Contacts of the helix formed by residues 145 - 165 (chain A) in PDB entry 5TWF
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 MET 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.7 33.2 - - + -
54A ASN* 4.2 3.4 - - - +
57A ILE* 4.9 8.1 - - - -
144A PHE* 1.3 89.5 - - + +
146A SER* 1.3 57.4 + - - +
147A VAL 3.8 3.0 - - - +
148A ALA* 3.8 18.5 - - + +
149A LYS* 3.2 23.7 + - - +
193A PHE* 3.9 11.0 - - + +
194A ASN 5.2 1.8 - - - +
195A LEU* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 2.2 36.0 + - - +
144A PHE 3.1 1.6 + - - -
145A MET* 1.3 75.8 - - - +
147A VAL* 1.3 66.3 + - - +
149A LYS* 3.6 3.8 + - - +
150A THR* 2.8 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 5.0 3.1 - - + -
125A GLN* 3.7 32.3 - - + +
131A LEU* 3.6 28.9 - - + -
132A PHE* 4.8 3.6 - - + -
143A ASN* 3.4 32.5 - - - +
144A PHE* 4.3 11.2 - - + -
146A SER* 1.3 80.6 - - - +
148A ALA* 1.3 61.7 + - - +
150A THR* 3.4 6.5 + - - -
151A ILE* 3.0 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.8 27.8 - - + -
61A THR* 4.5 6.7 - - - +
132A PHE* 5.3 2.5 - - + -
144A PHE* 4.1 15.6 - - + -
145A MET* 3.8 19.4 - - - +
146A SER 3.3 0.2 - - - -
147A VAL* 1.3 79.5 - - - +
149A LYS* 1.3 62.4 + - - +
151A ILE* 3.1 12.0 + - - +
152A LEU* 3.0 30.6 + - + +
195A LEU* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET 3.2 20.4 + - - +
146A SER* 3.9 4.5 - - - +
147A VAL 3.4 0.2 - - - -
148A ALA* 1.3 78.6 - - - +
150A THR* 1.3 63.2 + - - +
152A LEU* 3.3 0.9 + - - -
153A LYS* 3.1 23.6 + - - +
194A ASN 5.6 0.7 - - - +
195A LEU* 3.4 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 3.8 15.0 - - + -
146A SER 2.8 22.1 + - - -
147A VAL* 3.6 6.9 - - - -
148A ALA 3.2 0.2 - - - -
149A LYS* 1.3 75.4 - - - +
151A ILE* 1.3 65.1 + - - +
153A LYS* 3.1 26.4 + - - +
154A ARG* 3.0 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.7 23.6 - - + -
121A TRP* 3.9 24.5 - - + -
122A VAL* 3.6 27.7 - - + +
125A GLN* 3.6 29.2 - - + -
126A LEU* 4.4 2.2 - - + -
132A PHE* 4.0 23.1 - - + -
147A VAL* 3.0 20.4 + - + +
148A ALA* 3.4 8.1 - - - +
150A THR* 1.3 74.4 - - - +
152A LEU* 1.3 58.9 + - - +
154A ARG* 3.2 3.3 + - - +
155A LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.9 30.7 - - + +
64A PHE* 4.3 14.6 - - + -
148A ALA 3.0 16.8 + - - +
149A LYS* 3.9 3.8 - - - +
150A THR 3.2 0.2 - - - -
151A ILE* 1.3 74.8 - - + +
153A LYS* 1.3 61.0 - - - +
155A LEU* 3.4 11.8 + - + -
156A PHE 2.9 23.7 + - - -
186A PHE* 3.2 30.7 - - + -
189A PHE* 5.1 3.8 - - + -
190A VAL* 4.4 7.2 - - + -
195A LEU* 3.4 37.7 - - + +
196A ILE* 3.3 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS 3.1 11.3 + - - +
150A THR* 3.1 37.2 + - - +
152A LEU* 1.3 77.4 - - - +
154A ARG* 1.3 76.2 + - + +
156A PHE* 3.2 7.1 + - - +
157A ARG* 3.2 43.9 + - - +
195A LEU 5.4 0.7 - - - +
196A ILE* 3.9 17.1 - - + +
197A ASP 6.1 0.2 - - - +
200A GLU* 3.8 35.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
96A HIS 5.9 0.6 + - - -
97A TRP* 3.5 35.8 - - + -
98A ALA 3.6 15.0 + - - -
99A ASP* 3.1 25.9 + - - +
118A LEU* 3.3 34.5 - - + +
121A TRP* 4.1 17.2 - - + -
122A VAL* 5.1 4.0 - - + -
150A THR* 3.0 41.9 + - - +
151A ILE* 3.7 6.3 - - - +
153A LYS* 1.3 87.9 - - + +
155A LEU* 1.3 62.5 + - - +
157A ARG* 3.3 38.4 + - - +
158A VAL* 3.5 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR 4.5 1.1 - - - +
64A PHE* 4.2 7.0 - - + +
65A PHE* 3.9 33.2 - - + +
68A ILE* 4.2 17.4 - - + +
118A LEU* 4.5 7.6 - - + -
119A MET* 3.5 34.1 - - + -
122A VAL* 4.7 4.0 - - + -
151A ILE* 2.9 37.1 + - + +
152A LEU* 3.7 18.4 - - + +
154A ARG* 1.3 75.0 - - - +
156A PHE* 1.3 65.4 + - - +
158A VAL* 2.9 17.8 + - + +
159A TYR* 3.2 14.0 + - - -
186A PHE* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 5.5 1.1 - - - -
