Contacts of the helix formed by residues 159 - 177 (chain B) in PDB entry 3NA1
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 ILE 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE* 4.3 14.8 - - + -
143B LEU* 4.5 7.0 - - + -
146B ARG* 4.3 2.7 - - - +
155B TYR* 4.1 25.4 - - + -
157B GLY 3.5 6.2 + - - +
158B ASP* 1.3 75.0 + - - +
160B SER* 1.3 60.0 + - - +
161B ASP 3.3 2.7 - - - -
162B ASP* 3.1 24.4 + - + +
163B LEU* 2.8 50.4 + - + +
297B GLN* 5.0 1.1 + - - +
300B LEU* 4.0 15.0 - - + -
440B MET* 5.6 0.2 - - + -
468B ILE 4.6 1.6 + - - -
470B PHE* 4.0 15.9 - - + -
472B PHE* 3.6 31.0 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP* 2.6 27.8 + - - -
159B ILE* 1.3 77.9 - - - +
161B ASP* 1.3 64.3 + - - +
163B LEU* 3.1 9.5 + - - +
164B PHE* 2.9 47.3 + - - -
294B MET* 4.5 4.6 - - - +
297B GLN* 3.4 25.6 + - - -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP 5.0 2.2 + - - +
159B ILE 3.3 0.6 - - - -
160B SER* 1.3 83.9 + - - +
162B ASP* 1.3 58.9 + - - +
164B PHE* 3.4 17.7 + - - +
165B ARG* 3.1 54.5 + - - +
192B GLN* 5.6 2.7 + - - +
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Residues in contact with ASP 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.6 24.0 - - + -
142B VAL* 5.3 2.6 - - + +
143B LEU* 6.5 0.4 - - + -
146B ARG* 2.7 47.5 + - - -
158B ASP 4.5 2.3 - - - +
159B ILE* 3.1 22.1 + - + +
161B ASP* 1.3 74.5 - - - +
163B LEU* 1.3 55.4 + - - +
165B ARG* 3.0 30.9 + - - +
166B PHE* 2.7 33.6 + - - +
183B LEU* 4.3 3.5 - - + +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 4.0 11.9 - - + -
159B ILE* 2.8 39.8 + - + +
160B SER* 3.1 10.1 + - - +
162B ASP* 1.3 73.3 - - - +
164B PHE* 1.3 55.1 + - - +
166B PHE* 3.2 8.2 + - + +
167B ALA* 2.8 30.5 + - - +
293B SER* 3.5 24.3 - - - +
294B MET* 5.6 0.4 - - + -
296B LEU* 4.6 13.9 - - + -
297B GLN* 3.6 38.1 - - + -
300B LEU* 4.7 2.5 - - + -
436B PHE* 3.9 30.3 - - + -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B SER* 2.9 36.2 + - - -
161B ASP* 3.6 17.7 - - - +
162B ASP 3.4 0.2 - - - -
163B LEU* 1.3 72.8 - - - +
165B ARG* 1.3 59.7 + - - +
167B ALA 3.3 0.9 + - - -
168B PHE* 3.0 28.8 + - - +
192B GLN* 6.0 0.2 - - - +
195B ILE* 3.9 22.4 - - + +
199B TYR* 4.9 15.9 - + + -
289B VAL* 3.6 15.7 - - + +
290B ASP* 3.8 30.7 - - + -
293B SER* 3.2 25.1 - - - -
294B MET* 3.5 27.6 - - + -
463B MET* 5.2 2.2 - - + -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ARG* 4.9 0.8 - - - +
161B ASP* 3.1 42.2 + - - +
162B ASP* 3.0 34.6 + - - +
164B PHE* 1.3 72.1 - - + +
166B PHE* 1.3 60.5 + - - +
168B PHE* 3.3 1.7 + - - +
169B GLU* 2.9 31.9 + - - +
182B MET* 3.4 35.0 + - + +
183B LEU* 4.3 6.2 - - + +
187B VAL* 4.1 14.1 - - - +
192B GLN* 2.8 46.0 + - - +
195B ILE* 3.9 18.2 - - + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU 5.3 0.4 - - - -
135B VAL* 3.7 18.4 - - + -
136B SER* 3.4 31.9 - - - -
139B PHE* 3.8 29.8 - + + -
162B ASP 2.7 19.0 + - - +
163B LEU* 3.3 12.3 - - + +
165B ARG* 1.3 73.2 - - - +
167B ALA* 1.3 65.3 + - + +
169B GLU* 3.7 2.7 - - - +
170B SER* 3.0 43.2 + - - -
183B LEU* 4.0 8.4 - - + +
293B SER* 6.0 0.7 - - - -
296B LEU* 3.7 18.2 - - + -
432B GLU* 3.3 28.7 - - + -
436B PHE* 3.5 28.3 - + + -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU 2.8 19.1 + - - +
164B PHE 3.3 3.3 + - - +
166B PHE* 1.3 72.5 - - + +
168B PHE* 1.3 57.3 + - - +
170B SER* 3.4 2.6 + - - -
171B ILE* 3.1 30.0 + - - +
288B GLY 3.6 8.3 - - - +
289B VAL* 3.3 27.8 - - - +
292B THR* 3.3 20.0 - - - +
293B SER* 4.1 4.3 - - - +
432B GLU* 3.6 12.5 - - - +
