Contacts of the strand formed by residues 169 - 182 (chain A) in PDB entry 3AA6
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 TRP 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLN* 3.8 29.8 - - + -
164A GLN* 2.9 73.9 + - + +
167A ASN* 3.2 35.6 - - + +
168A PHE* 1.3 80.2 - - - +
170A ASN* 1.3 72.0 + - - +
197A HIS 3.1 13.2 - - - +
198A TYR* 4.2 11.2 - + + -
199A TYR* 3.7 3.4 - - - -
235B LYS* 5.0 9.3 - - + +
239B ILE* 3.6 54.3 - - + -
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Residues in contact with ASN 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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26A PRO* 3.1 28.1 - - + +
27A GLY* 4.3 4.8 + - - +
28A GLU* 2.8 34.8 + - - +
162A GLN 3.5 6.5 - - - -
163A PHE* 3.2 31.7 - - + +
164A GLN 3.4 2.1 + - - -
165A PRO* 4.1 6.2 - - - +
169A TRP* 1.3 82.4 - - - +
171A GLY* 1.3 59.3 + - - +
195A GLN 4.2 0.2 - - - +
196A VAL* 3.5 4.0 - - - +
197A HIS* 2.8 32.4 + - + +
199A TYR* 3.3 21.0 + - - -
239B ILE* 4.7 0.2 - - - -
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Residues in contact with GLY 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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26A PRO* 4.1 4.7 - - - -
161A HIS* 3.2 6.6 - - - +
162A GLN 2.8 32.3 + - - +
163A PHE* 4.0 2.3 - - - -
169A TRP* 4.4 1.0 - - - -
170A ASN* 1.3 77.5 - - - +
172A ARG* 1.3 61.2 + - - +
195A GLN 3.3 9.4 - - - -
196A VAL* 4.2 0.2 - - - -
239B ILE* 4.2 10.5 - - - -
243B LEU* 3.6 15.3 - - - -
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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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26A PRO* 3.6 31.0 - - + +
27A GLY 4.5 0.2 - - - +
57A TYR* 4.3 6.3 + - - -
61A GLN* 3.5 57.6 + - - +
63A THR* 4.8 6.1 + - - +
64A PRO* 4.1 9.9 - - - +
159A GLU* 2.8 26.8 + - - +
160A SER 3.4 7.4 - - - +
161A HIS* 3.3 16.8 + - + +
163A PHE* 3.5 18.1 - - - -
171A GLY* 1.3 75.3 - - - +
173A TRP* 1.3 72.7 + - - +
174A ARG* 4.0 13.2 + - + +
193A LYS 4.0 0.2 - - - +
194A ILE* 3.4 3.1 - - - -
195A GLN* 2.9 34.8 + - + +
243B LEU* 3.6 8.9 - - - +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.1 40.9 + + + -
158A ILE* 4.3 6.5 - - + -
159A GLU* 3.5 3.3 - - - -
160A SER* 2.8 38.0 + - - +
172A ARG* 1.3 75.5 - - - +
174A ARG* 1.3 73.4 + - - +
175A SER* 3.2 23.5 + - - -
192A LEU* 4.7 2.5 - - + -
193A LYS 3.4 7.0 - - - -
194A ILE* 3.7 24.5 - - + +
236A GLU* 3.7 28.5 - - + -
239A TYR* 3.5 36.1 - + - -
240A GLN* 4.9 8.7 - - + -
240B VAL* 5.9 2.2 - - + -
243B LEU* 3.9 18.1 - - + +
244B ARG* 3.7 26.9 - - + -
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Residues in contact with ARG 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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60A ASP* 2.9 31.8 + - - +
61A GLN* 3.7 45.7 + - - +
62A PHE* 4.0 21.3 - - + -
158A ILE 3.3 7.0 - - - -
159A GLU* 4.6 1.1 - - + -
172A ARG* 4.0 13.3 + - + +
173A TRP* 1.3 81.3 + - - +
175A SER* 1.3 62.1 + - - +
191A VAL 4.1 0.4 - - - +
192A LEU* 3.6 0.3 - - - -
193A LYS* 2.8 80.6 + - + +
194A ILE 5.4 0.6 - - - -
195A GLN* 4.7 18.0 + - - +
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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
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62A PHE* 3.5 4.1 - - - -
156A ALA 3.9 0.3 - - - +
157A CYS* 3.4 3.1 - - - -
158A ILE* 2.9 49.4 + - - +
173A TRP* 3.2 15.6 + - - +
174A ARG* 1.3 76.5 - - - +
176A GLU* 1.3 61.4 + - - +
177A TRP* 4.0 3.8 + - - -
191A VAL 3.3 4.9 - - - -
192A LEU* 3.5 17.7 - - - -
236A GLU* 2.6 29.2 + - - -
