Contacts of the strand formed by residues 242 - 248 (chain A) in PDB entry 2HRG
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 ARG 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.3 12.7 + - - -
67A GLY* 4.1 9.3 - - - -
105A THR* 2.9 45.6 + - + +
106A PHE* 3.9 2.8 - - - +
107A TRP* 3.8 13.9 - - - -
199A LEU 3.2 8.5 - - - +
200A VAL* 4.0 14.8 - - + -
221A GLU* 4.8 0.4 - - - +
222A ALA* 3.4 4.2 - - - -
223A ASP* 2.8 55.1 + - - +
224A SER* 3.0 23.0 + - - -
237A ILE* 4.3 0.2 - - - -
240A ALA 3.0 20.8 + - - -
241A GLN* 1.3 80.1 - - - +
243A TYR* 1.3 70.0 + - - +
422A ARG* 3.9 0.5 + - - -
423A ASP* 2.8 41.6 + - - -
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Residues in contact with TYR 243 (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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105A THR* 5.3 0.9 - - - -
197A PHE 4.0 0.3 - - - +
198A ARG* 3.7 1.0 - - - -
199A LEU* 2.7 41.0 + - + +
219A VAL* 3.7 12.8 - - + -
221A GLU* 3.2 20.9 - - - +
222A ALA* 3.8 16.6 - - + -
235A ILE* 3.6 38.8 - - + -
236A GLN 4.4 3.6 + - - -
237A ILE* 4.0 16.2 - - + -
241A GLN* 4.1 13.8 + - + -
242A ARG* 1.3 78.3 - - - +
244A SER* 1.3 61.8 + - - +
245A PHE* 4.2 1.1 + - + -
299A LEU* 3.6 35.1 - - + +
301A GLU* 4.8 0.7 + - - +
304A LEU* 4.2 6.6 - - + +
422A ARG* 2.8 34.1 + - - -
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Residues in contact with SER 244 (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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105A THR* 3.5 8.1 + - - -
196A ARG* 3.1 27.9 + - - -
197A PHE 3.2 7.4 - - - -
198A ARG* 3.5 5.5 - - - +
219A VAL* 3.4 6.8 - - - +
220A ILE* 2.9 31.9 + - - -
221A GLU* 2.5 43.7 + - - +
243A TYR* 1.3 73.4 - - - +
245A PHE* 1.3 60.0 + - - +
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Residues in contact with PHE 245 (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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146A ILE* 4.2 3.1 - - + -
195A TYR 3.6 0.2 - - - +
196A ARG* 3.7 2.5 - - - -
197A PHE* 2.9 70.8 + + + -
199A LEU* 4.3 20.2 - - + -
210A PHE* 3.7 36.6 - + - -
212A ILE* 4.2 7.6 - - + -
217A LEU* 3.8 35.7 - - + -
218A THR 3.1 18.4 - - - +
219A VAL* 4.1 7.9 - - + -
220A ILE* 4.6 1.6 - - - -
235A ILE* 4.2 15.3 - - + -
243A TYR 4.8 0.7 - - - -
244A SER* 1.3 76.5 - - - +
246A VAL* 1.3 68.8 + - - +
247A LEU* 4.2 4.3 - - + -
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Residues in contact with VAL 246 (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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136A LEU* 3.6 37.5 - - + +
137A TYR* 4.0 21.1 - - + -
195A TYR 3.2 10.1 - - - +
196A ARG* 4.9 1.1 - - - -
216A SER 4.3 1.0 - - - +
217A LEU* 3.9 4.0 - - - -
218A THR* 2.8 45.8 + - + +
220A ILE* 3.9 25.6 - - + -
245A PHE* 1.3 72.7 - - - +
247A LEU* 1.3 63.4 + - - +
248A ASN* 3.9 19.3 + - - +
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Residues in contact with LEU 247 (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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189A VAL* 4.6 7.9 - - + -
194A ARG* 3.5 1.7 - - - -
195A TYR* 2.9 32.7 + - + -
197A PHE* 3.8 31.2 - - + -
212A ILE* 3.7 29.6 - - + -
215A HIS* 4.0 33.4 - - + +
216A SER 4.7 5.2 - - - +
217A LEU* 4.4 7.2 - - + -
245A PHE* 3.8 5.3 + - + -
246A VAL* 1.3 73.4 - - - +
248A ASN* 1.3 77.7 + - - +
249A ALA* 3.6 15.4 + - + +
278A LEU* 4.3 9.4 - - + -
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Residues in contact with ASN 248 (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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136A LEU 4.5 0.8 + - - -
193A LYS 4.1 2.7 - - - -
194A ARG* 3.1 36.6 - - + +
215A HIS* 4.0 7.6 + - - -
216A SER 5.2 2.2 + - - -
246A VAL* 3.9 14.0 + - - +
247A LEU* 1.3 78.9 - - - +
249A ALA* 1.3 59.9 + - - +
250A ASP* 2.9 31.8 + - + +
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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