Contacts of the helix formed by residues 157 - 173 (chain A) in PDB entry 1M1I
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 PRO 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS 4.2 3.1 - - - +
156A VAL* 1.3 97.5 - - + +
158A PRO* 1.3 68.7 - - + +
159A LYS* 4.2 12.6 - - + +
160A VAL* 3.1 26.2 + - + +
161A SER* 2.9 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 5.6 6.1 - - - +
156A VAL 3.6 3.1 - - - +
157A PRO* 1.3 82.4 - - + +
159A LYS* 1.3 63.0 + - + +
161A SER* 2.6 29.4 + - - +
162A HIS* 2.7 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 4.3 9.2 - - + -
158A PRO* 1.3 80.6 - - + +
160A VAL* 1.3 69.7 + - + +
162A HIS* 3.5 13.7 - - - +
163A ILE* 2.9 28.6 + - + +
207A SER 3.5 21.1 - - - +
208A GLY* 4.2 16.0 + - - +
209A ASP* 2.7 26.3 + - - +
214A ASN* 4.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.8 9.0 - - + -
156A VAL* 3.1 25.6 - - + -
157A PRO* 3.1 28.3 + - + +
159A LYS* 1.3 79.3 - - + +
161A SER* 1.3 62.0 + - - +
162A HIS 3.2 0.2 - - - -
163A ILE* 2.9 39.2 - - + +
164A THR* 3.0 17.6 + - + +
205A ALA* 5.8 1.3 - - + -
206A THR 4.6 5.6 - - - +
207A SER* 3.7 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 4.5 9.2 + - - -
33A HIS* 2.9 29.4 + - - -
147A ILE* 5.5 0.2 - - - -
148A THR 5.9 0.4 - - - -
149A VAL* 4.0 31.6 - - - -
156A VAL* 4.0 3.3 - - - +
157A PRO 2.9 12.6 + - - -
158A PRO* 2.6 25.3 + - - +
160A VAL* 1.3 75.0 - - - +
162A HIS* 1.3 63.5 + - - +
164A THR* 2.6 27.4 + - - -
165A PHE 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 5.9 2.4 + - - -
32A SER* 4.4 2.2 - - - -
33A HIS* 3.6 36.1 + + + -
36A ALA* 3.3 34.7 - - + +
37A ILE* 4.6 6.2 - - + +
40A ILE* 5.5 8.8 - - + +
158A PRO* 2.7 39.2 + - - +
159A LYS* 3.5 12.3 - - - +
161A SER* 1.3 85.2 + - - +
163A ILE* 1.3 56.6 + - + +
165A PHE* 3.5 2.4 + - - +
166A ALA* 3.0 29.6 + - - +
214A ASN* 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 6.2 0.7 - - - -
159A LYS 2.9 19.3 - - - +
160A VAL* 2.9 29.7 + - + +
162A HIS* 1.3 79.1 - - + +
164A THR* 1.3 70.6 + - + +
166A ALA* 3.7 6.3 - - - +
167A HIS* 2.9 34.5 + - + +
200A ILE* 5.1 10.3 - - + +
205A ALA* 4.8 9.0 - - + -
206A THR* 4.1 38.4 - - + +
208A GLY* 4.7 15.0 - - - +
213A ASN 5.2 0.9 - - - +
214A ASN* 3.6 23.1 - - - +
243B VAL* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.9 45.8 - - + -
113A GLY* 6.0 0.4 - - - -
147A ILE* 3.0 29.9 - - + +
148A THR 4.8 2.0 - - - +
156A VAL* 5.4 1.1 - - + -
160A VAL* 3.0 22.3 + - + +
161A SER* 2.6 22.2 + - - -
163A ILE* 1.3 81.2 - - + +
165A PHE* 1.3 61.8 + - - +
167A HIS* 3.2 7.7 + - - +
168A GLU* 2.9 29.6 + - - +
243B VAL* 4.7 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.9 9.0 - - + -
33A HIS* 2.8 25.1 - + + +
34A VAL* 5.2 1.3 - - + -
37A ILE* 3.2 48.5 - - + -
54A PHE* 3.7 20.4 - + - -
100A TYR* 3.6 22.7 - + + -
102A PHE* 3.4 20.6 - + - -
147A ILE* 3.1 32.5 - - + -
161A SER 3.2 0.6 + - - -
162A HIS 3.7 1.1 - - - +
164A THR* 1.3 79.7 + - - +
166A ALA* 1.3 53.2 - - - +
168A GLU* 3.1 2.1 + - - +
169A VAL* 2.8 68.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 5.0 4.3 - - + -
40A ILE* 4.6 18.8 - - + -
