Contacts of the helix formed by residues 142 - 158 (chain A) in PDB entry 5KAL
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 ARG 142 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.0 10.3 - - + -
76A ASP* 3.2 40.5 + - - +
79A ASP* 3.4 35.6 + - - +
80A GLY 4.3 9.9 - - - -
82A GLY* 3.2 29.4 + - - +
83A GLY 2.7 29.3 + - - +
84A ASP* 3.2 11.4 + - - +
141A ARG* 1.3 77.0 - - - +
143A ASN* 1.3 68.4 + - - +
144A GLY 3.2 3.3 + - - -
145A VAL* 3.3 11.3 + - - +
146A ARG* 3.1 24.3 + - - +
215A VAL* 4.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 4.6 8.0 - - - +
83A GLY* 4.8 1.7 - - - -
84A ASP* 3.0 32.4 + - - +
141A ARG* 3.8 1.2 - - + +
142A ARG* 1.3 77.0 - - - +
144A GLY* 1.3 62.5 + - - +
146A ARG* 3.2 10.6 + - - +
147A ASN* 2.9 33.5 + - - +
297A ASP* 5.8 0.7 - - - +
299A TYR* 3.8 29.9 + - + +
300A GLU* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 4.0 22.0 - - - -
141A ARG* 5.4 2.4 - - - +
142A ARG 3.3 0.8 - - - -
143A ASN* 1.3 77.9 - - - +
145A VAL* 1.3 62.6 + - - +
147A ASN* 2.9 19.5 - - - +
148A SER* 2.9 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 4.3 19.1 - - + -
51A THR 4.5 6.3 - - - +
52A PHE* 4.1 19.6 - - + +
56A VAL* 6.0 0.2 - - - +
70A VAL* 3.9 28.3 - - + -
72A LEU* 5.2 4.5 - - + -
141A ARG 5.0 4.7 - - - +
142A ARG* 3.3 10.0 + - - +
144A GLY* 1.3 73.5 - - - +
146A ARG* 1.3 58.4 + - - +
148A SER* 3.5 2.1 + - - -
149A ALA* 2.9 28.2 + - + +
215A VAL* 4.8 13.2 - - + -
218A VAL* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 4.6 1.2 + - - -
81A LYS* 3.6 47.1 + - - +
82A GLY 4.2 7.6 + - - -
83A GLY* 5.9 0.4 - - - -
142A ARG* 3.1 16.0 + - - +
143A ASN* 3.5 13.9 + - - +
144A GLY 3.1 0.2 - - - -
145A VAL* 1.3 77.5 - - - +
147A ASN* 1.3 64.6 + - - +
149A ALA* 3.0 6.5 + - - +
150A LEU* 2.9 20.4 + - - +
210A PRO 4.0 9.5 + - - -
211A SER* 4.1 9.7 - - - +
213A ILE* 3.2 45.4 + - + +
215A VAL* 4.1 17.9 - - + +
299A TYR* 3.5 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 2.9 30.0 + - - +
144A GLY* 2.9 12.0 - - - +
146A ARG* 1.3 73.5 - - - +
148A SER* 1.3 84.4 + - - +
150A LEU* 3.2 7.8 + - + +
151A LEU* 3.0 31.1 + - + +
189A TYR* 3.2 45.7 + - + +
193A LEU* 6.2 0.4 - - + -
297A ASP* 5.0 3.0 + - - -
298A PRO* 4.9 4.9 - - + -
299A TYR* 3.7 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.6 18.0 - - - +
53A GLY* 3.4 23.4 + - - -
56A VAL* 4.6 9.4 - - - -
57A VAL* 3.9 19.4 - - - +
144A GLY 2.9 19.2 + - - -
145A VAL 3.7 4.0 - - - -
147A ASN* 1.3 88.0 + - - +
149A ALA* 1.3 57.1 + - - +
151A LEU* 3.4 2.6 + - - +
152A ARG* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.9 5.6 - - + +
145A VAL* 2.9 15.9 + - + +
146A ARG 3.4 7.9 - - - +
148A SER* 1.3 75.2 - - - +
150A LEU* 1.3 64.6 + - - +
152A ARG* 3.2 9.8 + - - +
153A ALA* 2.9 23.4 + - - +
213A ILE* 4.0 22.1 - - + +
218A VAL* 4.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG 2.9 12.0 + - - +
