Contacts of the helix formed by residues 162 - 180 (chain B) in PDB entry 3A3K
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 ARG 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.5 28.4 + - - +
156B ASP* 3.5 18.9 + - + +
159B GLY* 5.6 3.8 - - - +
160B ASP* 2.9 28.1 + - - +
161B ASP* 1.3 75.4 - - - +
163B PRO* 1.3 70.1 - - - +
164B CYS 3.3 2.1 + - - -
165B PHE* 3.4 56.2 + - + +
166B PHE* 3.2 27.0 + - + -
187B GLU* 4.3 19.2 + - - -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS* 4.4 2.4 + - - +
156B ASP* 3.2 12.8 - - - +
160B ASP* 3.7 14.4 - - - +
161B ASP* 3.4 10.9 - - + +
162B ARG* 1.3 91.0 - - - +
164B CYS* 1.3 59.7 + - + +
166B PHE* 3.4 5.2 + - + +
167B ILE* 3.0 41.3 + - + +
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Residues in contact with CYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 4.1 7.9 - - + -
155B ALA 3.3 23.6 - - - +
156B ASP* 3.0 8.1 + - - +
163B PRO* 1.3 76.6 - - - +
165B PHE* 1.3 66.1 + - - +
167B ILE* 3.6 1.9 - - - +
168B VAL* 3.0 29.3 + - - +
213B CYS* 2.1 65.7 - - + +
214B SER* 3.9 4.3 - - - -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 3.9 33.8 - + + -
156B ASP* 3.0 16.8 + - - +
162B ARG* 3.4 51.1 + - + +
164B CYS* 1.3 76.2 - - - +
166B PHE* 1.3 83.3 + + - +
168B VAL* 3.3 1.9 + - - +
169B GLU* 2.8 54.0 + - + +
187B GLU* 5.5 0.4 - - - +
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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
----------------------------------------------------------
87B VAL* 3.5 37.7 - - + -
88B TYR* 3.7 32.8 - + - -
111B ALA* 3.8 17.3 - - + -
112B LEU 5.2 1.9 + - - -
130B HIS* 3.5 21.6 - - + +
161B ASP* 3.2 21.3 - - - -
162B ARG* 3.2 24.2 + - + -
163B PRO* 3.8 6.5 - - + +
164B CYS 3.2 0.4 - - - -
165B PHE* 1.3 93.6 - + - +
167B ILE* 1.3 64.5 + - - +
169B GLU* 3.4 22.4 + - - +
170B GLY* 3.0 20.4 + - - -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS* 3.4 33.3 - - + +
133B LEU* 3.7 23.6 - - + +
163B PRO* 3.0 30.7 + - + +
164B CYS* 3.6 5.6 - - - +
166B PHE* 1.3 76.3 - - - +
168B VAL* 1.3 57.7 + - + +
170B GLY* 3.8 0.7 - - - -
171B LEU* 3.0 27.5 + - - +
213B CYS* 3.8 21.8 - - - -
241B LEU* 3.9 23.6 - - + +
243B VAL* 4.4 24.7 - - + -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 3.6 38.8 - - + -
154B TYR* 3.7 36.6 - - + -
164B CYS 3.0 20.8 + - - +
165B PHE 3.8 3.1 - - - +
167B ILE* 1.3 75.3 - - + +
169B GLU* 1.3 58.2 + - - +
171B LEU* 3.7 6.7 - - + +
172B TYR* 2.7 39.2 + - + +
185B HIS* 4.5 11.9 - - + -
213B CYS* 4.5 8.1 - - + -
241B LEU* 4.9 1.8 - - + -
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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
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111B ALA* 4.8 0.3 - - - +
112B LEU* 3.8 36.3 + - + +
113B GLY 4.6 3.1 + - - -
165B PHE* 2.8 45.0 + - + +
166B PHE* 3.6 23.8 - - - +
168B VAL* 1.3 75.9 - - - +
170B GLY* 1.3 63.2 + - - +
172B TYR* 3.7 4.3 - - - +
173B MET* 3.1 33.4 + - + +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 4.5 9.8 - - - +
130B HIS* 3.7 23.3 - - - -
131B VAL* 4.0 13.8 - - - +
166B PHE 3.0 14.9 + - - -
167B ILE 3.8 2.7 - - - -
169B GLU* 1.3 76.3 - - - +
171B LEU* 1.3 61.3 + - - +
173B MET* 4.3 1.0 - - - +
174B ARG* 3.3 26.5 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS 3.8 2.6 + - - -
133B LEU* 3.7 24.2 - - + -
134B GLY* 4.1 10.9 - - - +
137B VAL* 4.0 27.8 - - + -
152B VAL* 4.5 21.3 - - + -
167B ILE 3.0 16.5 + - - +
168B VAL* 3.7 6.1 - - - +
