Contacts of the helix formed by residues 190 - 204 (chain A) in PDB entry 1I73
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 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 3.4 9.7 + - - -
184A ASN* 3.5 21.6 + - - +
185A THR 3.0 24.5 + - - +
187A ALA 3.8 0.8 + - - -
189A TYR* 1.3 68.2 - - - +
191A LEU* 1.3 66.3 + - - +
192A PHE* 3.2 14.8 + - - +
193A LEU* 3.0 38.4 + - + +
194A VAL* 3.2 23.8 + - - +
219A TYR* 3.0 20.4 + - - +
221A PHE* 4.1 1.1 - - + -
224A THR* 3.8 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 5.0 0.9 - - + -
104A LEU* 3.9 24.7 - - + -
109A VAL* 4.1 15.5 - - + +
112A ALA* 3.9 20.2 - - + -
113A ILE* 4.8 6.5 - - + -
142A PHE* 4.1 28.5 - - + -
176A PHE* 3.9 30.5 - - + -
182A TRP* 3.8 23.8 - - + -
183A THR 2.9 15.8 + - - +
189A TYR 3.3 2.6 + - - -
190A ASN* 1.3 68.9 - - - +
192A PHE* 1.3 57.7 + - - +
194A VAL 3.2 0.3 + - - -
195A ALA* 2.7 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 3.6 38.5 - - + +
115A ASP* 3.6 21.5 - - + -
116A ALA* 3.6 21.9 - - - +
119A LEU* 3.7 25.4 - - + -
183A THR 4.7 0.8 + - - -
184A ASN* 6.4 2.2 - - + -
190A ASN* 3.2 7.5 + - - +
191A LEU* 1.3 77.3 - - - +
193A LEU* 1.3 74.0 + - + +
195A ALA* 3.8 1.4 - - - +
196A ALA* 2.9 29.6 + - + +
224A THR* 3.7 28.5 - - + -
227A TYR* 3.8 27.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASN* 3.0 24.3 + - + +
191A LEU 3.2 0.2 - - - -
192A PHE* 1.3 90.7 - - + +
194A VAL* 1.3 62.9 + - - +
196A ALA* 3.4 4.0 + - + +
197A HIS* 3.1 22.3 + - - +
214A LEU* 3.8 12.6 - - + +
219A TYR* 4.4 10.5 - - + +
220A ALA 4.1 6.1 - - - +
221A PHE* 3.8 20.4 - - + -
222A ARG* 3.6 36.8 - - + +
224A THR* 3.9 8.1 - - + -
227A TYR* 3.9 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.1 16.2 - - + -
161A ALA* 3.7 29.8 - - + -
176A PHE* 4.0 6.3 - - + -
182A TRP* 3.8 26.2 - - + -
189A TYR* 4.5 1.3 - - + -
190A ASN 3.2 16.4 + - - +
191A LEU 3.9 0.4 - - - +
193A LEU* 1.3 76.9 - - - +
195A ALA* 1.3 65.2 + - - +
197A HIS* 3.3 7.3 + - + +
198A GLU* 2.9 26.4 + - - +
219A TYR* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 4.9 0.4 - - - +
113A ILE* 3.8 22.2 - - + -
116A ALA* 3.9 11.7 - - + -
176A PHE* 3.6 28.4 - - + -
191A LEU 2.7 22.0 + - - +
192A PHE* 3.8 4.0 - - - +
194A VAL* 1.3 75.6 - - - +
196A ALA* 1.3 56.2 + - - +
198A GLU* 3.2 0.6 + - - +
199A PHE* 2.9 39.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 3.5 12.9 - - + +
119A LEU* 3.6 32.3 - - + -
120A TRP* 2.9 28.9 + - - +
192A PHE* 2.9 20.0 + - + +
193A LEU* 3.7 6.7 - - + +
195A ALA* 1.3 74.7 - - - +
197A HIS* 1.3 63.0 + - - +
199A PHE* 4.7 0.2 - - - -
200A GLY 3.3 6.1 + - - -
214A LEU* 3.6 13.5 - - + -
227A TYR* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU 3.1 13.4 + - - +
194A VAL* 3.5 9.6 - - + +
196A ALA* 1.3 74.0 - - - +
198A GLU* 1.3 84.5 + - - +
200A GLY 3.0 9.7 + - - -
201A HIS* 3.3 1.8 + - - -
207A HIS* 3.6 9.6 - + - -
214A LEU* 2.8 29.9 + - + +
215A MET* 3.4 34.5 - - + +