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Residues in contact with PHE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE 3.0 16.4 + - - +
165B ARG 3.7 3.1 - - - +
167B ALA* 1.3 75.0 - - - +
169B GLU* 1.3 58.1 + - - +
171B ILE* 3.4 7.2 + - + +
172B THR* 2.7 60.7 + - + +
180B GLN* 4.0 13.2 - - + -
182B MET* 3.6 30.5 - - + -
191B ALA* 4.0 13.0 - - + -
194B PHE* 3.4 39.0 - + - -
195B ILE* 3.7 21.5 - - + -
241B TYR* 3.7 26.0 - + - -
285B LEU* 5.2 0.9 - - + -
289B VAL* 4.0 13.4 - - + +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.7 17.5 - - + -
165B ARG 2.9 18.1 + - - +
166B PHE* 3.7 4.9 - - - +
168B PHE* 1.3 77.0 - - - +
170B SER* 1.3 57.8 + - - +
172B THR* 3.1 4.8 + - - -
173B ASN* 3.0 30.8 + - - +
179B ARG* 2.7 40.3 + - - +
180B GLN* 3.2 12.0 + - - +
181B GLY* 2.9 26.7 + - - -
182B MET* 2.9 34.1 + - + +
183B LEU* 4.6 5.4 - - + -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.0 16.8 + - - +
135B VAL* 3.6 13.3 - - - +
166B PHE* 3.0 42.1 + - - -
167B ALA 3.7 1.3 - - - -
168B PHE 3.2 0.2 - - - -
169B GLU* 1.3 74.1 - - - +
171B ILE* 1.3 65.9 + - - +
173B ASN* 3.3 2.4 + - - +
174B VAL* 3.1 24.6 + - - +
428B ILE* 6.0 0.2 - - - -
432B GLU* 3.5 29.5 - - - +
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ALA 3.1 18.4 + - - +
168B PHE* 3.4 15.7 - - + +
170B SER* 1.3 76.7 - - - +
172B THR* 1.3 61.2 + - + +
174B VAL* 3.3 17.6 - - + +
175B ILE* 3.0 46.4 + - + +
284B MET 3.8 15.9 - - - +
285B LEU* 4.1 24.9 - - + +
288B GLY* 4.8 7.9 - - - +
289B VAL* 4.4 4.0 - - + -
428B ILE* 4.1 24.7 - - + -
432B GLU* 4.8 4.0 + - - +
601B HEM 4.2 19.1 - - + -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PHE* 2.7 56.4 + - + +
169B GLU* 3.1 7.4 + - - -
171B ILE* 1.3 73.8 - - - +
173B ASN* 1.3 62.1 + - - +
176B PHE* 2.8 51.4 + - + +
178B GLU 3.9 2.7 + - - +
180B GLN* 3.2 27.3 + - + +
241B TYR* 5.2 2.5 - - + -
285B LEU* 3.7 18.2 - - + -
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 2.8 52.3 + - + +
134B ALA* 4.8 3.4 - - - +
135B VAL* 3.8 5.5 - - + +
169B GLU 3.0 21.1 + - - +
170B SER 3.7 4.0 - - - +
171B ILE 3.3 0.2 - - - -
172B THR* 1.3 76.6 + - - +
174B VAL* 1.3 58.1 + - - +
177B GLY* 2.8 32.4 + - - -
178B GLU 3.4 28.3 + - - +
179B ARG* 3.5 26.1 + - - +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.2 51.6 - - + -
131B LEU* 4.1 11.4 - - + +
132B LEU* 4.6 11.7 - - + -
170B SER 3.1 13.6 + - - +
171B ILE* 3.3 26.0 - - + +
173B ASN* 1.3 79.1 - - - +
175B ILE* 1.3 60.2 + - - +
259B TYR* 4.3 0.9 + - - -
261B GLY* 3.4 6.4 - - - -
262B ILE* 3.0 41.9 + - + +
428B ILE* 4.2 11.9 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ILE* 3.0 40.8 + - + +
172B THR 4.1 1.6 - - - +
174B VAL* 1.3 77.7 - - - +
176B PHE* 1.3 89.2 + - + +
177B GLY 3.6 0.2 - - - -
261B GLY 3.8 0.9 - - - -
262B ILE* 3.3 26.5 + - + -
263B LEU* 2.9 38.6 + - + +
264B TYR 4.5 0.3 + - - -
281B VAL* 4.3 15.7 - - + +
284B MET* 3.9 26.5 - - + -
285B LEU* 3.8 16.4 - - + -
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 2.8 41.1 + - + +
175B ILE* 1.3 87.8 - - + +
177B GLY* 1.3 61.4 + - - +
178B GLU* 3.3 24.1 + - + +
180B GLN* 4.6 8.7 - - - +
241B TYR* 3.5 42.2 - + + -
242B THR* 4.3 1.8 - - - -
245B PHE* 3.4 32.8 - + + -
260B ARG 3.5 7.6 - - - +
263B LEU* 3.5 32.1 - - + -
281B VAL* 4.1 13.9 - - + -
285B LEU* 4.1 22.9 - - + -
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.7 10.6 - - - +
173B ASN* 2.8 30.0 + - - +
175B ILE 3.6 1.6 - - - -
176B PHE* 1.3 72.8 - - - +
178B GLU* 1.3 61.5 + - - +
260B ARG* 3.5 23.2 + - - -
261B GLY* 4.4 1.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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