Contacts of the helix formed by residues 197 - 207 (chain L) in PDB entry 1H2I
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 GLU 197 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L LYS* 2.7 29.8 + - - +
195L ASP 3.4 8.7 + - - +
196L LEU* 1.3 82.1 - - - +
198L PRO* 1.3 60.3 - - - +
199L SER* 3.3 6.7 + - - -
200L VAL* 3.0 19.1 + - + +
201L GLU* 2.7 33.4 + - - +
42M ALA* 3.6 19.8 - - - +
45M GLN* 3.4 19.5 + - - +
77M GLU* 4.6 13.3 + - - +
78M MET* 4.0 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L GLN* 6.0 0.9 - - - +
196L LEU* 3.3 22.4 - - + +
197L GLU* 1.3 90.5 - - - +
199L SER* 1.3 60.8 + - - +
201L GLU* 3.3 7.5 + - + +
202L GLU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L GLU* 3.3 4.4 + - - -
198L PRO* 1.3 78.2 - - - +
200L VAL* 1.3 65.5 + - - +
202L GLU* 3.4 16.7 + - - +
203L ALA* 3.1 23.9 + - - +
34M GLU* 5.1 0.5 - - - +
38M ALA* 3.9 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L GLU* 3.0 17.8 + - + +
199L SER* 1.3 79.0 + - - +
201L GLU* 1.3 58.5 + - - +
203L ALA* 3.7 1.4 - - - +
204L ARG* 2.8 58.0 + - - +
35M GLU* 4.6 1.7 - - + +
38M ALA* 3.4 40.8 - - + +
39M ILE* 3.6 16.2 - - + +
42M ALA* 4.0 13.5 - - + -
77M GLU 4.5 1.3 - - - +
78M MET* 3.4 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L LEU* 5.1 8.3 - - + -
197L GLU 2.7 15.2 + - - +
198L PRO* 3.7 9.0 - - + +
199L SER 3.2 0.2 - - - -
200L VAL* 1.3 77.9 - - - +
202L GLU* 1.3 59.5 - - - +
204L ARG* 3.6 11.5 + - - +
205L TYR* 2.8 32.5 + - + +
77M GLU* 5.8 0.6 - - - +
36N TYR* 2.7 38.7 + - - -
37N GLN* 4.4 15.1 - - - +
40N GLN* 4.4 10.4 - - - +
41N LYS* 5.4 2.6 - - - +
44N ARG* 4.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198L PRO 2.9 21.6 + - - +
199L SER* 3.5 16.2 - - - +
200L VAL 3.2 0.2 - - - -
201L GLU* 1.3 74.9 - - - +
203L ALA* 1.3 66.8 + - - +
205L TYR* 3.0 9.0 + - - +
206L ASN* 2.9 36.8 + - - +
34M GLU* 4.7 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L SER 3.1 13.7 + - - +
200L VAL 3.8 2.7 - - - +
202L GLU* 1.3 81.3 - - - +
204L ARG* 1.3 62.5 + - - +
206L ASN* 3.2 12.2 + - - +
207L SER* 3.4 12.3 + - - -
32M THR* 4.8 2.1 + - - -
34M GLU* 3.7 31.2 - - + +
35M GLU* 3.6 34.3 - - - +
38M ALA* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200L VAL* 2.8 32.4 + - - +
201L GLU* 3.6 14.3 + - - +
203L ALA* 1.3 73.1 - - - +
205L TYR* 1.3 62.2 + - - +
207L SER* 2.5 23.6 + - - -
208L CYS* 4.0 6.6 - - - -
35M GLU* 2.7 49.4 + - - +
39M ILE* 4.1 0.8 - - - +
77M GLU 2.8 29.3 + - - -
78M MET 3.2 19.0 + - - -
79M PHE* 3.5 21.8 - - - +
80M GLY* 3.6 6.3 - - - +
82M ASN* 4.8 1.6 - - - +
116M LYS* 4.2 10.3 - - - +
36N TYR* 2.7 43.3 + - + +
40N GLN* 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L GLU* 2.8 25.0 + - + +
202L GLU* 3.3 6.3 - - - +
204L ARG* 1.3 79.0 - - - +
206L ASN* 1.3 72.0 + - - +
207L SER 3.2 1.2 + - - -
208L CYS* 3.6 12.5 + - - -
209L ARG* 3.1 34.8 + - - -
33N ALA* 3.5 40.7 - - + +
34N GLU* 4.5 7.3 + - - +
36N TYR* 4.6 10.3 - + - -
37N GLN* 3.1 40.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202L GLU* 2.9 27.7 + - - +
203L ALA 3.2 5.3 + - - +
205L TYR* 1.3 84.5 - - - +
207L SER* 1.3 59.7 + - - +
208L CYS 3.3 1.2 + - - -
209L ARG* 3.7 40.2 + - - +
34M GLU* 3.8 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ALA 3.4 8.1 + - - -
204L ARG* 2.5 24.9 + - - +
205L TYR 3.2 0.2 - - - -
206L ASN* 1.3 75.1 - - - +
208L CYS* 1.3 61.5 + - - +
209L ARG 3.3 11.2 + - - +
32M THR* 3.8 30.6 - - - +
35M GLU* 3.9 13.2 + - - -
116M LYS* 4.7 5.3 + - - -
30N GLN* 5.3 2.9 - - - +
----------------------------------------------------------
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