Contacts of the strand formed by residues 170 - 174 (chain O) in PDB entry 2DYS
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365N ILE* 4.1 1.8 - - - -
366N VAL* 4.7 1.5 - - - +
16O ILE* 6.5 0.2 - - + -
163O TRP* 3.8 28.5 - - + +
164O ALA* 3.3 3.4 - - - +
165O VAL* 3.0 37.5 + - + +
166O PRO* 4.3 1.8 - - - +
168O LEU* 4.0 24.5 - - + +
169O GLY* 1.3 86.8 - - - +
171O LYS* 1.3 66.9 + - - +
182O THR* 3.6 28.5 - - + +
183O THR 3.7 14.8 - - - +
184O LEU* 4.0 27.6 - - + -
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Residues in contact with LYS 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N THR* 3.7 20.7 - - + +
365N ILE* 2.6 51.4 + - - +
366N VAL* 3.1 22.6 + - - +
368N HIS* 3.0 40.1 + - + +
370N THR* 4.3 5.2 - - - +
162O SER* 3.4 17.9 - - - +
163O TRP 3.2 6.3 + - - -
164O ALA* 3.9 11.5 - - + +
166O PRO* 6.2 2.4 - - - +
170O LEU* 1.3 79.3 + - - +
172O THR* 1.3 63.4 + - - +
182O THR* 5.7 0.2 + - - -
197O SER* 3.7 26.2 - - - -
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Residues in contact with THR 172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N THR 4.1 4.3 - - - +
296N GLY* 6.3 0.2 - - - -
154O VAL* 3.8 22.9 - - + +
162O SER* 3.7 2.5 - - - -
163O TRP* 2.8 35.8 + - - +
170O LEU* 5.7 0.2 - - - +
171O LYS* 1.3 78.6 + - - +
173O ASP* 1.3 65.8 + - - +
180O ASN* 3.3 39.0 - - + +
181O GLN 4.6 4.4 + - - +
182O THR* 3.4 29.5 + - + +
23U GLN* 5.7 4.0 + - - +
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Residues in contact with ASP 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N GLN* 5.4 1.7 + - - -
294N THR* 3.1 39.1 + - - +
295N VAL* 3.7 19.5 - - - +
368N HIS* 4.9 2.4 + - - -
602N MG 4.2 9.4 - - - -
154O VAL* 3.7 7.4 - - - +
160O LEU* 5.9 0.7 - - + -
161O HIS 3.5 7.0 - - - +
162O SER* 2.7 30.4 + - - -
171O LYS* 4.7 0.2 - - - +
172O THR* 1.3 75.2 - - - +
174O ALA* 1.3 60.1 + - - +
175O ILE* 3.6 22.0 + - + +
180O ASN* 3.1 21.3 + - - +
198O GLU* 4.5 6.9 - - + +
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Residues in contact with ALA 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O TRP* 4.1 7.4 - - + -
154O VAL* 3.4 16.8 - - + -
155O SER* 3.1 24.9 - - - +
156O SER* 3.4 8.5 - - - -
160O LEU* 3.3 8.0 - - - +
161O HIS* 2.6 52.0 + - + +
172O THR 3.6 0.4 + - - -
173O ASP* 1.3 69.0 - - - +
175O ILE* 1.3 62.0 + - - +
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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