216A TYR 3.1 24.1 + - - -
217A PRO* 4.5 4.4 + - + -
999A ZN 2.0 37.0 - - - -
3B PAT 3.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 5.9 0.3 - - - +
161A ALA* 3.5 30.9 - - + +
162A HIS* 3.3 20.4 - - - +
163A ALA* 3.4 14.5 + - + +
174A ALA* 4.4 11.4 - - + -
176A PHE* 4.3 6.3 - - + -
194A VAL* 2.9 25.9 + - + +
195A ALA 3.2 4.4 + - - +
197A HIS* 1.3 84.3 - - - +
199A PHE* 1.3 59.6 + - - +
201A HIS* 2.9 22.6 + - - +
202A SER 3.0 9.4 + - - -
2B LEU 3.5 0.7 - - - +
3B PAT 2.5 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.9 17.0 - - + -
116A ALA* 3.8 26.9 - - + -
117A PHE* 3.5 59.9 - + + -
120A TRP* 4.0 13.0 - - + +
138A ILE* 4.5 1.8 - - + -
140A ILE* 3.7 17.9 - - + -
174A ALA* 3.8 21.5 - - + -
176A PHE* 4.6 3.8 - + - -
195A ALA* 2.9 25.9 + - + +
196A ALA 3.9 4.5 - - - +
197A HIS 3.2 0.4 - - - -
198A GLU* 1.3 74.5 - - - +
200A GLY* 1.3 66.7 + - - +
202A SER* 3.3 15.9 - - - -
203A LEU* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TRP* 3.5 29.3 - - - +
196A ALA 3.3 6.9 + - - -
197A HIS 3.0 9.0 + - - -
199A PHE* 1.3 77.0 - - - +
201A HIS* 1.3 59.7 + - - +
203A LEU* 3.2 5.4 + - - +
204A GLY 3.1 5.7 + - - -
205A LEU* 2.9 31.3 + - - +
215A MET* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 5.3 0.5 + - - -
163A ALA* 4.0 15.7 - - + +
164A PHE 4.3 1.8 - - - -
165A GLN* 3.7 15.1 - - - +
197A HIS* 3.3 10.5 + + - -
198A GLU* 2.9 13.2 + - - +
200A GLY* 1.3 77.1 - - - +
202A SER* 1.3 62.0 + - - +
204A GLY* 3.0 14.6 + - - -
205A LEU 2.8 25.5 + - - +
206A ALA 4.2 1.8 - - - -
207A HIS* 3.1 10.7 + + - -
215A MET* 3.3 16.0 - - + +
999A ZN 2.1 31.0 - - - -
2B LEU* 3.3 38.0 - - + +
3B PAT 3.1 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 2.9 23.7 + - - -
138A ILE* 4.2 15.2 - - - +
163A ALA* 3.7 9.6 - - - +
164A PHE 3.5 12.1 + - - -
166A PRO* 3.3 12.0 - - - +
172A GLY* 2.8 24.6 + - - -
174A ALA* 4.3 1.0 - - - +
198A GLU 3.0 11.9 + - - -
199A PHE* 3.1 25.0 + - - -
201A HIS* 1.3 76.6 - - - +
203A LEU* 1.3 57.0 + - - +
204A GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO 4.3 1.0 - - - +
88A TRP* 4.0 18.8 - - + +
93A LEU* 4.0 7.4 - - + -
117A PHE* 5.8 0.4 - - + -
120A TRP* 3.8 37.5 - - + -
126A LEU* 3.6 31.2 - - + -
128A PHE* 3.9 18.6 - - + -
138A ILE* 4.7 5.2 - - + -
166A PRO* 3.5 7.9 - - - +
199A PHE* 2.9 21.8 + - + +
200A GLY* 3.7 5.2 - - - +
201A HIS 3.0 0.4 - - - -
202A SER* 1.3 76.5 - - - +
204A GLY* 1.3 58.5 + - - +
205A LEU* 3.7 1.8 - - + -
237A ILE* 4.7 5.8 - - + -
240A ILE* 4.1 3.4 - - - +
241A TYR* 2.7 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.2 0.2 - - - +
82A THR* 3.0 31.2 + - - -
85A ASN* 5.7 0.5 - - - -
86A PRO* 3.7 12.6 - - - +
165A GLN* 5.4 0.4 - - - -
166A PRO* 3.6 17.5 - - - +
201A HIS 3.0 7.8 + - - -
202A SER 3.4 0.4 - - - -
203A LEU* 1.3 80.4 - - - +
205A LEU* 1.3 61.0 + - - +
240A ILE* 3.6 15.0 - - - +
----------------------------------------------------------
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