Contacts of the strand formed by residues 162 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.9 13.3 + - - +
136A TRP 3.5 3.1 - - - +
139A ILE* 3.7 23.3 - - + +
158A PHE 3.8 7.0 - - - +
159A HIS* 3.2 38.8 + - + +
160A SER 4.5 0.3 - - - +
161A LEU* 1.3 79.3 - - - +
163A GLY* 1.3 64.0 + - - +
166A ALA* 3.7 11.2 - - + -
167A LYS 3.4 25.8 - - - +
168A MET* 3.9 24.0 - - + +
290A ILE 4.2 3.1 - - - +
292A ALA* 3.8 29.3 - - + +
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Residues in contact with GLY 163 (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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51A LYS* 5.0 0.4 - - - -
135A LYS* 4.2 20.4 - - - -
136A TRP 2.8 19.3 + - - -
137A ASP* 5.0 3.8 - - - -
161A LEU 3.6 1.4 + - - -
162A LEU* 1.3 74.6 - - - +
164A THR* 1.3 67.1 + - - -
166A ALA* 3.1 15.2 + - - +
292A ALA* 3.3 10.6 - - - +
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Residues in contact with THR 164 (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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51A LYS* 2.7 39.7 + - - +
163A GLY* 1.3 69.7 - - - -
165A ASN* 1.3 82.5 + - - +
166A ALA 3.0 3.6 + - - -
292A ALA* 5.4 0.2 - - - -
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Residues in contact with ASN 165 (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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46A ARG* 3.8 27.5 + - + +
47A ILE* 3.5 20.4 + - - +
49A ASP* 4.6 17.4 + - - +
50A THR* 5.5 3.6 + - - +
51A LYS* 4.7 1.0 - - - +
163A GLY 3.3 1.2 + - - -
164A THR* 1.3 89.8 + - - +
166A ALA* 1.3 63.2 + - - +
167A LYS* 4.4 10.6 + - - +
291A GLU* 5.9 0.2 - - - -
292A ALA* 4.9 3.7 - - - +
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Residues in contact with ALA 166 (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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47A ILE* 4.5 0.9 - - - -
136A TRP 3.3 21.5 - - - +
137A ASP* 3.2 23.3 - - - +
162A LEU* 3.7 10.8 - - + -
163A GLY 3.1 23.3 + - - +
164A THR 3.0 2.9 - - - +
165A ASN* 1.3 81.6 - - - +
167A LYS* 1.3 64.7 + - - +
291A GLU* 4.2 1.7 - - - +
292A ALA* 3.4 21.4 + - - +
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Residues in contact with LYS 167 (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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42A GLY 5.4 1.6 - - - -
43A ILE* 3.1 35.6 + - + +
46A ARG* 6.3 1.0 - - - +
47A ILE* 4.5 4.4 - - + +
137A ASP 3.2 5.3 + - - -
138A PHE* 3.3 22.3 - - + -
139A ILE 3.1 20.6 + - - -
162A LEU* 3.4 6.4 - - - +
165A ASN* 4.0 12.3 + - - +
166A ALA* 1.3 79.1 - - - +
168A MET* 1.3 60.6 + - - +
289A VAL* 3.6 21.3 - - + -
290A ILE 3.4 5.8 - - - +
291A GLU* 2.9 37.8 + - - +
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Residues in contact with MET 168 (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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138A PHE* 4.9 0.2 - - - -
139A ILE* 3.1 18.6 - - + +
140A HIS* 5.2 0.4 - - - -
141A MET* 3.8 15.0 - - + +
155A LEU* 3.9 9.6 - - - +
158A PHE* 3.8 27.8 - - - +
159A HIS* 3.7 33.2 - - + +
162A LEU* 3.9 12.3 - - + -
167A LYS* 1.3 77.2 - - - +
169A LEU* 1.3 61.6 + - - +
170A ILE* 4.5 10.8 - - + -
