Contacts of the helix formed by residues 162 - 175 (chain B) in PDB entry 3N3B
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 PHE 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.6 26.7 - - + +
66B LEU* 3.5 40.2 - - + -
67B ASP* 3.2 32.8 - - - -
105B TYR* 3.9 6.5 - - - -
157B LEU* 2.8 39.4 + - + +
158B GLU* 3.6 42.8 - - + +
160B PHE 3.4 0.4 - - - -
161B LEU* 1.3 72.9 - - - +
163B TYR* 1.3 56.9 + - + +
164B SER 3.2 0.4 - - - -
165B GLY* 3.0 8.4 + - - -
166B PHE* 3.0 57.3 + + + -
188B ILE* 5.7 0.9 - - + -
192B GLU* 5.7 1.1 - - + -
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU 3.5 21.0 + - - -
159B SER* 3.5 27.4 - - - -
160B PHE 3.3 10.5 + - - +
161B LEU 3.0 2.2 + - - -
162B PHE* 1.3 73.2 - - + +
164B SER* 1.3 63.5 - - - +
165B GLY 3.1 1.3 - - - -
166B PHE* 3.6 28.4 - + + -
167B TRP* 3.1 18.0 + - - +
189B ILE* 3.8 22.6 + - + +
192B GLU* 5.0 3.3 - - - +
250B VAL* 4.9 0.3 - - - +
253B PHE* 3.4 30.7 - + + +
254B LEU* 4.3 4.7 - - + +
257B ASN* 3.4 44.0 - - + +
286B LEU* 5.2 1.3 - - + -
322B PEO 4.2 3.5 + - - -
85C ASN* 2.9 33.1 + - - -
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 5.0 0.5 - - - +
63B LEU* 6.0 0.3 - - - +
134B LYS* 4.5 0.3 + - - -
161B LEU 3.0 8.8 + - - -
162B PHE 4.5 0.2 - - - -
163B TYR* 1.3 76.4 - - - +
165B GLY* 1.3 58.7 + - - +
167B TRP* 4.2 1.2 - - - +
233B GLU* 2.6 28.7 + - - -
236B TYR* 4.0 13.7 - - - -
237B THR* 4.1 9.6 - - - -
240B LEU* 5.0 2.9 - - - +
241B TYR* 2.8 32.6 + - - -
250B VAL* 3.8 13.2 - - - +
254B LEU* 3.7 24.5 - - - +
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 3.4 33.3 - - - +
63B LEU* 4.4 11.7 - - - +
162B PHE 3.0 7.8 + - - -
164B SER* 1.3 81.4 + - - +
166B PHE* 1.3 64.3 + - - +
167B TRP 3.2 2.8 + - - -
168B LEU* 3.5 4.0 + - - +
169B PRO* 3.2 17.5 - - - +
236B TYR* 6.3 0.2 - - - -
240B LEU* 5.6 1.8 - - - -
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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
----------------------------------------------------------
63B LEU* 4.1 20.4 - - + -
105B TYR* 4.3 3.4 - - - -
158B GLU 4.8 3.6 - - - -
162B PHE* 3.0 50.3 + + + -
163B TYR* 3.5 43.0 + + + -
165B GLY* 1.3 74.2 - - - +
167B TRP* 1.3 63.5 + - - +
168B LEU 3.3 0.2 - - - -
169B PRO* 3.3 11.6 - - + +
170B MET* 3.3 21.2 - - - +
185B ILE* 3.6 28.9 - - + +
188B ILE* 3.7 27.8 - - + -
189B ILE* 3.9 20.6 - - + -
192B GLU* 5.0 5.8 - - + -
253B PHE* 4.4 2.0 - - + -
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Residues in contact with TRP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR 3.1 18.4 + - - +
164B SER 4.2 8.5 - - - +
165B GLY 3.2 0.8 - - - -
166B PHE* 1.3 76.7 - - - +
168B LEU* 1.3 67.1 + - + +
170B MET* 3.2 7.8 + - - +
171B TYR* 2.9 59.4 + + + -
241B TYR* 3.9 8.5 - + - +
246B TRP* 3.4 49.8 - + + -
249B ASP* 2.8 44.3 + - + -
250B VAL* 3.6 21.8 - - + -
253B PHE* 3.6 36.3 - + + -
282B ILE* 3.8 17.4 - - + +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 33.4 - - + -
56B THR* 3.6 40.6 - - + +
