Contacts of the helix formed by residues 143 - 156 (chain B) in PDB entry 1KNY
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 LEU 143 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 2.9 39.5 + - + -
139B ILE* 3.4 15.0 - - + +
142B GLU* 1.3 78.8 - - - +
144B PHE* 1.3 63.4 + - - +
146B TYR* 3.1 20.4 + - + +
147B ALA* 3.1 21.1 + - - +
150B TRP* 4.8 5.3 - - + -
169B VAL* 4.3 13.2 - - + +
172B ALA* 4.4 11.0 - - + -
173B GLY* 4.4 7.9 - - - +
176B LEU* 4.5 17.9 - - + -
230B PHE* 3.8 25.1 - - + -
231B TRP* 4.0 17.2 - - + -
234B ILE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 21.8 - - + -
3A GLY* 3.9 9.4 - - - -
4A PRO* 3.5 27.8 - - + +
69A THR* 2.9 30.3 - - - -
71A GLY* 3.5 24.7 - - - -
73A TRP 3.9 10.5 - - - -
74A LYS* 3.6 32.1 - - + -
139B ILE 2.6 19.0 + - - +
140B VAL* 3.3 12.3 - - - +
143B LEU* 1.3 72.6 - - - +
145B GLU* 1.3 63.0 + - - +
147B ALA* 3.2 16.0 - - - +
148B GLY 3.5 4.9 + - - -
231B TRP* 3.7 19.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 3.1 29.9 - - + +
74A LYS* 3.0 30.3 + - + +
76A GLU* 4.5 1.6 - - - +
556A APC 3.1 14.3 + - - +
140B VAL 3.9 1.0 + - - -
141B GLU 3.1 11.6 - - - +
142B GLU* 2.7 10.7 + - - +
144B PHE* 1.3 79.8 - - - +
146B TYR* 1.3 71.2 + - + +
147B ALA 3.1 2.3 + - - -
148B GLY* 3.6 2.1 + - - +
149B LYS* 3.5 29.6 + - - +
559B KAN 2.3 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 2.8 46.6 + - + +
143B LEU* 3.1 16.4 + - + +
145B GLU* 1.3 78.7 - - + +
147B ALA* 1.3 56.7 + - - +
149B LYS* 3.3 21.7 - - + +
150B TRP* 3.0 35.4 + - + +
165B LEU* 3.6 20.8 - - + +
168B GLN* 4.4 27.2 + - + +
169B VAL* 3.8 28.5 - - + -
172B ALA* 4.2 17.3 - - + -
559B KAN 4.4 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.7 15.9 - - + -
143B LEU 3.1 10.4 + - - +
144B PHE* 3.2 16.2 - - - +
145B GLU 3.1 0.4 - - - -
146B TYR* 1.3 73.4 - - - +
148B GLY* 1.3 63.8 + - - +
150B TRP* 3.4 29.0 + - + -
151B ARG* 2.8 34.6 + - - +
231B TRP* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.4 18.7 - - - +
48A TYR* 3.3 31.4 - - - +
144B PHE 3.5 3.4 + - - -
145B GLU 3.6 2.5 + - - -
146B TYR 3.6 0.2 - - - -
147B ALA* 1.3 75.4 - - - +
149B LYS* 1.3 51.3 + - - +
151B ARG* 2.6 24.4 + - - +
152B ASN* 2.6 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 5.5 1.1 - - - -
188A SER* 4.0 16.7 + - - -
556A APC 3.4 55.7 + - - +
145B GLU* 3.5 25.0 + - + +
146B TYR* 3.3 32.8 + - + +
148B GLY* 1.3 73.7 - - - +
150B TRP* 1.3 58.8 + - - +
152B ASN* 3.2 9.2 + - - +
153B ILE* 2.8 36.6 + - + +
161B PHE* 4.8 12.0 - - + -
165B LEU* 3.9 15.3 - - + -
559B KAN 5.1 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.8 4.3 - - + -
146B TYR* 3.0 26.7 + - + -
147B ALA* 3.7 32.3 + - + -
149B LYS* 1.3 80.4 - - - +
151B ARG* 1.3 65.2 + - + +
153B ILE* 3.7 5.9 - - - +
154B ARG* 3.2 10.8 + - - +
162B LEU* 4.9 2.2 - - + -
165B LEU* 3.5 17.0 - - + -
169B VAL* 3.8 25.1 - - + -
224B LEU* 2.9 43.6 - - + +
227B LEU* 3.6 55.5 - - + +
228B GLU* 3.3 30.2 + - - -
230B PHE* 5.2 4.5 - + - -
231B TRP* 3.9 25.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN 3.3 16.7 + - - -
3A GLY* 3.1 4.8 - - - -
4A PRO* 2.6 52.2 + - - +
48A TYR* 3.3 40.1 - - + -
147B ALA* 2.8 22.2 + - - +
148B GLY* 2.6 19.1 + - - +
150B TRP* 1.3 74.1 - - + +
152B ASN* 1.3 64.1 + - - +
153B ILE 3.0 0.9 - - - -
154B ARG* 2.8 31.1 + - - +
155B VAL* 3.1 10.9 + - - +
228B GLU* 2.8 32.1 + - - +
231B TRP* 3.6 19.8 - - - -
232B ASN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 4.2 0.2 - - - -
47A PRO* 3.4 11.5 - - - +
48A TYR* 2.9 33.6 + - - -
49A SER* 3.4 29.5 + - - +
556A APC 4.1 12.9 + - - -
148B GLY 2.6 11.7 + - - +
149B LYS* 3.5 10.9 - - - +
151B ARG* 1.3 73.2 - - - +
153B ILE* 1.3 55.1 + - + +
155B VAL* 3.1 3.4 + - - -
156B GLN* 2.6 63.4 + - - +
157B GLY 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 5.6 1.3 - - + -
149B LYS* 2.8 22.6 + - + +
150B TRP* 3.7 8.3 - - + +
151B ARG 3.0 0.2 - - - -
152B ASN* 1.3 78.0 - - + +
154B ARG* 1.4 61.1 + - - +
155B VAL 4.1 0.2 - - - -
156B GLN 3.7 0.2 + - - -
157B GLY* 3.0 32.0 + - - +
158B PRO* 3.2 35.9 - - + +
159B THR* 4.2 14.4 - - + +
161B PHE* 4.0 25.6 - - + -
162B LEU* 4.0 31.0 - - + +
165B LEU* 4.7 8.5 - - + -
224B LEU* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.8 26.1 + - - -
150B TRP 3.2 7.7 + - - +
151B ARG* 2.8 30.6 + - - +
153B ILE* 1.4 72.2 - - - +
155B VAL* 1.3 60.7 + - - +
224B LEU* 3.1 37.8 - - + +
228B GLU* 3.3 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.9 27.6 - - + -
48A TYR* 4.5 9.0 - - + -
151B ARG 3.1 6.4 + - - +
152B ASN* 3.1 21.0 + - - +
153B ILE 4.1 0.2 - - - -
154B ARG* 1.3 85.2 - - + +
156B GLN* 1.3 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR 5.1 4.4 + - - +
46A GLY* 3.8 10.1 - - - +
47A PRO* 3.8 18.3 - - + +
556A APC 5.2 2.6 + - - -
152B ASN* 2.6 53.9 + - - +
155B VAL* 1.3 79.7 - - + +
157B GLY* 1.3 66.9 + - - +
----------------------------------------------------------
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