Contacts of the helix formed by residues 142 - 158 (chain A) in PDB entry 5F0L
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 HIS 142 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 4.2 10.2 + - - -
140A VAL* 3.4 3.7 - - + -
141A GLN* 1.3 76.5 - - - +
143A PRO* 1.4 65.1 - - + +
144A LEU* 3.3 27.0 + - + -
145A ARG* 3.3 58.7 + - + +
146A GLY* 2.8 34.3 + - - -
193A LEU* 4.4 0.6 - - - +
200A GLN* 4.3 14.8 + - - -
237B ASP* 2.9 17.6 + - - +
238B GLY* 4.1 8.7 - - - -
239B ALA 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN 3.3 8.9 - - - +
142A HIS* 1.4 88.1 - - + +
144A LEU* 1.3 62.9 + - - +
147A LEU* 3.0 31.3 + - - +
193A LEU* 3.5 26.5 - - + +
196A ARG* 4.4 15.3 - - + -
197A MET* 3.4 33.9 - - + +
200A GLN* 3.4 28.3 - - + +
239B ALA 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 5.4 2.9 - - - +
56A SER* 5.8 2.5 - - - +
58A LEU 4.3 14.4 - - - +
59A SER 4.5 3.6 - - - +
60A PRO* 4.4 13.7 - - + -
63A TYR* 3.9 32.3 - - + -
142A HIS* 3.4 19.3 + - + -
143A PRO* 1.3 79.7 - - - +
145A ARG* 1.3 65.9 + - + +
147A LEU* 3.3 3.3 + - - +
148A PHE* 3.2 53.4 + - + -
197A MET* 3.9 14.5 - - + +
200A GLN* 5.2 2.0 - - - +
216A LEU* 4.0 21.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
53A LEU 3.1 20.9 - - - +
54A ARG* 3.2 25.5 + - - +
55A THR 3.2 10.7 + - - +
56A SER* 2.7 27.9 + - - +
63A TYR* 3.6 27.9 + - + +
105A ILE* 4.2 15.0 - - + +
109A TYR* 4.4 2.6 + - - -
140A VAL* 4.0 5.6 - - + -
142A HIS* 3.3 42.2 + - + +
144A LEU* 1.3 81.9 - - + +
146A GLY* 1.3 57.2 + - - +
148A PHE* 3.5 2.6 + - - +
149A LEU* 3.0 27.9 + - - +
205B GLN* 5.8 1.4 - - - +
237B ASP* 2.9 39.4 + - - -
238B GLY* 5.6 0.4 - - - -
407B EDO 3.9 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 3.5 20.8 - - - +
142A HIS 2.8 22.1 + - - -
145A ARG* 1.3 70.5 - - - +
147A LEU* 1.3 58.5 + - - +
149A LEU* 3.6 3.5 - - - +
150A ARG* 2.8 35.1 + - - +
193A LEU* 3.5 15.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
143A PRO 3.0 27.2 + - - +
144A LEU* 3.3 4.9 + - + +
146A GLY* 1.3 75.1 - - - +
148A PHE* 1.3 51.9 + - + +
150A ARG* 3.2 1.3 + - - -
151A ASN* 2.7 31.9 + - - +
190A MET* 3.2 61.5 - - + +
193A LEU* 3.5 7.7 - - + +
194A TRP* 4.1 23.3 - - + -
197A MET* 4.6 2.9 - - - -
216A LEU* 4.1 29.8 - - + +
219A LEU* 4.0 13.5 - - + -
220A VAL* 4.0 10.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
60A PRO 4.6 1.1 - - - -
63A TYR* 3.4 31.9 - + + -
64A TYR* 3.8 47.6 - + + -
67A TYR* 3.4 40.2 - + + -
109A TYR* 3.5 12.8 - - - +
144A LEU* 3.2 39.3 + - + +
145A ARG 4.0 1.6 - - - +
147A LEU* 1.3 75.3 - - + +
149A LEU* 1.3 60.2 + - - +
151A ASN* 3.5 6.0 - - + +
152A TYR* 2.8 22.9 + - - +
216A LEU* 3.8 17.0 - - + -
219A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 4.9 3.4 - - + +
108A LEU* 3.6 28.7 - - + -
109A TYR* 3.4 35.8 + - + +
112A ILE* 3.6 25.6 - - + -
137A CYS* 3.9 20.2 - - + +
140A VAL* 3.4 33.9 - - + -
145A ARG 3.0 18.3 + - - +
146A GLY 3.6 4.5 - - - +
148A PHE* 1.3 76.7 - - - +
150A ARG* 1.3 57.9 + - + +
152A TYR* 2.9 5.4 + - - +
153A LEU* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.4 29.1 + - - +
137A CYS* 3.5 22.2 + - + +