59B VAL* 4.1 10.8 - - + -
60B PHE* 6.1 0.2 - - + -
165B GLY 3.5 5.2 + - - +
167B TRP* 1.3 93.2 - - + +
169B PRO* 1.4 65.1 - - + +
171B TYR* 3.0 4.9 + - + +
172B PHE* 2.9 55.9 + - + -
241B TYR* 3.8 11.8 + - + +
246B TRP* 4.0 12.1 - - + -
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 5.3 0.7 - - + -
60B PHE* 3.8 29.6 - - + -
165B GLY 3.2 16.4 - - - +
166B PHE* 3.3 9.6 - - + +
168B LEU* 1.4 94.1 - - + +
170B MET* 1.3 65.3 + - + +
172B PHE* 4.0 9.8 - - + +
173B SER* 3.1 26.0 + - - -
178B LEU* 5.0 1.5 - - + +
181B THR* 5.2 2.9 - - + -
182B ALA* 3.6 14.8 - - + +
185B ILE* 3.8 26.2 - - + -
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Residues in contact with MET 170 (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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166B PHE 3.3 14.6 + - - +
167B TRP* 3.2 8.2 + - - +
168B LEU 3.1 0.8 - - - -
169B PRO* 1.3 83.0 - - + +
171B TYR* 1.3 64.6 + - - +
173B SER* 3.5 2.8 - - - -
174B SER* 3.2 18.4 + - - -
182B ALA* 3.7 24.2 - - + +
185B ILE* 4.0 18.4 - - + -
186B ARG* 4.0 17.9 - - + +
189B ILE* 4.6 2.7 - - + -
253B PHE* 5.1 3.1 - - + -
282B ILE* 4.3 22.6 - - + +
285B ALA* 3.4 35.3 - - + +
286B LEU* 3.9 31.2 - - + -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 5.3 1.1 - - - -
167B TRP* 2.9 46.1 + + + +
168B LEU* 3.0 7.8 + - + +
170B MET* 1.3 74.7 - - - +
172B PHE* 1.3 81.5 + + - +
174B SER* 2.6 25.5 + - - -
175B ARG* 3.3 46.8 + - + +
246B TRP* 3.4 50.5 + + - -
279B ASN* 5.9 2.2 - - - -
282B ILE* 3.8 17.0 - - + +
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 28.9 - - + -
52B GLU* 4.1 27.4 - - + -
56B THR* 3.5 26.2 - - + -
168B LEU* 2.9 46.8 + - + +
169B PRO* 4.0 8.3 - - + +
171B TYR* 1.3 88.1 - + - +
173B SER* 1.3 57.5 + - - +
175B ARG* 3.2 5.9 + - + +
176B GLY 3.1 5.0 + - - -
177B LYS* 2.7 53.3 + - + +
178B LEU* 3.8 26.0 - - + -
246B TRP* 4.8 1.3 - + - -
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Residues in contact with SER 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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169B PRO 3.1 19.5 + - - -
170B MET* 3.5 9.6 - - - -
172B PHE* 1.3 77.9 - - - +
174B SER* 1.3 58.8 + - - +
176B GLY* 3.2 13.4 + - - +
177B LYS 3.5 7.3 + - - +
179B THR* 5.1 8.2 - - - +
182B ALA* 3.8 13.6 - - - +
186B ARG* 3.4 25.8 + - - -
285B ALA* 4.0 8.3 - - - +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET 3.2 8.9 + - - -
171B TYR* 2.6 30.1 + - - -
173B SER* 1.3 76.9 - - - +
175B ARG* 1.3 70.9 + - - +
176B GLY 3.3 0.8 + - - -
281B ALA* 3.7 39.5 - - - +
282B ILE* 4.6 1.4 - - - +
285B ALA* 4.5 2.9 - - - +
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Residues in contact with ARG 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 TYR* 3.3 50.8 + - + +
172B PHE* 3.2 9.0 + - + +
173B SER 3.2 0.6 - - - -
174B SER* 1.3 86.6 + - - +
176B GLY* 1.3 60.3 + - - +
177B LYS* 3.4 15.7 - - + +
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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