213A LEU* 5.5 0.2 - - + -
288A ILE 3.5 1.7 - - - +
289A VAL* 3.4 4.7 - - - -
290A ILE* 2.8 69.2 + - + +
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Residues in contact with LEU 169 (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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35A PHE* 4.2 24.5 - - + -
36A MET* 4.6 5.8 - - + -
40A LEU* 4.6 6.7 - - + -
43A ILE* 5.9 0.4 - - + -
70A ILE* 5.1 2.9 - - + -
138A PHE* 3.8 31.8 - - + -
139A ILE 2.8 8.3 + - - -
140A HIS* 3.1 6.3 - - + -
141A MET 2.8 26.5 + - - -
142A ILE* 4.6 12.3 - - + -
167A LYS 4.2 0.4 - - - -
168A MET* 1.3 73.7 - - - +
170A ILE* 1.3 76.3 + - - +
171A ILE* 4.1 25.4 - - + -
287A PHE* 4.4 2.0 - - + -
288A ILE 3.4 13.5 - - - +
289A VAL* 4.2 17.9 - - + +
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Residues in contact with ILE 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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141A MET* 3.4 20.9 - - + +
145A LEU* 3.5 24.2 - - + -
155A LEU* 3.3 34.3 - - + -
168A MET* 4.5 8.1 - - + -
169A LEU* 1.3 79.2 - - - +
171A ILE* 1.3 69.4 + - - +
172A VAL* 4.3 4.3 - - + +
204A LEU* 3.7 19.7 - - + -
208A LEU* 5.3 2.7 - - + -
286A SER 3.7 0.9 - - - +
287A PHE* 3.7 0.3 - - - -
288A ILE* 2.9 45.9 + - + +
290A ILE* 3.5 26.0 - - + -
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Residues in contact with ILE 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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32A MET* 3.8 26.5 - - + -
35A PHE* 5.4 0.9 - - + -
36A MET* 6.0 2.2 - - + -
66A ILE* 6.0 0.2 - - + -
141A MET 3.1 9.0 + - - +
142A ILE* 3.8 37.7 - - + -
143A GLN* 2.8 31.2 + - + -
144A MET 4.5 0.2 + - - -
145A LEU* 6.0 0.2 - - - +
169A LEU* 4.1 15.7 - - + -
170A ILE* 1.3 79.5 - - - +
172A VAL* 1.3 75.0 + - - +
285A LEU* 4.6 7.9 - - + -
286A SER 3.4 9.6 - - - +
287A PHE* 3.5 38.6 - - + -
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Residues in contact with VAL 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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143A GLN* 3.3 6.3 - - - -
145A LEU* 4.4 14.1 - - + +
146A TYR* 3.3 25.6 - - + +
170A ILE* 4.3 5.2 - - + -
171A ILE* 1.3 79.7 - - - +
173A VAL* 1.3 71.8 + - - +
199A ILE* 4.4 10.8 - - + +
200A THR 3.9 3.1 - - - -
201A SER* 3.7 18.8 - - - +
204A LEU* 3.7 34.3 - - + -
285A LEU* 3.8 3.7 - - - +
286A SER* 2.9 28.5 + - - +
288A ILE* 5.3 1.6 - - + -
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Residues in contact with VAL 173 (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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143A GLN* 4.3 7.2 - - - +
146A TYR* 2.9 19.5 + - - +
172A VAL* 1.3 75.3 - - - +
174A SER* 1.3 59.8 + - - +
177A SER* 3.9 16.4 - - - +
179A TRP* 3.7 23.1 - - + +
183A TRP* 3.6 22.2 - - + -
199A ILE 3.6 18.6 - - - +
200A THR* 3.3 5.6 - - + -
201A SER* 3.0 21.8 + - - -
283A ASN* 4.5 0.7 - - - +
284A THR 3.7 7.2 - - - +
285A LEU* 4.4 8.5 - - + +
286A SER* 4.3 0.2 - - - -
400A 2PM 3.9 17.9 - - - +
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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
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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