152A LEU 2.9 13.5 + - - +
153A LYS* 3.2 9.6 + - - +
155A LEU* 1.3 75.9 - - - +
157A ARG* 1.3 63.4 + - + +
159A TYR* 3.1 13.7 + - - +
160A ALA* 2.9 29.5 + - + -
183A PHE* 3.7 22.4 - + - -
186A PHE* 3.7 16.7 - + + -
187A ILE* 4.2 0.9 - - + -
196A ILE* 3.9 5.4 - - + -
200A GLU* 3.0 33.0 - - + -
201A LEU* 3.6 28.9 - - + -
203A PRO* 3.6 28.9 - - + -
204A LEU* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 4.6 5.9 - - + +
95A TYR* 3.7 49.8 - - + +
96A HIS 5.0 4.4 + - - -
97A TRP* 5.0 0.2 - - - -
114A TYR* 2.4 41.1 + - + +
115A ILE* 6.4 0.2 - - + -
118A LEU* 5.2 2.2 - - + -
153A LYS* 3.2 25.7 + - - +
154A ARG* 3.4 40.4 - - - +
155A LEU 3.1 0.6 - - - -
156A PHE* 1.3 80.8 - - + +
158A VAL* 1.3 59.4 + - + +
160A ALA* 2.9 23.6 + - - +
161A HIS* 2.9 15.6 + - - +
200A GLU* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.5 24.9 - - + -
72A TYR* 4.2 22.9 - - + -
115A ILE* 4.0 40.8 - - + -
118A LEU* 4.1 20.0 - - + -
119A MET* 4.6 2.7 - - - -
154A ARG 3.6 12.6 - - - +
155A LEU* 2.9 13.8 + - + +
157A ARG* 1.3 75.4 - - - +
159A TYR* 1.3 63.8 + - - +
161A HIS* 3.4 3.5 + - + +
162A ILE* 3.2 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.5 2.6 - - - -
68A ILE* 3.1 32.8 - - + +
71A LEU* 5.1 4.3 - - + -
155A LEU 3.2 7.9 + - - -
156A PHE* 3.1 29.1 + - + +
158A VAL* 1.3 78.9 - - - +
160A ALA* 1.3 54.3 + - - +
162A ILE* 3.1 8.3 + - + +
163A TYR* 2.9 39.1 + + + -
179A LEU* 4.5 10.5 - - + -
182A SER* 3.0 31.6 + - - -
183A PHE* 3.1 48.9 - + + -
186A PHE* 3.2 44.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA* 6.3 0.4 - - + -
95A TYR* 5.3 8.3 - - + +
156A PHE* 2.9 17.4 + - + +
157A ARG* 2.9 13.7 + - - +
159A TYR* 1.3 73.6 - - - +
161A HIS* 1.3 67.5 + - - +
163A TYR* 3.2 1.4 + - - -
164A HIS* 2.9 32.8 + - + +
203A PRO* 4.5 21.1 - - + -
204A LEU* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 4.2 14.6 - + - -
79A CYS* 3.0 16.3 - - - -
84A CYS* 3.3 6.4 - - + -
86A VAL 5.0 2.0 - - - -
87A MET* 3.3 31.0 - - + +
88A SER 3.7 18.1 + - - +
111A ALA* 3.6 9.5 - - + +
115A ILE* 5.2 0.4 - - + -
157A ARG 2.9 6.8 + - - +
158A VAL* 3.8 8.7 - - + +
160A ALA* 1.3 74.7 - - - +
162A ILE* 1.3 63.7 + - + +
164A HIS* 5.1 0.4 - - - -
165A GLN* 2.8 45.4 + - - -
166A HIS* 3.8 10.3 + + - -
301A ZN 2.2 37.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 5.4 1.6 - - + +
71A LEU* 4.5 3.6 - - + +
72A TYR* 3.6 41.1 - - + +
75A ILE* 3.6 36.1 - - + -
158A VAL* 3.2 18.3 + - + +
159A TYR* 3.1 10.8 + - + +
161A HIS* 1.3 79.0 - - + +
163A TYR* 1.3 62.5 + - - +
166A HIS* 3.7 3.1 - - - +
167A PHE* 3.3 22.2 + - - -
170A VAL* 4.3 11.2 - - + -
179A LEU* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 2.9 25.1 + + + +
160A ALA 3.2 3.5 + - - +
162A ILE* 1.3 79.2 - - - +
164A HIS* 1.3 66.3 + - + +
167A PHE* 3.3 48.7 - + - +
179A LEU* 3.3 31.1 - - + +
180A ASN* 2.8 37.9 + - - +
183A PHE* 3.9 26.3 - + - +
204A LEU* 3.5 31.2 - - + -
207A LEU* 3.3 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER 4.9 0.7 - - - +
89A ALA* 3.3 44.6 + - + +
93A TYR* 4.7 4.8 - + - -
160A ALA* 2.9 25.7 + - + +
161A HIS 4.5 0.4 - - - +
163A TYR* 1.3 85.0 - - + +
165A GLN* 1.3 65.1 + - + +
167A PHE* 4.8 1.9 + - - +
203A PRO* 3.6 29.6 - - + +
204A LEU* 4.2 10.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER 4.6 7.8 + - - +
84A CYS* 3.9 8.4 - - - +
85A PRO* 6.2 0.8 - - - +
86A VAL 4.8 3.1 + - - +
88A SER* 3.9 28.3 + - - +
89A ALA 4.6 9.1 - - - -
161A HIS* 2.8 36.4 + - - +
164A HIS* 1.3 85.8 - - + +
166A HIS* 1.3 76.2 + - + +
167A PHE* 3.4 1.4 + - - -
168A ASP* 4.6 4.9 + - - +
169A SER* 5.0 0.2 + - - -
301A ZN 3.9 2.9 - - - -
----------------------------------------------------------
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