Contacts of the helix formed by residues 202 - 212 (chain A) in PDB entry 3V30
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 HIS 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER 3.5 7.2 - - - -
166A THR 2.9 28.9 + - - -
167A GLY* 3.8 14.8 - - - -
168A GLY* 3.3 26.7 + - - +
196A TYR 4.4 0.2 - - - -
197A ALA* 2.9 14.4 + - - +
200A GLY* 3.4 32.3 + - - -
201A ASN* 1.3 74.4 + - - +
203A VAL* 1.3 64.9 + - - +
204A LYS 3.4 2.7 - - - -
205A CYS* 3.2 8.9 + - + +
206A VAL* 2.9 26.0 + - - +
238A VAL* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASN* 3.1 10.8 + - - +
202A HIS* 1.3 71.7 - - - +
204A LYS* 1.3 62.4 + - + +
206A VAL* 3.3 6.0 + - - +
207A GLU* 2.9 35.9 + - - +
237A LYS* 3.7 40.8 - - + -
238A VAL* 3.7 26.0 - - + +
241A VAL* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 3.5 20.9 - - + +
202A HIS 3.4 0.6 - - - -
203A VAL* 1.3 79.5 - - + +
205A CYS* 1.3 57.0 + - - +
207A GLU* 3.3 18.9 + - - +
208A ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER* 4.0 20.2 - - - -
168A GLY* 4.2 7.8 + - - -
170A THR* 3.2 24.3 + - - +
173A VAL* 3.5 35.7 - - - -
197A ALA* 4.1 9.0 - - + -
202A HIS* 3.2 22.4 + - + +
204A LYS* 1.3 73.7 - - - +
206A VAL* 1.3 64.2 + - - +
208A ALA* 3.2 1.4 + - - +
209A LEU* 3.0 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.1 13.7 - - + -
197A ALA* 3.7 9.4 - - + +
198A VAL* 3.7 37.0 - - + +
202A HIS 2.9 19.6 + - - +
203A VAL* 3.5 9.2 - - - +
205A CYS* 1.3 75.5 - - - +
207A GLU* 1.3 63.2 + - - +
209A LEU* 3.3 2.8 + - - +
210A LEU* 2.9 43.6 + - + +
238A VAL* 4.3 12.3 - - + -
241A VAL* 3.9 10.5 - - + -
242A ILE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 2.9 18.7 + - - +
204A LYS* 3.4 26.7 - - - +
206A VAL* 1.3 77.7 - - - +
208A ALA* 1.3 56.4 + - - +
210A LEU* 3.4 3.1 + - - +
211A ALA* 2.9 29.9 + - - +
237A LYS* 5.6 3.0 + - - -
241A VAL* 3.3 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 3.8 20.6 - - + +
173A VAL* 4.9 9.2 - - + -
177A LEU* 5.5 0.7 - - - -
204A LYS 3.0 17.2 + - - +
205A CYS* 3.7 4.7 - - - +
207A GLU* 1.3 74.0 - - - +
209A LEU* 1.3 65.7 + - - +
211A ALA* 3.3 7.6 + - - +
212A ARG* 3.2 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.6 2.5 - - + -
165A SER* 3.9 9.9 - - - +
173A VAL* 3.9 23.1 - - + -
177A LEU* 3.9 4.5 - - + -
183A ILE* 3.5 30.8 - - + +
193A PRO* 3.6 42.8 - - + +
194A LEU* 3.8 12.8 - - + +
197A ALA* 3.9 9.9 - - + -
205A CYS* 3.0 22.6 + - - +
206A VAL 3.7 3.6 - - - +
208A ALA* 1.3 77.2 - - - +
210A LEU* 1.3 58.5 + - - +
212A ARG* 3.3 7.2 + - - -
213A GLY 3.3 0.3 + - - -
214A ALA* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.9 21.1 - - + -
206A VAL* 2.9 35.8 + - + +
207A GLU* 3.9 3.4 - - - +
209A LEU* 1.3 74.8 - - - +
211A ALA* 1.3 60.0 + - - +
213A GLY* 2.9 16.3 + - - -
214A ALA 4.0 10.1 - - - +
216A LEU* 3.7 27.4 - - + -
241A VAL* 4.1 7.4 - - + -
242A ILE* 4.0 20.4 - - + -
245A HIS* 3.0 57.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU 2.9 18.5 + - - +
208A ALA* 3.3 8.7 + - - +
210A LEU* 1.3 75.2 - - - +
212A ARG* 1.3 61.6 + - + +
213A GLY 3.3 0.6 + - - -
245A HIS* 5.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY* 3.4 39.8 + - - +
177A LEU* 3.3 34.0 - - + +
178A GLU* 3.1 28.3 + - - +
183A ILE* 3.7 20.8 - - + +
208A ALA* 3.2 29.5 + - - +
210A LEU 3.1 0.8 - - - -
211A ALA* 1.3 82.1 - - + +
213A GLY* 1.3 57.6 + - - +
214A ALA 3.6 1.6 - - - -
----------------------------------------------------------
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