Contacts of the helix formed by residues 140 - 154 (chain A) in PDB entry 3IKH
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 SER 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 1.3 73.9 - - - +
141A LEU* 1.3 65.2 + - - +
142A ASP* 3.8 7.6 + - - +
143A LYS* 3.3 27.1 + - - +
144A THR* 2.9 23.2 + - - -
166A ASN* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE 3.8 0.6 + - - -
140A SER* 1.3 72.3 - - - +
142A ASP* 1.3 61.2 + - - +
144A THR* 3.7 0.2 - - - -
145A ARG* 2.8 55.6 + - - +
166A ASN* 4.5 9.1 - - - +
168A ASP* 3.4 48.9 - - + +
169A PHE* 4.1 18.1 - - + -
171A HIS* 4.7 5.8 - - + +
172A LEU* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 5.9 0.2 - - - -
140A SER* 3.2 7.0 + - - +
141A LEU* 1.3 80.6 - - - +
143A LYS* 1.3 60.0 + - + +
145A ARG* 3.2 28.4 + - - +
146A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 6.1 0.9 - - - -
115A PHE 4.6 8.3 - - - +
116A SER* 3.7 14.9 - - - +
117A LEU* 3.2 56.5 - - + +
120A MSE 5.0 2.7 - - + -
139A PHE* 4.1 17.3 - - + -
140A SER* 3.2 21.0 + - - +
142A ASP* 1.3 78.7 - - + +
144A THR* 1.3 64.4 + - - +
146A ALA* 3.2 5.3 + - - +
147A LEU* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 3.3 33.4 + - + +
136A GLN 4.8 1.5 + - - +
139A PHE* 3.2 24.0 + - - +
140A SER 2.9 19.9 + - - -
141A LEU 3.7 4.0 - - - -
143A LYS* 1.3 76.2 - - - +
145A ARG* 1.3 63.3 + - - +
147A LEU 3.2 1.7 + - - -
148A PHE* 3.2 35.0 + - + -
160A PHE* 4.0 14.4 - - + -
169A PHE* 4.2 6.8 - - + -
172A LEU* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 2.8 45.4 + - - +
142A ASP* 3.2 28.9 + - - +
144A THR* 1.3 72.7 - - - +
146A ALA* 1.3 58.4 + - - +
148A PHE* 3.2 4.9 + - - +
149A GLN* 3.0 55.8 + - - +
171A HIS* 5.0 11.3 + - - +
172A LEU* 3.4 31.4 - - + +
175A LEU* 3.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.8 28.0 - - + -
142A ASP 2.9 19.8 + - - +
143A LYS 3.5 3.8 - - - +
145A ARG* 1.3 77.2 - - - +
147A LEU* 1.3 57.5 + - - +
149A GLN* 3.4 15.5 + - - +
150A TYR* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.7 17.0 - - + +
117A LEU* 3.8 7.4 - - + -
120A MSE 4.0 26.0 - - + -
121A ILE* 3.7 29.4 - - + -
124A MSE 3.8 18.3 - - + +
133A LEU* 3.4 14.7 - - + +
135A GLN* 3.0 36.1 - - - +
139A PHE* 4.0 6.3 - - + -
143A LYS 2.9 18.3 + - - +
144A THR 3.2 0.2 + - - -
146A ALA* 1.3 76.1 - - - +
148A PHE* 1.3 59.8 + - - +
150A TYR* 3.2 7.2 + - - +
151A ALA 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.7 15.9 - - + -
135A GLN* 3.5 25.6 - - + -
144A THR* 3.2 28.8 + - + -
145A ARG* 3.2 6.7 + - - +
147A LEU* 1.3 76.1 - - - +
149A GLN* 1.3 57.9 + - - +
151A ALA* 3.3 3.0 + - - +
152A ARG* 2.9 33.5 + - - +
158A THR* 3.4 31.5 - - + +
159A VAL 3.7 13.7 - - - -
160A PHE* 3.5 49.4 - + + -
172A LEU* 4.7 7.9 - - + -
175A LEU* 4.1 22.2 - - + -
176A ILE* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 3.0 43.2 + - - +
146A ALA* 3.7 14.8 - - - +
148A PHE* 1.3 73.2 - - - +
150A TYR* 1.3 66.2 + - - +
152A ARG* 3.4 7.5 + - - +
153A SER* 3.0 23.6 + - - -
175A LEU* 3.9 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.8 40.9 + - + +
124A MSE 3.7 52.2 + - + -
125A ALA* 4.6 4.5 - - - -
146A ALA 3.0 14.7 + - - +
147A LEU* 3.4 11.7 - - - +
149A GLN* 1.3 77.6 - - - +
151A ALA* 1.3 67.0 + - - +
153A SER* 2.6 24.8 + - - -
154A ARG* 3.2 60.3 + - + +
156A MSE 4.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.7 31.0 - - + -
147A LEU 3.0 5.3 + - - -
148A PHE 3.3 8.3 + - - +
150A TYR* 1.3 78.2 - - + +
152A ARG* 1.3 62.7 + - - +
154A ARG* 3.0 8.0 + - - -
156A MSE 2.9 52.5 + - + +
158A THR* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE 2.9 19.2 + - - +
149A GLN* 3.7 7.9 - - - +
151A ALA* 1.3 75.3 - - - +
153A SER* 1.3 61.8 + - - +
154A ARG 3.1 0.2 - - - -
155A GLY* 3.2 13.0 + - - +
156A MSE 4.6 8.0 + - - -
158A THR* 4.2 4.0 + - + +
174A PRO 3.0 22.8 + - - -
175A LEU* 3.2 50.5 + - + +
176A ILE 3.5 6.1 + - - +
177A ASP* 3.2 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN 3.0 11.9 + - - -
150A TYR* 2.6 25.6 + - - -
152A ARG* 1.3 75.4 - - - +
154A ARG* 1.3 83.6 + - - +
155A GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MSE 6.0 0.4 - - - +
127A ALA* 5.6 10.1 - - + +
128A VAL* 4.2 1.6 - - - -
129A ALA* 3.5 21.1 + - - +
150A TYR* 3.2 60.6 + - + +
151A ALA 3.0 8.5 + - - +
153A SER* 1.3 106.9 + - - +
155A GLY* 1.3 62.0 + - - +
156A MSE 3.5 14.3 + - + -
----------------------------------------------------------
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