Contacts of the strand formed by residues 194 - 201 (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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A SER* 2.8 27.6 + - - +
136A LEU* 3.3 22.9 - - - +
137A TYR* 3.7 18.2 + - - -
138A ASP* 2.7 64.5 + - - +
139A VAL* 3.1 8.0 + - - +
192A GLY 4.8 3.8 + - - +
193A LYS* 1.3 77.0 - - - +
195A TYR* 1.3 63.2 + - - +
246A VAL* 4.7 0.4 - - + -
247A LEU 3.5 4.9 - - - -
248A ASN* 3.1 28.5 - - + +
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Residues in contact with TYR 195 (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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137A TYR* 3.9 4.0 - - - +
139A VAL* 3.5 37.2 - - + +
144A THR* 4.0 9.6 - - + -
188A THR 4.4 5.6 - - - -
189A VAL* 3.3 32.7 - - + -
190A THR* 2.6 34.4 + - - -
193A LYS* 3.6 35.9 - - + +
194A ARG* 1.3 75.5 - - - +
196A ARG* 1.3 61.1 + - - +
197A PHE* 3.4 26.0 + + + -
245A PHE 3.6 0.3 - - - +
246A VAL* 3.2 6.3 - - - +
247A LEU* 2.9 39.0 + - + +
249A ALA* 4.0 5.4 - - + -
1001A CA 4.7 4.7 - - - -
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Residues in contact with ARG 196 (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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104A GLY* 4.9 3.6 - - - -
131A ASP* 2.8 33.3 + - - -
133A HIS* 5.4 1.2 - - - -
137A TYR* 3.0 52.0 + - + +
139A VAL 2.9 11.0 + - - +
140A ASP* 3.6 18.8 - - + +
144A THR* 2.9 23.9 + - - -
195A TYR* 1.3 69.9 - - - +
197A PHE* 1.3 63.2 + - - +
198A ARG* 3.4 23.3 + - + +
220A ILE* 4.0 16.2 - - + +
221A GLU* 3.2 32.1 + - - +
226A ASN* 4.8 6.7 + - - -
244A SER* 3.1 26.3 + - - +
245A PHE 3.7 4.5 - - - +
246A VAL* 4.6 0.4 - - - +
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Residues in contact with PHE 197 (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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143A SER 4.3 0.7 - - - -
144A THR* 3.2 32.8 - - + -
146A ILE* 3.6 19.7 - - + -
187A ILE* 3.5 33.7 - - + -
188A THR 5.4 0.2 - - - -
189A VAL* 3.9 12.8 - - + -
195A TYR* 3.4 28.0 - + + -
196A ARG* 1.3 72.8 - - - +
198A ARG* 1.3 60.4 + - - +
199A LEU 3.9 1.3 + - - -
212A ILE* 5.7 1.3 - - + -
244A SER* 3.2 4.9 - - - -
245A PHE* 2.9 69.3 + + + -
247A LEU* 3.8 28.0 - - + -
278A LEU* 4.7 3.1 - - + -
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Residues in contact with ARG 198 (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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104A GLY* 3.6 19.4 - - - -
105A THR* 3.0 35.6 + - + +
125A VAL* 3.5 32.2 - - - +
126A VAL 5.0 0.8 + - - -
127A TYR* 3.8 16.3 - - - +
131A ASP* 4.6 3.6 + - - -
137A TYR* 4.8 0.2 + - - -
140A ASP* 2.8 41.5 + - - +
144A THR* 2.9 12.1 + - - +
145A VAL* 3.5 12.3 - - + -
146A ILE* 2.8 30.7 + - - +
196A ARG* 3.4 39.7 - - - +
197A PHE* 1.3 72.8 - - - +
199A LEU* 1.3 58.9 + - - +
200A VAL* 3.7 6.1 + - - +
243A TYR 3.7 4.0 - - - -
244A SER* 3.5 12.6 - - - +
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Residues in contact with LEU 199 (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* 3.3 25.8 - - + +
148A LEU* 3.9 17.5 - - + -
197A PHE 3.9 0.4 - - - -
198A ARG* 1.3 70.4 - - - +
200A VAL* 1.3 60.1 + - - +
210A PHE* 3.8 53.8 - - + -
235A ILE* 4.5 16.4 - - + -
237A ILE* 4.0 27.3 - - + +
242A ARG* 3.2 8.0 - - - +
243A TYR* 2.7 43.0 + - + +
245A PHE* 4.3 11.7 - - + -
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Residues in contact with VAL 200 (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 30.1 - - + -
106A PHE 4.2 0.9 - - - +
107A TRP* 3.9 22.2 - - + -
123A PRO* 4.3 17.7 - - + -
145A VAL* 4.3 4.5 - - + -
146A ILE 2.9 12.1 + - - +
147A THR* 3.3 8.0 - - + -
148A LEU* 2.9 27.4 + - - -
198A ARG 3.9 8.7 - - - +
199A LEU* 1.3 74.7 - - - +
201A SER* 1.3 63.5 + - - +
202A LEU* 3.5 23.7 + - + -
237A ILE* 4.5 1.1 - - - -
241A GLN 4.0 2.2 - - - -
242A ARG* 4.0 11.4 - - + -
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Residues in contact with SER 201 (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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107A TRP* 3.7 8.0 + - - -
148A LEU* 3.8 12.8 - - - +
200A VAL* 1.3 70.2 - - - +
202A LEU* 1.3 58.5 + - - +
203A SER* 3.2 10.3 + - - -
208A HIS* 4.8 1.2 + - - -
237A ILE* 3.2 32.9 + - - +
238A PHE 3.5 23.7 + - - -
239A ALA* 4.3 2.2 - - - -
240A ALA* 3.1 26.7 + - - -
241A GLN 3.0 15.5 + - - -
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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