Contacts of the helix formed by residues 198 - 210 (chain Y) in PDB entry 1GNG
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 ASP 198 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Y PRO* 1.4 69.3 - - - +
200Y HIS* 3.0 33.4 + - - +
201Y ARG* 3.2 48.9 + - - +
202Y LEU* 3.5 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 199 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B SER* 3.5 33.7 - - - +
262B GLY* 4.6 6.9 + - - -
263B VAL* 3.9 7.8 - - + +
198Y ASP* 1.4 85.8 - - - +
200Y HIS* 1.3 57.8 + - - +
202Y LEU* 3.6 26.5 - - + -
203Y LEU* 3.4 21.0 + - - +
219Y ARG* 5.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 200 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PTR 4.2 50.0 + + + +
198Y ASP* 3.0 20.5 + - - +
199Y PRO* 1.3 77.9 - - - +
201Y ARG* 1.3 66.8 + - + +
202Y LEU 3.2 0.7 - - - -
203Y LEU* 3.3 8.6 + - + +
204Y GLN* 3.2 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Y ASP* 3.2 43.7 + - - +
200Y HIS* 1.3 76.7 - - + +
202Y LEU* 1.3 56.8 + - - +
204Y GLN* 2.9 20.6 + - - +
205Y GLN* 2.7 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 4.3 3.4 - - + -
198Y ASP 3.5 6.7 + - - +
199Y PRO* 3.6 27.6 - - + -
201Y ARG* 1.3 77.7 - - - +
203Y LEU* 1.3 57.2 + - - +
205Y GLN* 3.1 9.3 + - + +
206Y LEU* 2.8 56.8 + - + +
215Y GLU* 6.0 1.1 - - + -
219Y ARG* 3.2 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PTR 5.4 13.9 - - + -
223B ARG* 5.9 1.6 - - - +
227B LEU 5.7 0.7 - - - +
228B ILE* 3.8 31.0 - - + +
262B GLY* 4.3 20.6 - - - +
263B VAL* 4.1 15.7 - - + -
199Y PRO 3.4 13.8 + - - +
200Y HIS* 3.3 13.6 + - + +
201Y ARG 3.1 0.4 - - - -
202Y LEU* 1.3 79.4 - - - +
204Y GLN* 1.3 66.0 + - + +
206Y LEU* 3.1 4.9 + - - +
207Y VAL* 2.9 33.9 + - + +
212Y LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200Y HIS* 3.2 29.8 + - + +
201Y ARG* 2.9 26.7 + - - +
203Y LEU* 1.3 79.8 - - + +
205Y GLN* 1.3 57.4 + - - +
207Y VAL* 3.6 7.2 + - - +
208Y LEU* 3.1 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201Y ARG* 2.7 18.5 + - + +
202Y LEU* 3.4 13.9 - - + +
204Y GLN* 1.3 71.8 - - - +
206Y LEU* 1.3 58.9 - - + +
208Y LEU* 3.0 17.6 + - - +
209Y SER* 2.6 48.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 3.9 29.6 - - + -
202Y LEU* 2.8 40.6 + - + +
203Y LEU* 3.6 3.8 - - - +
205Y GLN* 1.3 74.1 - - + +
207Y VAL* 1.3 57.4 + - - +
209Y SER* 3.4 5.6 - - - +
210Y GLY* 2.9 7.4 + - - -
211Y ASN* 2.8 47.6 + - + +
212Y LEU* 3.4 22.5 + - + +
215Y GLU* 3.9 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE 3.8 20.4 - - - +
229B PHE 3.3 27.8 - - - +
230B GLY* 4.3 6.1 - - - +
285B ASN* 5.1 1.6 - - - +
288B TYR* 3.1 36.2 - - + -
203Y LEU* 2.9 33.8 + - + +
204Y GLN* 3.7 8.1 - - - +
206Y LEU* 1.3 77.6 - - - +
208Y LEU* 1.3 64.8 - - + +
210Y GLY* 3.4 2.4 + - - -
212Y LEU* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204Y GLN* 3.1 31.1 + - + +
205Y GLN* 3.0 21.0 + - - +
207Y VAL* 1.3 79.0 - - + +
209Y SER* 1.3 64.5 + - - +
210Y GLY* 3.1 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B THR 4.8 0.3 - - - +
291B PHE* 6.0 1.9 - - - -
205Y GLN* 2.6 36.1 + - - -
206Y LEU* 3.2 12.8 + - - +
208Y LEU* 1.3 73.7 - - - +
210Y GLY* 1.3 62.2 + - - +
211Y ASN* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 3.5 13.5 - - - -
289B THR 3.4 20.8 - - - +
290B GLU* 3.2 21.5 - - - +
291B PHE* 5.1 1.2 + - - -
206Y LEU 2.9 8.1 + - - -
207Y VAL 3.4 6.7 + - - -
208Y LEU 3.1 4.4 - - - -
209Y SER* 1.3 80.2 - - - +
211Y ASN* 1.3 61.8 + - - +
214Y LYS* 3.2 5.5 + - - -
----------------------------------------------------------
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