Contacts of the strand formed by residues 174 - 177 (chain A) in PDB entry 2RHG
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PHE 4.1 5.2 - - - +
154A CYS* 4.2 15.3 - - + -
166A VAL* 3.7 30.4 + - + +
170A GLY* 5.9 1.9 - - - -
173A TYR* 1.3 74.5 - - - +
175A TYR* 1.3 62.0 + - - +
176A LEU* 3.1 3.6 + - - +
200A LEU* 4.3 16.6 - - + -
205A ALA* 3.9 6.6 - - - +
206A ALA* 2.8 32.4 + - - +
207A PRO 2.8 8.2 + - - -
208A ALA* 3.4 7.6 - - + -
209A LEU 2.9 25.6 + - - -
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Residues in contact with TYR 175 (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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49A GLU* 5.5 2.7 - - + -
100A LEU* 5.9 0.2 - - + -
127A LEU* 3.6 21.1 - - + -
151A ILE* 4.1 5.3 - - + +
152A PHE 3.1 17.1 + - - +
153A ILE* 3.9 19.0 - - + +
154A CYS 2.9 25.7 + - - -
173A TYR* 3.9 16.5 + - + -
174A THR* 1.3 70.5 - - - +
176A LEU* 1.3 62.7 + - - +
177A LEU* 3.4 25.4 + - + +
209A LEU 3.8 5.2 - - - -
211A GLY* 4.0 21.7 - - - -
212A PHE* 4.1 1.4 + - - +
232A ILE* 3.8 25.6 - - + +
269A IGP 2.8 57.8 + + - -
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Residues in contact with LEU 176 (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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154A CYS* 4.0 18.4 - - + +
155A PRO 6.0 0.2 - - - -
174A THR* 3.1 3.3 + - + -
175A TYR* 1.3 69.3 - - - +
177A LEU* 1.3 66.5 + - - +
178A SER 3.6 0.7 + - - -
196A LEU* 3.5 34.8 - - + -
197A ILE* 3.8 33.2 - - + -
200A LEU* 4.4 4.9 - - + -
208A ALA* 4.4 15.3 - - + -
209A LEU 2.8 18.3 + - - +
210A GLN* 3.2 23.5 - - + +
211A GLY 2.8 27.9 + - - -
228A ALA* 5.2 1.3 - - + -
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Residues in contact with LEU 177 (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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153A ILE* 3.9 21.8 - - + -
154A CYS 3.2 19.3 + - - +
155A PRO* 4.2 4.5 - - + -
156A PRO* 4.0 23.6 - - + +
175A TYR* 3.4 20.0 + - + +
176A LEU* 1.3 77.8 - - - +
178A SER* 1.3 68.3 + - - +
211A GLY 4.0 0.9 - - - -
212A PHE* 3.7 26.7 - - + -
269A IGP 5.8 6.3 - - + -
20B ILE* 4.1 30.7 - - + -
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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