Contacts of the strand formed by residues 162 - 165 (chain H) in PDB entry 2YMX
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 THR 162 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H PRO* 5.1 10.8 - - + -
161H VAL* 1.3 76.7 - - - +
163H VAL* 1.3 64.8 + - - +
164H THR* 5.9 3.2 - - - +
207H ASN 3.7 0.7 - - - +
208H VAL* 3.3 4.5 - - - -
209H ALA* 2.8 48.5 + - - +
211H PRO* 5.7 5.7 - - + +
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Residues in contact with VAL 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H CYS* 5.3 1.8 - - + -
153H VAL* 4.5 1.6 - - + -
161H VAL* 4.1 9.2 - - + -
162H THR* 1.3 80.6 - - - +
164H THR* 1.3 81.3 + - - +
165H TRP* 4.2 6.5 - - + +
176H THR* 4.2 21.9 + - + +
188H LEU* 3.6 31.9 - - + -
190H SER* 3.8 25.4 - - - +
206H CYS* 4.6 9.9 - - + -
207H ASN 3.2 5.8 - - - +
208H VAL* 4.3 12.6 - - + -
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Residues in contact with THR 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H THR* 5.8 3.4 - - - +
163H VAL* 1.3 82.3 - - - +
165H TRP* 1.3 67.1 - - - +
167H SER* 4.0 3.3 - - - -
168H GLY* 3.6 23.7 + - - +
206H CYS* 3.4 4.9 - - - -
207H ASN* 2.8 57.8 + - - +
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Residues in contact with TRP 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 5.0 0.2 - - + -
150H GLY* 3.4 31.2 - - - -
151H CYS* 3.6 5.4 - - + -
163H VAL* 4.2 3.1 - - + +
164H THR* 1.3 77.9 - - - +
166H ASN* 1.3 68.8 + - - +
167H SER 3.2 0.9 - - - -
168H GLY* 3.1 8.7 + - - +
170H LEU* 3.1 44.2 + - + +
174H VAL* 3.7 29.7 - - + +
176H THR* 5.1 0.2 - - - -
190H SER* 2.9 43.8 + - - -
191H SER 4.1 0.4 + - - -
192H VAL* 3.7 20.0 - - + +
204H VAL* 3.6 27.6 - - + -
205H THR 3.4 17.7 - - - -
206H CYS* 3.5 29.8 - - + -
221H ILE* 3.8 11.0 - - + -
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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