147A ASN* 3.2 10.7 + - + +
149A ALA* 1.3 75.5 - - - +
151A LEU* 1.3 66.3 + - + +
153A ALA* 3.1 6.9 + - + +
154A TYR* 3.0 47.5 + - + -
208A VAL* 4.1 29.8 - - + +
210A PRO* 4.5 20.6 - - + -
213A ILE* 4.3 22.8 - - + +
261A LEU* 4.6 15.7 - - + -
298A PRO* 4.8 13.2 - - + -
299A TYR* 4.5 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.7 28.5 - - + -
147A ASN* 3.0 23.4 + - + +
148A SER* 3.8 2.5 - - - +
150A LEU* 1.3 77.5 - - + +
152A ARG* 1.3 63.9 + - - +
154A TYR* 3.2 8.1 + - + +
155A PHE* 2.9 31.7 + - + -
189A TYR* 4.3 24.0 - - + -
192A ASN* 4.2 25.6 - - + +
193A LEU* 4.5 17.9 - - + -
196A VAL* 3.9 25.8 - - + -
261A LEU* 4.5 8.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
55A THR 4.2 0.4 + - - -
56A VAL* 2.7 62.1 + - - +
57A VAL* 3.7 13.4 - - - +
59A GLY* 3.9 12.5 - - - -
148A SER 2.9 17.4 + - - +
149A ALA* 3.4 9.6 - - - +
151A LEU* 1.3 77.5 - - - +
153A ALA* 1.3 57.3 + - - +
155A PHE* 3.3 2.4 + - - +
156A GLU* 2.9 46.4 + - + +
222A PRO* 3.6 25.9 - - - +
223A PRO* 2.9 33.3 + - - +
225A LEU* 3.7 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA 2.9 13.5 + - - +
150A LEU* 3.1 10.7 + - + +
152A ARG* 1.3 73.7 - - - +
154A TYR* 1.3 67.4 + - - +
156A GLU* 2.9 27.0 + - - +
157A GLN* 3.0 16.8 + - - +
208A VAL* 5.7 11.7 - - + -
213A ILE* 5.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.0 45.6 + - + -
151A LEU* 3.2 11.6 + - + +
153A ALA* 1.3 75.3 - - - +
155A PHE* 1.3 64.7 + - + +
157A GLN* 3.1 29.8 + - - +
196A VAL* 3.8 28.5 - - + -
200A LEU* 3.7 22.1 - - + +
205A LEU* 3.5 31.4 - - + +
206A GLN 3.4 24.0 - - - -
207A PHE* 3.8 13.0 - - - -
208A VAL* 3.0 36.3 + - + +
261A LEU* 4.5 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.8 35.0 - - + +
58A TYR* 4.4 5.4 - + - -
151A LEU* 2.9 27.4 + - + +
152A ARG 3.9 3.4 - - - +
154A TYR* 1.3 75.1 - - - +
156A GLU* 1.3 64.8 + - - +
158A ASN 3.2 22.7 + - - +
159A PRO* 3.3 7.1 - - - +
161A CYS* 4.3 14.1 - - + -
162A ARG* 3.9 44.8 + - + +
165A SER* 3.8 24.9 - - - -
192A ASN* 4.3 9.2 - - - -
195A VAL* 4.6 6.1 - - + -
196A VAL* 4.4 23.1 - - + -
199A LEU* 4.8 11.2 - - + -
205A LEU* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 2.9 30.0 + - - +
153A ALA* 2.9 20.9 + - - +
155A PHE* 1.3 74.1 - - - +
157A GLN* 1.3 66.9 + - - +
158A ASN 3.3 0.3 + - - -
159A PRO* 3.9 13.8 - - - +
225A LEU* 3.9 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 3.0 16.7 + - - +
154A TYR* 3.1 18.2 + - - +
156A GLU* 1.3 79.1 - - - +
158A ASN* 1.3 60.0 + - - +
159A PRO* 4.0 2.6 - - - +
205A LEU* 3.6 15.0 - - + +
206A GLN* 3.2 47.3 + - - +
208A VAL* 3.5 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR 3.8 0.6 + - - -
155A PHE* 3.2 11.0 + - - +
157A GLN* 1.3 80.5 - - - +
159A PRO* 1.3 69.1 - - - +
160A PRO* 3.4 17.2 - - - +
161A CYS* 3.2 40.4 + - + +
162A ARG 4.3 0.3 + - - -
204A HIS* 3.9 20.7 + - - +
205A LEU* 4.1 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