C LEU* 3.7 26.7 - - + +
277C TRP* 3.8 23.8 - + + -
283C THR* 4.6 4.2 - - + +
285C VAL* 3.5 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 5.9 2.2 - - + -
81C TRP* 5.6 11.2 - - + -
86C LEU* 4.0 24.9 - - + -
89C ASN* 3.9 21.8 - - + +
90C SER* 3.8 25.8 - - - +
93C ALA* 3.4 19.1 - - + +
117C PRO* 3.2 20.6 + - + +
118C GLU* 3.7 17.0 - - + +
120C TRP* 1.3 77.8 - - + +
122C VAL* 1.3 57.7 + - + +
124C LEU* 3.5 4.0 + - - +
125C GLY 2.8 22.3 + - - -
194C PHE* 5.1 3.4 - - + -
198C LEU* 4.2 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA* 4.7 4.5 - - - -
97C LEU* 3.9 8.5 - - + +
109C VAL* 5.2 0.2 - - + -
111C VAL* 4.0 29.6 - - + -
113C LEU* 4.5 2.9 - - + -
118C GLU* 2.8 31.8 + - + +
119C TRP* 3.8 5.2 - - - +
121C LEU* 1.3 70.8 - - - +
123C ILE* 1.3 60.1 + - - +
125C GLY* 3.1 2.1 + - - -
126C CYS* 2.9 34.7 + - - -
158C VAL* 4.1 28.9 - - + -
194C PHE* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 4.1 22.0 - - + -
119C TRP* 3.0 50.6 + - + +
120C TRP 4.0 2.9 - - - +
122C VAL* 1.3 75.5 - - - +
124C LEU* 1.3 61.9 + - - +
126C CYS* 3.2 7.8 + - - +
127C ILE* 3.0 27.0 + - + +
133C PHE* 3.4 49.1 - - + -
135C PRO* 4.4 1.1 - - + -
269C ILE* 3.8 28.5 - - + -
273C LEU* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.8 7.0 - - + -
47C ALA* 4.7 9.4 - - + +
51C LEU* 3.9 24.7 - - + -
86C LEU* 3.9 12.6 - - + -
90C SER* 3.7 25.6 - - - +
120C TRP 3.0 21.4 + - - +
121C LEU* 3.7 4.3 - - - +
123C ILE* 1.3 75.7 - - - +
125C GLY* 1.3 63.5 + - - +
127C ILE* 3.2 14.8 + - + +
128C ARG* 3.0 30.5 + - - +
273C LEU* 4.5 16.6 - - + -
277C TRP* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C SER 3.9 5.1 + - - -
93C ALA* 4.1 2.7 - - - -
94C ALA* 3.6 28.4 - - - +
97C LEU* 3.8 8.7 - - - -
121C LEU 2.8 16.9 + - - -
122C VAL 3.1 4.4 + - - -
124C LEU* 1.3 77.3 - - - +
126C CYS* 1.3 61.6 + - - +
128C ARG 3.4 0.5 + - - -
129C ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 3.9 15.3 - - - -
109C VAL* 4.2 20.6 - - - -
111C VAL* 5.1 0.2 - - - -
122C VAL* 2.9 21.0 + - - -
123C ILE 3.4 8.3 - - - +
125C GLY* 1.3 73.5 - - - +
127C ILE* 1.3 65.8 + - - +
129C ALA 3.1 1.0 + - - -
130C GLY 2.9 4.9 + - - -
131C LEU* 2.8 56.9 + - - +
133C PHE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASN* 2.8 47.0 + - - +
46C PHE* 4.2 9.6 - - + +
47C ALA* 3.8 14.4 - - + +
123C ILE* 3.0 33.6 + - + +
124C LEU* 3.2 18.1 + - + +
126C CYS* 1.3 76.9 - - - +
128C ARG* 1.3 63.0 + - - +
130C GLY* 3.5 5.4 + - - -
131C LEU 4.8 0.7 - - - -
133C PHE* 3.9 18.8 - - + -
210C THR* 4.2 0.2 - - - +
216C SER* 4.2 9.2 - - - +
235C TYR* 3.8 16.2 - - + -
269C ILE* 5.1 1.3 - - + -
273C LEU* 5.4 0.4 - - + -
274C MET* 4.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 3.6 18.1 - - + +
51C LEU* 3.4 16.8 - - - +
52C ASP* 2.9 40.8 + - - -
87C SER* 3.7 7.9 + - - -
90C SER* 2.9 46.3 + - - -
91C GLN* 3.6 26.6 - - - +
94C ALA* 3.8 5.2 - - + -
124C LEU* 3.0 19.2 + - - +
125C GLY 3.7 3.8 - - - +
127C ILE* 1.3 76.8 - - - +
129C ALA* 1.3 59.2 + - - +
130C GLY 3.2 3.4 + - - -
205C HIS* 3.5 19.4 + - - +
207C CYS* 3.9 19.3 - - - +
208C VAL* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ALA* 4.4 9.6 - - + +
98C SER* 4.1 22.7 - - - -
103C LEU 5.4 0.2 - - - +
105C ARG* 4.1 8.8 + - - +
125C GLY 3.0 18.0 + - - +
128C ARG* 1.3 75.2 - - - +
130C GLY* 1.3 62.2 + - - +
131C LEU* 3.5 31.0 + - + +
205C HIS* 3.9 8.3 - - - +
208C VAL* 3.7 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 3.6 6.9 - - - +
106C GLY* 3.0 25.6 + - - -
126C CYS 2.9 3.0 + - - -
127C ILE 3.5 2.6 + - - -
128C ARG 3.2 5.1 + - - -
129C ALA* 1.3 79.3 - - - +
131C LEU* 1.3 58.2 - - - +
132C ILE* 4.1 1.6 + - - +
208C VAL* 4.4 6.7 - - - -
210C THR* 4.2 12.1 - - - -
214C GLU* 4.9 2.0 - - - +
215C ALA 5.2 0.9 - - - +
235C TYR* 3.2 24.0 + - - -
----------------------------------------------------------
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