Contacts of the strand formed by residues 162 - 173 (chain B) in PDB entry 2AOT
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 LEU 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 3.5 13.8 - - - +
136B TRP 3.6 2.5 - - - +
139B ILE* 3.7 25.1 - - + +
158B PHE 3.9 5.6 - - - +
159B HIS* 3.1 35.4 + - + +
160B SER 4.6 0.5 - - - +
161B LEU* 1.3 76.9 - - - +
163B GLY* 1.3 63.2 + - - +
166B ALA* 3.9 11.0 - - + +
167B LYS 3.5 24.2 - - - +
168B MET* 4.1 21.1 - - + +
290B ILE 4.2 0.9 - - - +
291B GLU 4.2 2.9 - - - -
292B ALA* 3.8 38.8 - - + +
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Residues in contact with GLY 163 (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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51B LYS* 4.9 0.4 - - - -
135B LYS* 4.0 20.0 - - - -
136B TRP 2.8 19.8 + - - -
137B ASP* 5.1 4.0 - - - -
161B LEU 3.6 1.6 + - - -
162B LEU* 1.3 77.0 - - - +
164B THR* 1.3 67.2 + - - -
165B ASN 3.3 1.0 + - - -
166B ALA* 3.1 13.7 + - - +
292B ALA* 3.4 9.0 - - - +
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Residues in contact with THR 164 (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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51B LYS* 2.8 39.3 + - - +
163B GLY* 1.3 68.7 - - - -
165B ASN* 1.3 84.4 + - - +
166B ALA 3.2 0.2 + - - -
292B ALA* 5.4 0.4 - - - -
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Residues in contact with ASN 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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46B ARG* 4.0 47.1 + - + +
47B ILE* 3.7 20.3 + - - +
49B ASP* 5.4 8.5 + - - +
51B LYS* 5.0 0.4 - - - +
163B GLY 3.3 1.4 + - - -
164B THR* 1.3 92.1 + - - +
166B ALA* 1.3 63.1 + - - +
167B LYS* 4.6 9.6 + - - +
291B GLU* 5.9 0.2 - - - -
292B ALA* 4.7 5.3 - - - +
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Residues in contact with ALA 166 (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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47B ILE* 4.4 0.7 - - - -
51B LYS* 5.2 0.2 - - - +
136B TRP 3.3 20.9 - - - +
137B ASP* 3.2 24.5 - - - +
162B LEU* 3.9 11.2 - - + -
163B GLY 3.1 22.6 + - - +
164B THR 3.1 2.3 - - - +
165B ASN* 1.3 81.9 - - - +
167B LYS* 1.3 65.3 + - - +
291B GLU* 4.2 1.9 - - - +
292B ALA* 3.3 23.6 + - - +
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Residues in contact with LYS 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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42B GLY 5.4 0.9 - - - -
43B ILE* 2.9 43.5 + - + +
46B ARG* 6.1 2.6 - - - +
47B ILE* 4.3 6.4 - - + +
137B ASP 3.4 4.8 + - - -
138B PHE* 3.3 22.4 - - + -
139B ILE 3.1 21.0 + - - -
162B LEU* 3.5 6.3 - - - +
165B ASN* 4.6 10.2 + - - +
166B ALA* 1.3 79.5 + - - +
168B MET* 1.3 59.7 + - - +
289B VAL* 4.0 11.0 - - + -
290B ILE 3.4 6.3 - - - +
291B GLU* 2.6 45.1 + - - +
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Residues in contact with MET 168 (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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139B ILE* 3.1 22.7 - - + +
140B HIS* 5.2 0.2 - - - -
141B MET* 4.4 12.6 - - - +
155B LEU* 4.0 12.6 - - - +
158B PHE* 3.7 27.6 - - + +
159B HIS* 3.8 28.3 - - + +
162B LEU* 4.1 14.3 - - + +
167B LYS* 1.3 76.3 - - - +
169B LEU* 1.3 62.0 + - - +
170B ILE* 4.1 16.1 + - + -
288B ILE 3.5 1.6 - - - +
289B VAL* 3.4 4.1 - - - -
290B ILE* 2.8 66.5 + - + +
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Residues in contact with LEU 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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35B PHE* 4.4 16.6 - - + -
36B MET* 6.4 1.3 - - + -
40B LEU* 4.7 7.4 - - + -
43B ILE* 5.1 2.0 - - + -
70B ILE* 4.9 4.3 - - + -
138B PHE* 3.8 29.6 - - + -
139B ILE 2.8 9.1 + - - -
140B HIS* 3.2 13.0 - - + +
141B MET 2.9 25.8 + - - +
142B ILE* 4.7 7.9 - - + -
167B LYS 4.2 0.2 - - - -
168B MET* 1.3 72.5 - - - +
170B ILE* 1.3 69.5 + - - +
171B ILE* 4.3 20.9 - - + -
287B PHE* 4.3 12.3 - - + -
288B ILE 3.4 19.1 - - - +
289B VAL* 4.0 19.5 - - + +
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Residues in contact with ILE 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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141B MET* 3.5 27.1 - - + +
145B LEU* 3.5 26.2 - - + -
155B LEU* 3.3 34.1 - - + -
168B MET* 4.3 8.7 - - + -
169B LEU* 1.3 79.7 - - - +
171B ILE* 1.3 67.4 + - - +
172B VAL* 4.3 4.2 + - + -
204B LEU* 4.0 16.8 - - + -
208B LEU* 5.5 3.8 - - + -
286B SER 3.7 1.4 - - - +
288B ILE* 2.8 43.2 + - + +
290B ILE* 3.8 22.0 - - + -
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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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32B MET* 3.3 39.3 - - + -
35B PHE* 5.2 0.9 - - + -
141B MET 3.2 9.3 + - - +
142B ILE* 4.0 20.8 - - + +
143B GLN* 2.8 40.5 + - + -
144B MET 4.5 0.2 + - - -
169B LEU* 4.3 16.2 - - + -
170B ILE* 1.3 78.5 - - - +
172B VAL* 1.3 75.4 + - - +
285B LEU* 4.5 7.4 - - + -
286B SER 3.3 9.4 - - - +
287B PHE* 3.2 36.8 - - + -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B MET 5.6 0.2 - - - +
143B GLN* 3.3 13.2 - - - -
145B LEU* 4.3 17.0 - - + +
146B TYR* 3.7 19.1 - - + +
170B ILE* 4.3 6.3 - - + +
171B ILE* 1.3 81.7 - - - +
173B VAL* 1.3 71.0 + - - +
199B ILE* 4.5 5.8 - - + +
200B THR 3.9 2.2 - - - -
201B SER* 3.7 17.9 - - - +
204B LEU* 3.4 36.1 - - + -
285B LEU* 3.8 3.5 - - - +
286B SER* 2.9 28.8 + - - +
288B ILE* 5.4 1.8 - - + -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLN* 4.4 1.6 - - - +
146B TYR* 3.0 13.6 + - - +
172B VAL* 1.3 75.5 - - - +
174B SER* 1.3 60.3 + - - +
177B SER* 3.9 3.8 - - - +
179B TRP* 3.5 34.8 - - + +
183B TRP* 3.7 33.0 - - + -
199B ILE 3.7 7.6 - - - +
200B THR* 3.2 5.3 - - + -
201B SER 3.0 21.7 + - - -
283B ASN* 4.2 1.3 - - - +
284B THR 3.6 6.7 - - - +
285B LEU* 4.1 17.3 - - + -
401B 2PM 3.9 16.6 - - - -
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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