41A TYR* 2.8 32.9 + - + -
162A HIS 3.0 15.6 + - - +
163A ILE* 3.7 8.1 - - - +
165A PHE* 1.3 80.2 - - - +
167A HIS* 1.3 56.5 + - - +
169A VAL* 3.4 8.3 - - - -
170A GLY* 2.9 11.3 + - - -
200A ILE* 4.7 16.8 - - + -
216A PHE* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ZN 2.0 37.0 - - - -
163A ILE* 2.9 16.6 + - + +
164A THR 3.2 9.6 - - - +
166A ALA* 1.3 77.2 - - - +
168A GLU* 1.3 63.9 + - - +
170A GLY 3.1 12.3 + - - -
171A HIS* 3.1 12.4 + - - -
177A HIS* 3.8 2.7 - + - -
200A ILE* 2.7 26.4 + - - +
201A MET* 3.2 36.1 - - + +
202A TYR 3.3 24.3 + - - -
242B ALA 3.1 1.1 + - - -
243B VAL* 2.5 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 5.0 5.2 - - + -
113A GLY* 3.3 7.3 - - - +
114A LEU* 2.9 39.7 + - - +
115A ALA* 2.8 22.6 - - + +
146A ILE 3.3 19.3 - - - +
147A ILE* 4.5 6.1 - - + -
164A THR 2.9 18.0 + - - +
165A PHE 3.8 2.9 - - - +
167A HIS* 1.3 74.0 - - - +
169A VAL* 1.3 65.7 + - - +
171A HIS* 2.9 26.8 + - - +
172A ASN* 3.2 4.3 + - - -
241B GLY 2.2 31.7 - - - +
242B ALA* 3.7 6.6 - - - -
243B VAL* 3.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.2 1.1 - - + -
41A TYR* 2.8 39.9 - - + +
54A PHE* 5.6 0.9 - - + -
100A TYR* 3.0 35.0 - - + +
165A PHE* 2.8 62.7 + - + +
166A ALA* 3.1 9.2 - - - +
168A GLU* 1.3 75.9 - - + +
170A GLY* 1.3 50.9 + - - +
172A ASN* 3.0 2.4 + - - +
173A PHE* 2.8 44.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 2.9 18.5 + - - -
166A ALA 2.9 7.7 + - - -
167A HIS 3.1 7.3 + - - -
169A VAL* 1.3 75.8 - - - +
171A HIS* 1.3 58.1 + - - +
173A PHE* 3.3 7.9 + - - +
174A GLY 3.1 6.6 + - - -
175A SER* 2.9 30.4 + - - -
201A MET* 4.0 9.0 - - - -
216A PHE* 4.0 8.7 - - - -
224A ILE* 3.8 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ZN 2.0 34.7 - - - -
115A ALA* 3.9 3.8 - - + -
117A VAL 1.7 45.7 - - - +
167A HIS* 3.1 14.3 + - - -
168A GLU* 2.9 20.3 + - - +
170A GLY* 1.3 72.4 - - - +
172A ASN* 1.3 50.7 + - - +
174A GLY 2.9 1.7 + - - -
175A SER 2.6 26.3 + - - -
176A PRO* 4.1 6.5 - - + -
177A HIS* 3.5 13.0 - + - -
201A MET* 3.5 10.0 - - + +
239B LEU* 2.5 9.8 - - - +
240B ALA 2.5 22.7 + - - +
241B GLY 2.6 23.6 - - - -
242B ALA 2.9 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.5 22.2 - - + +
100A TYR* 2.6 43.0 + - - +
115A ALA* 3.6 8.6 - - - +
116A TRP 3.3 14.1 + - - -
117A VAL 3.4 2.5 - - - -
118A GLY* 3.2 9.7 - - - -
126A GLY* 3.7 7.6 - - - -
127A ILE* 2.9 24.6 + - - +
144A THR 3.0 25.4 + - - +
168A GLU 3.2 5.4 + - - +
169A VAL 3.0 9.0 + - - +
171A HIS* 1.3 76.0 - - - +
173A PHE* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A CYS* 3.7 26.9 - - + -
8A LEU* 5.9 0.2 - - + -
41A TYR* 4.0 23.6 - + + -
52A ILE* 3.4 25.8 - - + -
53A SER 4.3 7.4 - - - -
54A PHE* 5.3 4.5 - - + -
98A LEU* 3.8 26.2 - - + -
100A TYR* 4.8 1.6 - - - -
127A ILE* 4.5 5.4 - - + -
169A VAL* 2.8 27.0 + - + +
170A GLY* 3.5 7.6 - - - +
171A HIS 3.2 0.2 - - - -
172A ASN* 1.3 77.8 - - - +
174A GLY* 1.3 48.3 + - - +
224A ILE* 3.6 17.2 - - + -
227A VAL* 2.6 37.9 - - - +
228A LEU* 3.3 26.7 - - + +
236A PHE* 3.8 14.4 - + - -
----------------------------------------------------------
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