170B GLY* 1.3 72.9 - - - +
172B TYR* 1.3 70.5 + - - +
174B ARG 4.0 0.2 - - - -
175B VAL* 3.0 43.3 + - + +
183B VAL* 5.1 4.7 - - + -
211B TYR* 4.9 10.1 - - + -
241B LEU* 3.8 24.7 - - + -
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Residues in contact with TYR 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 VAL* 2.7 29.3 + - + +
169B GLU* 3.7 4.7 - - - +
171B LEU* 1.3 78.3 - - + +
173B MET* 1.3 83.1 + - + +
175B VAL* 3.8 1.4 - - - +
176B ARG* 2.9 70.9 + - + +
183B VAL* 3.5 44.0 - - + -
185B HIS* 4.1 22.6 - + - -
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.6 36.6 - - + -
169B GLU* 3.1 20.6 + - + +
170B GLY 4.4 1.8 - - - +
172B TYR* 1.3 102.4 - - + +
174B ARG* 1.3 58.3 + - - +
176B ARG* 4.0 3.6 - - - +
177B GLU* 3.1 30.4 + - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.5 53.6 + - + +
132B LYS* 5.2 2.8 - - - +
134B GLY* 3.7 13.2 - - - +
135B ASP* 2.9 43.1 + - - +
170B GLY 3.3 16.8 + - - +
173B MET* 1.3 76.0 - - - +
175B VAL* 1.3 60.5 + - - +
177B GLU* 3.4 21.0 + - - +
178B ARG* 3.1 42.6 + - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY* 3.4 24.0 - - - +
137B VAL* 3.8 27.4 - - + -
138B THR* 3.9 9.0 - - - +
171B LEU* 3.0 29.9 + - + +
172B TYR* 4.0 1.6 - - - +
174B ARG* 1.3 72.2 - - - +
176B ARG* 1.3 65.5 + - - +
177B GLU 3.1 1.3 - - - -
178B ARG 3.1 0.5 + - - -
179B LEU* 2.9 36.4 + - + +
181B ILE* 3.9 30.3 - - + -
183B VAL* 4.2 8.5 - - + -
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 2.9 64.9 + - + +
173B MET* 4.0 5.2 - - - +
175B VAL* 1.3 76.8 - - - +
177B GLU* 1.3 58.3 + - - +
180B ASN* 2.9 61.7 + - - +
181B ILE 3.1 32.1 + - - +
182B THR* 4.5 11.3 + - - +
183B VAL* 4.4 8.8 - - + +
1E NAG 4.4 6.1 + - - -
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Residues in contact with GLU 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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173B MET 3.1 21.3 + - - +
174B ARG* 3.4 31.5 + - - +
175B VAL 3.1 0.6 - - - -
176B ARG* 1.3 79.1 - - - +
178B ARG* 1.3 61.6 + - + +
180B ASN* 4.7 1.1 + - - +
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Residues in contact with ARG 178 (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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135B ASP* 2.8 38.7 + - - +
138B THR* 4.0 26.4 - - + +
142B ARG* 3.3 26.8 + - - +
174B ARG* 3.1 37.5 + - - +
175B VAL 4.3 0.2 - - - +
177B GLU* 1.3 84.5 - - + +
179B LEU* 1.3 60.8 + - - +
180B ASN 3.8 0.2 - - - -
399B GLN* 2.9 38.3 + - - +
507B SO4 2.6 45.8 + - - +
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Residues in contact with LEU 179 (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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138B THR* 3.8 26.2 - - + +
141B HIS* 3.6 35.9 - - + +
142B ARG* 3.6 37.7 - - + +
146B TRP 4.8 2.2 - - - +
147B GLU* 4.9 5.1 - - + +
175B VAL* 2.9 26.5 + - + +
178B ARG* 1.3 78.2 - - - +
180B ASN* 1.3 72.1 + - - +
181B ILE* 3.2 21.7 + - + +
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Residues in contact with ASN 180 (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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147B GLU 5.0 1.9 - - - +
175B VAL 3.8 0.4 + - - -
176B ARG* 2.9 41.9 + - - +
177B GLU 4.7 0.6 - - - +
178B ARG 3.8 1.0 - - - -
179B LEU* 1.3 79.7 - - - +
181B ILE* 1.3 59.9 + - - +
1E NAG 1.4 83.9 + - - +
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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