Contacts of the helix formed by residues 202 - 215 (chain C) in PDB entry 3EVK
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 ASN 202 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.1 27.6 - - - +
96C ASN 2.6 15.4 + - - +
97C MET 3.6 12.8 - - - +
98C ALA* 3.8 11.8 - - + +
102C LYS* 3.7 34.2 + - - +
200C VAL 3.2 1.8 + - - -
201C VAL* 1.3 71.3 - - - +
203C TRP* 1.3 62.2 + - - +
204C ASP* 3.4 21.2 - - - +
205C ASP* 3.0 23.2 + - - +
206C VAL* 3.3 13.0 + - - +
208C ARG* 4.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS 4.7 3.4 + - - -
104C GLY 3.5 21.7 + - - -
105C GLY 3.1 19.2 + - - -
106C LYS 4.1 2.9 - - - +
107C PRO* 3.6 39.7 - - + -
108C GLY 5.2 1.6 - - - +
111C ILE* 4.2 13.3 - - + +
115C ILE* 4.3 4.5 - - + -
122C PHE* 3.6 32.1 - + - -
125C PHE* 4.1 10.5 - + - -
144C LEU* 5.8 0.4 - - + -
173C LEU* 4.0 23.1 - - + -
198C TRP* 4.0 10.4 + + - -
201C VAL* 3.2 26.7 + - + +
202C ASN* 1.3 70.5 - - - +
204C ASP* 1.3 62.7 + - - +
205C ASP 3.3 0.2 - - - -
206C VAL* 3.4 30.4 + - + +
207C GLU* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 4.9 15.9 + - - +
202C ASN* 3.2 12.0 + - - +
203C TRP* 1.3 79.8 - - - +
205C ASP* 1.3 57.4 + - - +
207C GLU* 3.2 7.8 + - - +
208C ARG* 2.9 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.2 35.1 - - - +
96C ASN* 2.7 28.5 + - - -
202C ASN* 3.0 16.4 + - - +
204C ASP* 1.3 78.4 - - - +
206C VAL* 1.3 61.0 + - - +
208C ARG* 3.2 25.9 + - - +
209C ARG* 2.8 54.8 + - - +
222C LEU* 5.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN* 4.3 4.9 - - - +
111C ILE* 3.8 30.1 - - + -
144C LEU* 4.9 1.3 - - + -
172C LEU* 3.8 34.9 - - + +
173C LEU* 3.9 26.5 - - + -
201C VAL* 4.5 0.2 - - + -
202C ASN 3.3 15.4 + - - +
203C TRP* 3.7 27.1 - - + +
204C ASP 3.3 0.2 - - - -
205C ASP* 1.3 75.4 - - - +
207C GLU* 1.3 58.3 + - - +
209C ARG* 3.4 3.1 + - - +
210C LEU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLY 4.7 0.9 - - - -
109C GLY* 4.0 6.8 - - - -
110C LYS* 3.1 24.1 + - - +
111C ILE* 2.9 37.5 + - + +
203C TRP 2.8 18.3 + - - +
204C ASP* 3.2 8.5 + - - +
206C VAL* 1.3 76.5 - - - +
208C ARG* 1.3 58.0 + - + +
210C LEU* 3.3 4.3 + - - +
211C GLN* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 5.7 1.4 - - - +
102C LYS* 5.6 6.7 - - - +
202C ASN* 4.6 5.3 + - - -
204C ASP* 2.9 45.1 + - + +
205C ASP* 3.2 35.7 + - - +
207C GLU* 1.3 77.9 - - + +
209C ARG* 1.3 62.8 + - - +
211C GLN* 3.4 8.8 + - - +
212C LYS* 3.4 24.8 + - - +
222C LEU* 3.2 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER 4.8 0.6 + - - -
92C ILE* 4.0 24.5 - - - +
95C PRO* 3.6 20.4 - - - +
96C ASN* 3.9 4.0 - - - +
171C VAL 3.7 13.4 + - - +
172C LEU* 3.5 34.5 - - + -
205C ASP* 2.8 44.6 + - - +
206C VAL 3.7 4.5 - - - +
208C ARG* 1.3 74.1 - - - +
210C LEU* 1.3 64.9 + - - +
212C LYS* 3.3 3.0 + - - -
213C ALA* 3.1 18.5 + - - +
219C ALA* 3.2 36.5 + - - +
220C LEU* 3.1 29.3 + - - +
222C LEU 4.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS* 3.7 16.4 - - + +
111C ILE* 3.5 44.6 - - + +
114C LEU* 4.2 9.6 - - + -
146C TYR* 4.2 11.4 - - + -
153C LEU* 4.2 12.3 - - + -
172C LEU* 3.7 30.4 - - + +
206C VAL 2.9 16.9 + - - +
207C GLU* 3.7 5.4 - - - +
209C ARG* 1.3 76.3 - - - +
211C GLN* 1.3 57.6 + - - +
213C ALA* 3.1 1.0 + - - -
214C LEU* 2.8 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS* 3.0 43.4 - - - +
207C GLU* 2.9 35.9 + - + +
208C ARG* 3.6 10.3 - - - +
209C ARG 3.3 0.2 - - - -
210C LEU* 1.3 78.0 - - - +
212C LYS* 1.3 63.6 + - + +
214C LEU* 3.7 10.6 + - - +
215C ASN* 3.7 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLY* 4.8 5.7 + - - -
208C ARG 3.4 12.3 + - - +
209C ARG* 3.3 7.4 + - - +
210C LEU 3.3 0.4 - - - -
211C GLN* 1.3 75.8 - - + +
213C ALA* 1.3 66.2 + - - +
215C ASN* 3.1 9.5 + - - -
217C GLN* 3.0 54.0 + - + +
218C ILE* 2.7 27.2 + - - +
219C ALA* 3.9 15.0 - - + +
221C LYS* 4.9 12.1 + - - +
222C LEU* 3.7 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 5.5 1.1 - - - +
146C TYR* 3.3 49.7 - - + -
170C GLN* 4.3 11.9 - - + -
172C LEU* 4.1 9.6 - - + -
209C ARG 3.1 16.4 + - - +
210C LEU* 3.7 4.0 - - - +
212C LYS* 1.3 76.4 - - - +
214C LEU* 1.3 58.0 + - - +
216C GLY* 2.9 19.6 + - - -
217C GLN 3.5 11.2 + - - +
219C ALA* 4.2 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS* 4.3 28.9 - - + -
114C LEU* 4.4 22.7 - - + -
146C TYR* 3.9 30.7 + - + +
151C GLU* 5.9 1.6 - - - -
210C LEU* 2.8 46.8 + - + +
211C GLN* 3.9 11.2 - - - +
212C LYS 3.2 0.2 - - - -
213C ALA* 1.3 77.2 - - - +
215C ASN* 1.3 54.6 + - - +
216C GLY 3.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 5.8 1.7 + - - +
211C GLN 3.7 8.1 + - - +
212C LYS 3.1 6.1 + - - +
214C LEU* 1.3 75.7 - - - +
216C GLY* 1.3 61.5 + - - +
217C GLN* 2.7 32.1 + - - +
----------------------------------------------------------
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