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Residues in contact with GLU 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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62A PHE* 3.3 27.8 - - + -
78A GLU* 4.5 7.4 - - - +
79A HIS* 2.9 28.0 + - - -
155A ILE* 4.2 7.9 - - + -
156A ALA 3.3 9.2 - - - +
157A CYS* 3.7 5.8 - - - -
175A SER* 1.3 75.8 - - - +
177A TRP* 1.3 63.8 + - - +
178A LYS* 3.2 27.8 + - + +
189A ALA 4.1 0.2 - - - +
190A ALA* 3.1 5.0 - - - +
191A VAL* 2.9 46.8 + - + +
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Residues in contact with TRP 177 (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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154A ILE 3.6 1.7 - - - +
155A ILE* 3.4 2.1 - - - +
156A ALA* 2.7 47.6 + - + +
158A ILE* 4.8 4.5 - - + -
175A SER* 4.1 4.0 - - - -
176A GLU* 1.3 84.7 - - - +
178A LYS* 1.3 62.0 + - - +
179A PHE* 3.7 16.9 - + + -
188A VAL* 3.4 30.1 - - + -
189A ALA 3.7 2.5 - - - -
190A ALA* 3.3 18.4 - - + -
192A LEU* 3.6 19.0 - - + +
212A ILE* 3.9 16.8 - - + -
231A ILE* 3.8 14.8 - - + -
232A ILE* 3.6 44.3 - - + +
235A ALA* 3.6 29.8 - - + -
236A GLU* 2.9 24.0 + - + -
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Residues in contact with LYS 178 (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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78A GLU* 5.3 2.4 + - - -
79A HIS* 4.0 20.8 - - - -
148A ILE* 6.1 2.5 - - + +
153A THR* 4.5 9.9 - - + -
154A ILE 3.3 5.2 - - - +
155A ILE* 4.0 20.6 - - + +
176A GLU* 3.2 28.8 + - + +
177A TRP* 1.3 77.0 - - - +
179A PHE* 1.3 61.4 - - - +
180A THR* 3.9 4.5 + - - +
187A GLN 3.5 2.1 - - - +
188A VAL* 3.4 4.5 - - - +
189A ALA* 2.8 47.9 + - + +
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Residues in contact with PHE 179 (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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152A GLN 4.0 0.2 - - - +
153A THR* 3.3 4.4 - - - -
154A ILE* 2.8 51.5 + - + +
156A ALA* 4.6 7.2 - - + -
177A TRP* 3.7 28.3 - + + -
178A LYS* 1.3 73.6 - - - +
180A THR* 1.3 62.3 + - - +
181A ILE* 3.7 5.0 + - + +
186A ALA* 4.7 2.2 - - + -
187A GLN 3.4 5.6 - - - +
188A VAL* 3.7 32.8 - - + -
228A PHE* 3.5 73.6 - + + -
231A ILE* 5.0 3.8 - - + -
232A ILE* 3.8 26.0 - - + -
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Residues in contact with THR 180 (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 GLN* 3.3 47.6 - - + +
152A GLN 3.8 2.5 - - - -
153A THR* 4.1 17.2 + - - +
178A LYS* 4.9 4.5 + - - +
179A PHE* 1.3 71.6 - - - +
181A ILE* 1.3 63.2 + - - +
182A THR* 3.4 6.9 + - + -
186A ALA* 3.2 4.4 - - - -
187A GLN* 2.9 43.3 + - - +
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Residues in contact with ILE 181 (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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117A LEU* 4.4 15.5 - - + -
120A TRP* 3.9 34.8 - - + -
151A GLN* 5.1 2.9 - - - +
152A GLN* 3.0 35.1 + - + +
154A ILE* 4.3 18.4 - - + -
179A PHE 4.1 8.3 - - - +
180A THR* 1.3 73.8 - - - +
182A THR* 1.3 63.3 + - - +
183A PRO* 3.6 24.9 - - + +
185A THR 4.1 2.7 - - - +
186A ALA* 4.3 6.7 - - + -
218A VAL* 4.3 16.2 - - + -
228A PHE* 5.0 7.0 - - + -
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Residues in contact with THR 182 (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 GLN* 3.8 24.7 - - - +
180A THR* 3.4 3.5 + - + +
181A ILE* 1.3 77.3 - - - +
183A PRO* 1.4 71.3 - - - +
184A PRO* 4.1 0.9 - - - +
185A THR* 2.9 32.3 + - - +
187A GLN* 2.4 39.6 + - - +
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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