Contacts of the helix formed by residues 154 - 176 (chain A) in PDB entry 1V0D
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 ASN 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLU* 2.6 50.5 + - - +
137A THR* 4.6 4.2 - - + +
145A PHE* 3.6 10.3 - - - -
152A PHE* 4.7 1.0 - - - +
153A ARG* 1.3 83.2 + - + +
155A LYS* 1.3 82.1 + - - +
156A SER* 3.9 9.7 - - - -
157A GLY* 3.9 10.3 + - - +
158A TYR* 3.2 17.2 + - - +
160A ARG* 5.1 2.9 + - - -
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN 3.1 16.0 + - - -
135A ALA 2.8 32.5 + - - +
136A GLU* 2.9 16.0 + - - +
141A ASP* 3.1 26.6 + - - -
144A TRP* 3.6 34.5 - - + -
145A PHE* 3.6 16.8 - - + -
154A ASN* 1.3 74.9 - - - +
156A SER* 1.3 67.5 + - - +
157A GLY 3.0 1.1 - - - -
158A TYR* 2.8 14.9 + - - +
159A LEU* 3.0 13.0 + - - +
247A TYR* 2.6 48.9 + - + +
248A GLY* 4.4 0.2 - - - -
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 2.7 29.4 + - - -
154A ASN* 4.0 4.7 - - - -
155A LYS* 1.3 71.4 - - - +
157A GLY* 1.3 57.5 - - - +
159A LEU 3.3 0.9 + - - -
160A ARG* 2.8 39.8 + - - +
211A ASP* 3.4 28.4 + - - +
212A ARG* 3.7 11.8 + - - +
247A TYR* 3.5 24.0 - - - -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 4.8 5.8 - - - -
154A ASN* 3.6 16.2 + - - -
155A LYS 3.0 1.4 - - - -
156A SER* 1.3 80.9 - - - +
158A TYR* 1.3 60.6 + - - +
160A ARG* 3.4 20.1 + - - +
161A TYR* 3.1 22.3 + - - +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 3.6 27.6 - + + -
148A LEU* 3.7 27.7 - - + +
152A PHE* 3.6 46.1 - + + -
154A ASN 3.2 12.2 + - - +
155A LYS 2.8 13.6 + - - +
157A GLY* 1.3 72.1 - - - -
159A LEU* 1.3 60.5 + - + +
161A TYR* 3.0 17.2 + + - +
162A SER* 2.8 42.3 + - - -
253A ARG* 3.8 24.6 + - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 4.1 14.1 - - + -
155A LYS 3.0 7.4 + - - +
156A SER 3.8 6.3 - - - +
158A TYR* 1.3 95.9 - - + +
160A ARG* 1.3 65.6 + - - +
162A SER* 3.3 8.8 + - - -
163A CYS 3.0 18.4 + - - -
210A PHE* 3.4 30.5 - - + +
227A PHE* 5.0 0.7 - - + -
246A PRO* 3.5 28.3 - - + -
247A TYR* 3.3 41.3 - - + +
253A ARG* 4.4 7.2 - - + +
256A PHE* 4.8 11.0 - - + -
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 5.1 3.0 + - - -
156A SER* 2.8 30.8 + - - +
157A GLY* 3.5 16.7 - - - +
159A LEU* 1.3 72.1 - - - +
161A TYR* 1.3 64.3 + - - +
163A CYS 3.1 2.6 + - - -
164A GLU* 3.0 42.4 + - - +
204A GLN* 5.7 5.2 - - - -
207A GLY* 3.5 31.6 - - - +
208A SER* 4.3 1.8 - - - +
211A ASP* 3.4 37.3 + - + +
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.5 32.8 + - - -
152A PHE* 3.7 29.8 - + + -
157A GLY 3.1 9.5 + - - +
158A TYR* 3.0 19.2 + + - +
160A ARG* 1.3 79.8 - - - +
162A SER* 1.3 65.7 + - - +
164A GLU* 3.2 19.5 + - + +
165A SER* 2.8 46.6 + - - -
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 2.8 31.8 + - - -
159A LEU* 3.4 17.4 - - - +
161A TYR* 1.3 80.2 - - - +
163A CYS* 1.3 62.1 + - - +
165A SER* 3.1 19.6 + - - -
166A ARG* 3.3 19.5 + - - +
210A PHE* 4.4 10.6 - - - -
256A PHE* 5.5 2.4 - - - -
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Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU 3.0 7.3 + - - +
160A ARG 3.5 7.4 - - - +
162A SER* 1.3 76.1 - - - +
164A GLU* 1.3 64.2 + - - +
165A SER 3.1 1.0 + - - -
166A ARG* 3.1 15.1 + - - +
167A ILE* 3.2 24.8 + - - +
206A ASN 3.4 25.1 - - - -
207A GLY* 3.8 5.8 - - - -
209A TYR* 3.8 19.1 - - - -
210A PHE* 3.3 37.9 - - + -
261A LEU* 4.6 4.5 - - - -
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 3.0 40.2 + - - +
161A TYR* 3.4 19.3 + - + +
163A CYS* 1.3 76.8 - - - +
165A SER* 1.3 56.9 + - - +
167A ILE* 3.6 1.4 + - - +
168A ARG* 2.8 47.4 + - - +
204A GLN* 3.6 21.9 - - - +
205A TYR* 3.9 24.7 - - + +
207A GLY* 3.5 14.1 - - - -
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 2.8 39.6 + - - -
162A SER* 3.2 11.4 - - - -
163A CYS 3.0 0.4 - - - -
