Contacts of the strand formed by residues 170 - 174 (chain B) in PDB entry 3AG2
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 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ILE* 4.1 1.1 - - - -
366A VAL* 4.6 1.6 - - - +
163B TRP* 3.8 21.8 - - + -
164B ALA* 3.2 4.1 - - - +
165B VAL* 2.9 40.7 + - + +
166B PRO* 4.4 1.6 - - - +
168B LEU* 3.8 27.8 - - + +
169B GLY* 1.3 81.9 - - - +
171B LYS* 1.3 63.9 + - - +
182B THR* 3.9 21.1 - - + +
183B THR 3.5 22.0 - - - +
184B LEU* 3.6 39.0 - - + -
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR* 3.7 18.7 - - + +
365A ILE* 2.8 52.7 + - - +
366A VAL* 3.1 19.8 + - - +
368A HIS* 2.7 45.3 + - + +
369A ASP 5.3 0.2 - - - -
370A THR* 4.0 6.3 - - - +
162B SER* 3.4 17.9 - - - +
163B TRP 3.3 6.3 - - - -
164B ALA* 3.9 12.3 - - + -
166B PRO* 6.3 1.7 - - - +
170B LEU* 1.3 75.9 - - - +
172B THR* 1.3 63.3 + - - +
182B THR* 5.8 0.2 + - - -
197B SER* 3.6 28.7 - - - -
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Residues in contact with THR 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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294A THR 3.9 3.8 - - - +
296A GLY* 6.0 1.1 - - - -
154B VAL* 3.7 26.1 - - + +
162B SER* 3.5 2.9 - - - -
163B TRP* 2.9 30.2 + - - -
170B LEU* 6.5 0.2 - - - -
171B LYS* 1.3 75.8 + - - +
173B ASP* 1.3 66.2 + - - +
180B ASN* 3.4 37.0 - - + +
181B GLN 4.7 3.8 + - - +
182B THR* 3.5 27.9 + - - +
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Residues in contact with ASP 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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129A TYR* 6.1 0.5 - - - -
232A GLN* 5.1 3.6 + - - +
294A THR* 2.9 38.6 + - - +
295A VAL* 3.4 23.5 - - - +
368A HIS* 4.8 5.0 + - - -
154B VAL* 3.8 3.2 - - - +
160B LEU* 6.1 1.6 - - + +
161B HIS 3.7 3.6 - - - +
162B SER* 2.8 31.5 + - - -
171B LYS* 4.7 0.2 - - - +
172B THR* 1.3 80.6 - - - +
174B ALA* 1.4 59.8 + - - +
175B ILE* 3.9 21.0 + - + +
180B ASN* 3.0 23.1 + - - +
197B SER 4.9 1.0 - - - +
198B GLU* 4.7 12.5 - - - +
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Residues in contact with ALA 174 (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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101B GLY 4.6 0.2 - - - +
106B TRP* 4.0 8.3 - - + -
154B VAL* 3.6 17.3 - - + -
155B SER* 3.3 23.8 - - - +
156B SER* 3.4 8.3 - - - -
160B LEU* 3.3 8.1 - - - -
161B HIS* 2.8 50.9 + - + +
162B SER 4.3 0.2 - - - +
172B THR 3.6 0.4 + - - -
173B ASP* 1.4 69.2 - - - +
175B ILE* 1.3 61.0 + - - +
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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