Contacts of the strand formed by residues 200 - 204 (chain C) in PDB entry 5AYR
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 VAL 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C CYS* 5.7 0.8 - - - -
139C VAL* 3.4 17.3 - - + +
141C ILE* 4.0 17.9 - - + -
195C TRP* 3.2 33.7 + - + +
196C ALA* 3.5 18.3 + - - +
199C GLY* 1.3 76.5 - - - +
201C LEU* 1.3 62.5 + - - +
202C LEU* 3.3 29.5 + - + +
299C ILE* 3.7 37.0 - - + -
301C TRP* 4.5 7.0 - - + -
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TRP* 4.1 19.5 - - + -
128C TRP* 3.8 38.6 - - + +
137C VAL* 4.2 15.5 - - + -
139C VAL 2.6 17.4 + - - +
140C VAL* 4.2 8.5 - - + -
141C ILE* 2.8 32.7 + - - +
199C GLY 3.7 2.4 + - - -
200C VAL* 1.3 68.8 - - - +
202C LEU* 1.3 61.0 - - - +
203C LEU* 3.8 30.7 - - + -
229C VAL* 4.4 0.4 - - + -
233C LEU* 3.6 31.0 - - + -
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TRP* 4.2 6.6 - - - +
141C ILE* 3.8 23.6 - - + -
155C GLY 4.2 4.3 - - - +
156C LEU* 3.7 31.5 - - + +
157C CYS* 3.1 41.5 + - - +
158C PHE* 5.5 1.3 - - + -
192C LEU* 3.6 43.1 - - + +
195C TRP* 4.6 13.5 - - + -
196C ALA* 4.6 2.0 - - + -
200C VAL* 3.3 31.2 + - + +
201C LEU* 1.3 73.7 - - - +
203C LEU* 1.3 57.3 + - - +
204C ASN 3.9 1.0 + - - -
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TRP* 3.8 39.7 - - + +
141C ILE 3.0 12.9 + - - +
142C LEU* 3.4 13.5 - - + +
143C GLY 2.7 28.5 + - - -
157C CYS* 3.4 1.3 - - - -
201C LEU* 3.7 20.6 + - + -
202C LEU* 1.3 71.4 - - - +
204C ASN* 1.3 73.0 + - - +
205C ALA* 5.7 0.2 - - - -
207C LEU* 4.2 3.8 - - + -
226C THR* 4.2 19.5 - - + +
229C VAL* 3.6 34.3 - - + -
230C VAL* 4.4 12.6 - - + -
252C LYS* 5.9 0.6 - - - -
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Residues in contact with ASN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TRP* 6.1 0.4 - - - -
143C GLY* 3.6 2.6 - - - -
144C GLN 3.2 27.0 + - - +
145C ASP 3.7 8.1 + - - +
146C PRO* 3.8 24.7 - - - +
147C TYR* 6.2 1.4 - - - -
155C GLY* 5.5 1.6 - - - -
156C LEU 4.3 5.5 + - - +
157C CYS* 3.2 34.1 - - - +
158C PHE 4.9 1.1 + - - +
202C LEU 3.9 1.4 + - - -
203C LEU* 1.3 80.3 - - - +
205C ALA* 1.3 64.3 + - - +
206C VAL 3.4 11.0 - - - +
207C LEU* 3.3 21.9 - - + +
226C THR* 3.5 8.5 - - - +
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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