164A GLU* 1.3 74.7 - - - +
166A ARG* 1.3 61.1 + - - +
168A ARG* 3.7 7.0 - - - +
169A GLY* 2.7 27.5 + - - -
172A ARG* 3.7 10.2 + - - +
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.5 18.5 + - - +
163A CYS 3.1 5.3 + - - +
165A SER* 1.3 76.0 - - - +
167A ILE* 1.3 59.8 + - + +
169A GLY* 3.0 4.6 + - - -
170A TYR* 2.9 50.4 + - + +
210A PHE* 3.6 39.0 - - - -
256A PHE* 2.9 32.9 + - - -
257A SER* 4.0 10.9 + - - +
259A TRP* 2.7 22.8 + - - +
260A ASN* 3.7 15.4 - - - +
261A LEU* 3.8 16.6 - - + +
302A LEU* 5.3 0.6 - - - +
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A CYS* 3.2 25.3 + - - +
164A GLU 3.9 1.1 - - - +
166A ARG* 1.3 74.7 - - - +
168A ARG* 1.3 63.3 + - - +
170A TYR* 3.1 23.6 + - + +
171A LEU* 3.1 19.6 + - - +
200A LEU* 4.1 25.1 - - + -
205A TYR* 3.2 33.2 - - + +
206A ASN* 3.5 17.7 - - + -
209A TYR* 4.3 7.0 - - + -
261A LEU* 4.7 9.0 - - + -
295A PHE* 4.1 25.7 - - + +
300A LEU* 5.0 1.8 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 2.8 32.4 + - - +
165A SER* 3.7 5.8 - - - +
167A ILE* 1.3 77.4 - - - +
169A GLY* 1.3 57.6 + - - +
171A LEU* 3.2 10.0 + - + +
172A ARG* 3.0 46.0 + - + +
201A LYS* 5.8 1.0 - - - +
205A TYR* 3.3 58.3 + - + -
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER 2.7 13.7 + - - -
166A ARG* 3.0 6.7 + - - -
168A ARG* 1.3 75.5 - - - +
170A TYR* 1.3 63.3 + - - +
172A ARG* 3.3 27.3 + - - +
173A GLU* 3.0 34.4 + - - +
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Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 2.9 36.9 + - + +
167A ILE* 3.1 25.1 + - + +
169A GLY* 1.3 78.0 - - - +
171A LEU* 1.3 60.6 + - - +
173A GLU* 3.4 9.6 + - - -
174A VAL* 3.0 27.4 + - - +
260A ASN* 5.0 5.0 + - - -
261A LEU* 3.1 32.6 + - + +
263A HIS* 3.6 26.7 - + - -
267A LYS* 2.9 38.4 + - + +
294A LEU* 4.0 11.4 - - + +
295A PHE* 4.0 12.6 - + + -
300A LEU* 4.5 9.6 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE 3.1 12.0 + - - +
168A ARG* 3.2 12.5 + - + +
170A TYR* 1.3 75.1 - - - +
172A ARG* 1.3 68.1 + - + +
174A VAL* 3.1 12.3 + - + +
175A SER* 3.2 8.4 + - - +
193A LEU* 3.9 32.8 - - + +
196A MET* 5.6 2.0 - - + -
197A CYS* 3.9 32.3 - - + +
200A LEU* 3.9 22.9 - - + -
205A TYR* 5.0 8.1 - - + -
295A PHE* 3.7 18.3 - - + -
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.7 24.2 + - - +
168A ARG* 3.0 26.3 + - + +
169A GLY* 3.3 29.7 + - - +
171A LEU* 1.3 75.2 - - + +
173A GLU* 1.3 57.6 + - + +
175A SER* 2.7 31.3 + - - -
176A ALA* 3.0 13.0 + - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLY 3.0 17.2 + - - +
170A TYR* 3.6 17.6 - - - +
172A ARG* 1.3 77.6 - - + +
174A VAL* 1.3 61.4 + - - +
175A SER 3.6 0.2 + - - -
176A ALA* 3.7 17.5 + - - +
177A TYR* 3.8 7.4 + - - +
267A LYS* 3.1 34.5 + - - +
268A LYS* 4.4 24.5 + - + +
272A VAL* 5.4 3.1 - - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TYR* 3.0 18.3 + - + +
171A LEU* 3.4 13.7 - - + +
172A ARG 2.8 1.8 + - - -
173A GLU* 1.3 76.4 - - + +
175A SER* 1.3 62.8 + - - +
177A TYR* 3.3 6.7 + - - +
189A TYR* 2.9 37.8 + - + +
193A LEU* 3.9 15.0 - - + -
196A MET* 4.7 13.9 - - + -
267A LYS* 5.2 2.7 - - + -
272A VAL* 4.0 26.2 - - + -
275A LEU* 5.3 3.8 - - + -
294A LEU* 4.0 22.9 - - + -
295A PHE* 4.6 4.9 - - + -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.2 9.4 + - - +
172A ARG* 2.7 17.3 + - - -
174A VAL* 1.3 67.6 - - - +
176A ALA* 1.3 53.2 + - - -
177A TYR 2.5 17.8 + - - -
178A THR* 2.6 26.6 + - - -
190A LEU* 5.9 1.5 - - - +
193A LEU* 3.2 35.6 - - - +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG 3.0 8.0 + - - +
173A GLU* 3.7 15.7 - - - +
175A SER* 1.3 77.2 - - - +
177A TYR* 1.3 57.9 + - - +
178A THR 3.4 0.4 - - - -
179A SER* 3.7 15.5 + - - -
180A MET* 4.3 8.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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