138A ARG* 3.4 35.2 - - - +
140A VAL 5.3 2.0 + - - -
146A GLY* 2.8 23.3 + - - +
147A LEU 3.7 0.2 - - - +
149A LEU* 1.3 73.7 - - + +
151A ASN* 1.3 59.9 + - - +
153A LEU* 3.5 6.9 - - - +
154A LEU* 3.4 9.5 + - - +
186A ASN* 3.1 49.2 + - - +
189A GLU* 3.4 39.5 + - - +
190A MET* 3.4 30.7 - - + +
193A LEU* 4.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.5 17.5 + - - -
147A LEU 2.7 19.8 + - - +
148A PHE* 3.5 12.1 - - + +
150A ARG* 1.3 71.2 - - - +
152A TYR* 1.3 60.4 + - - +
153A LEU 3.2 0.2 - - - -
154A LEU* 3.0 9.2 + - - +
155A GLN* 3.0 43.0 + - - +
190A MET* 3.8 7.5 - - + +
219A LEU* 4.2 26.2 + - + +
222A THR* 4.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.3 22.4 + + - +
71A SER* 4.1 18.4 - - - -
74A LEU* 3.4 31.6 + - + +
78A GLU* 5.6 1.4 - - - +
109A TYR* 3.5 49.1 - + + -
112A ILE* 3.6 19.1 - - + -
113A THR* 2.7 21.8 + - - +
148A PHE 2.8 15.6 + - - +
149A LEU 2.9 7.1 + - - +
151A ASN* 1.3 72.6 - - - +
153A LEU* 1.3 61.3 + - - +
155A GLN* 4.8 4.0 - - + -
156A CYS* 3.0 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 4.1 23.6 - - + -
133A LEU* 3.7 31.2 - - + +
134A VAL* 3.7 27.8 - - + +
137A CYS* 4.4 7.4 - - - -
149A LEU 2.8 11.5 + - - +
150A ARG* 3.5 10.5 - - - +
152A TYR* 1.3 78.3 - - - +
154A LEU* 1.3 54.0 + - - +
156A CYS* 4.0 0.7 - - - +
157A THR* 2.8 46.3 + - + +
182A PHE* 3.7 24.0 - - + -
186A ASN* 3.6 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG 3.4 9.3 + - - +
151A ASN* 3.0 13.1 + - - +
153A LEU* 1.3 81.9 - - - +
155A GLN* 1.3 59.7 + - - +
157A THR* 3.0 15.7 + - - +
158A ARG* 3.2 16.1 + - - +
161A LEU* 5.6 0.4 - - + -
182A PHE* 4.7 7.6 - - + -
183A VAL* 4.3 13.5 - - + -
186A ASN* 3.8 7.2 - - - +
190A MET* 5.2 0.9 - - - -
219A LEU 4.9 0.9 - - - +
222A THR* 3.7 24.9 - - + +
223A ASN* 3.5 50.9 - - - +
226A ARG* 4.1 28.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 5.1 2.9 - - - +
151A ASN* 3.0 34.0 + - - +
152A TYR* 4.3 5.8 - - + +
154A LEU* 1.3 76.8 - - - +
156A CYS* 1.3 63.4 + - - +
158A ARG* 3.4 55.6 + - - +
222A THR* 3.3 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 5.9 3.6 - - - -
112A ILE* 3.9 13.5 - - + -
113A THR* 4.9 3.4 - - - -
116A VAL* 3.6 32.6 - - + +
120A LYS* 6.1 0.2 - - - -
152A TYR* 3.0 66.1 + - - +
153A LEU 4.0 0.9 - - - +
155A GLN* 1.3 77.5 - - - +
157A THR* 1.3 60.5 + - - +
158A ARG 3.5 0.3 + - - -
159A ASN 4.7 2.1 + - - -
160A ILE* 4.5 3.6 - - - +
505A GOL 4.8 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.2 12.8 - - + -
130A LEU* 3.7 24.5 - - + -
133A LEU* 5.0 2.9 - - + -
153A LEU* 2.8 31.3 + - + +
154A LEU* 3.0 12.8 + - - +
156A CYS* 1.3 75.8 - - + +
158A ARG* 1.3 65.5 + - - +
159A ASN 3.3 2.0 - - - -
160A ILE* 2.9 21.5 + - - +
161A LEU* 3.3 26.8 + - - +
182A PHE* 3.7 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU 3.2 10.5 + - - +
155A GLN* 3.4 50.2 + - - +
156A CYS 3.3 2.4 - - - -
157A THR* 1.3 74.9 - - - +
159A ASN* 1.3 90.4 + - - +
160A ILE 3.5 0.2 + - - -
226A ARG* 2.6 53.4 + - - +
229A GLN* 4.3 12.8 - - - +
505A GOL 4.8 6.9 - - - -
----------------------------------------------------------
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