Contacts of the helix formed by residues 155 - 170 (chain B) in PDB entry 1IC8
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 LYS 155 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B MET* 1.3 77.4 - - - +
156B THR* 1.3 65.3 + - - +
157B GLN* 4.2 26.3 - - + +
158B LYS* 3.3 25.7 + - + +
159B ARG* 3.1 16.5 + - - +
305E G 4.0 20.9 + - - +
306E T 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.9 29.3 + - + +
154B MET 3.7 1.2 + - - -
155B LYS* 1.3 71.0 - - - +
157B GLN* 1.3 55.1 + - - +
159B ARG* 3.0 21.2 + - - +
160B ALA* 2.7 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LYS* 3.4 25.5 + - + +
156B THR* 1.3 79.2 - - - +
158B LYS* 1.3 58.6 + - + +
160B ALA* 2.9 24.7 - - + +
161B ALA* 3.0 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.2 29.7 - - + +
140B ASN 6.3 0.2 - - - +
143B HIS* 4.5 8.7 - - + -
154B MET* 3.1 15.9 - - + +
155B LYS* 3.3 20.5 + - + +
156B THR 3.2 0.8 - - - -
157B GLN* 1.3 74.2 - - + +
159B ARG* 1.3 55.8 + - - +
160B ALA 2.6 5.6 + - - -
161B ALA* 2.5 29.4 + - - +
162B LEU 2.8 9.0 + - - -
306E T 2.5 65.4 + - - +
307E T 4.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 3.6 18.4 + - - -
108B LEU* 3.6 25.0 + - + +
110B GLU 4.1 1.8 + - - -
112B PRO* 3.4 36.0 - - - +
147B HIS* 3.7 19.3 - - + -
154B MET* 2.9 58.3 + - + +
155B LYS 3.1 3.5 + - - +
156B THR* 3.0 22.4 + - - +
158B LYS* 1.3 74.2 - - - +
160B ALA* 1.3 55.5 + - - +
162B LEU* 3.6 3.6 - - - -
163B TYR* 2.6 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 5.1 0.6 - - + +
108B LEU* 3.9 24.2 - - + -
156B THR* 2.7 13.3 + - + +
157B GLN* 2.9 22.0 - - + +
158B LYS 2.6 0.4 + - - -
159B ARG* 1.3 76.2 - - - +
161B ALA* 1.3 58.3 + - - -
162B LEU 3.0 1.6 - - - -
163B TYR* 3.5 2.4 + - - +
164B THR* 2.5 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.8 30.4 - - - +
139B LEU* 4.6 1.8 - - + -
157B GLN 3.0 11.2 + - - +
158B LYS* 2.5 20.2 + - - +
160B ALA* 1.3 71.4 - - - +
162B LEU* 1.3 62.4 + - - +
164B THR* 3.9 5.8 - - - -
165B TRP* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 5.8 0.9 - - - -
119B VAL* 4.5 20.0 - - + -
133B VAL* 4.2 15.3 - - + -
137B THR* 4.6 1.1 - - + -
139B LEU* 3.9 9.6 - - + +
144B LEU* 3.8 31.4 - - + -
147B HIS* 4.3 14.1 - - + +
148B LEU* 4.3 14.6 - - + -
154B MET* 4.1 13.0 - - + -
158B LYS 2.8 6.5 + - - +
159B ARG* 3.3 14.4 - - - +
160B ALA 3.0 0.8 - - - -
161B ALA* 1.3 76.2 - - - +
163B TYR* 1.3 69.2 + - + +
165B TRP* 2.7 14.3 + - + +
166B TYR* 2.7 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.9 17.9 - - + -
107B LEU* 3.7 26.9 - - + -
108B LEU* 3.5 44.4 - - + -
112B PRO 3.9 6.1 + - - -
115B VAL* 3.3 36.0 - - + +
116B ALA* 5.4 0.4 - - - -
119B VAL* 4.6 5.2 - - + -
147B HIS* 4.7 1.8 - + - -
159B ARG* 2.6 51.2 + - + +
160B ALA* 4.0 2.2 - - - +
162B LEU* 1.3 88.7 - - + +
164B THR* 1.3 56.4 + - - +
166B TYR* 2.7 10.1 + - - +
167B VAL* 2.6 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.6 23.2 - - + +
160B ALA* 2.5 25.9 + - - +
161B ALA* 3.9 6.4 - - - -
163B TYR* 1.3 75.8 - - - +
165B TRP* 1.3 56.9 + - - +
167B VAL* 3.2 1.8 - - + +
168B ARG* 2.9 69.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 4.8 5.8 - - + -
122B TYR* 5.5 1.3 - + - -
123B LEU* 3.4 26.2 - - + -
128B ILE* 4.2 4.5 - - + -
132B GLU* 4.3 21.9 + - - +
133B VAL* 3.3 38.8 - - + +
136B THR* 3.3 27.8 + - - +
137B THR* 3.7 14.4 - - + -
161B ALA 3.0 14.9 + - - +
162B LEU* 2.7 25.1 + - + +
164B THR* 1.3 72.6 - - - +
166B TYR* 1.3 76.8 + + + -
168B ARG* 3.4 9.4 + - + +
169B LYS* 2.7 71.5 + - + +
171B ARG* 5.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.7 19.1 - - + -
118B MET* 3.8 27.7 + - + +
119B VAL* 3.8 39.3 - - + -
122B TYR* 3.6 35.0 - + + +
162B LEU 2.7 14.6 + - - +
163B TYR* 2.7 16.5 + + - +
165B TRP* 1.3 84.9 - + + +
167B VAL* 1.3 74.1 + - + +
169B LYS* 3.2 5.0 + - - +
170B GLN* 3.1 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLN* 4.2 27.1 + - + +
103B VAL* 3.8 24.0 - - + -
104B VAL* 3.9 19.3 - - + -
107B LEU* 4.6 7.6 - - + -
163B TYR 2.6 20.0 + - - +
164B THR* 3.2 13.2 - - + +
166B TYR* 1.3 82.9 - - + +
168B ARG* 1.3 73.9 + - + +
170B GLN* 3.3 29.3 + - - +
171B ARG* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLN* 4.1 22.4 - - + +
164B THR* 2.9 51.8 + - + +
165B TRP* 3.8 8.5 - - + +
167B VAL* 1.3 81.7 - - + +
169B LYS* 1.3 63.3 + - - +
171B ARG* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 4.1 13.0 - - + -
128B ILE* 3.8 20.8 - - - +
132B GLU* 3.0 29.1 + - - +
165B TRP* 2.7 52.0 + - + +
166B TYR* 3.3 7.9 - - - +
167B VAL 3.1 0.2 - - - -
168B ARG* 1.3 73.3 - - - +
170B GLN* 1.3 48.5 + - - +
171B ARG* 2.4 38.4 + - - +
172B GLU* 2.7 50.0 + - - +
175B GLN* 5.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 4.2 24.7 - - + -
166B TYR* 3.1 48.4 + - + +
167B VAL* 3.6 23.0 - - - +
168B ARG 3.2 1.2 - - - -
169B LYS* 1.3 71.0 - - - +
171B ARG* 1.3 57.7 + - - +
172B GLU* 3.5 3.8 - - - -
173B VAL* 3.0 30.2 - - + +
----------------------------------------------------------
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