Contacts of the strand formed by residues 255 - 262 (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 ASN 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLY* 1.3 75.8 - - - -
256A TYR* 1.3 64.0 + - - +
277A ILE* 4.0 1.5 - - + +
278A LEU 3.4 3.8 - - - +
279A ARG* 2.7 39.3 + - - +
283A ALA* 4.1 4.8 - - - +
284A ALA* 2.9 23.6 + - - +
286A VAL* 3.3 26.1 + - - +
288A PRO* 3.4 35.3 - - + +
289A THR 4.5 0.3 + - - -
290A THR* 3.4 14.6 - - - +
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Residues in contact with TYR 256 (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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212A ILE* 4.6 0.7 - - + -
213A ASP* 3.3 29.4 - - + +
214A GLY* 4.5 6.5 - - - -
215A HIS* 3.8 14.8 - + + -
251A GLN* 3.4 11.7 - - + +
252A ASP* 2.5 47.2 + - - +
254A GLY* 3.8 15.7 - - - -
255A ASN* 1.3 76.0 - - - +
257A TRP* 1.3 63.2 + - - +
278A LEU* 2.8 45.1 + - + +
280A TYR* 3.5 23.3 - + - -
288A PRO* 3.6 5.8 - - - +
290A THR* 3.8 22.7 - - + -
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Residues in contact with TRP 257 (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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184A LEU* 3.9 22.9 - - + -
212A ILE* 3.5 2.4 - - - +
213A ASP* 2.9 38.1 + - - +
256A TYR* 1.3 71.4 - - - +
258A ILE* 1.3 61.7 + - - +
259A ARG* 3.5 25.2 + - + +
272A GLY* 4.3 14.6 - - - -
275A SER* 3.7 24.9 - - - -
276A ALA 3.4 19.5 - - - -
277A ILE* 4.1 0.9 - - + -
287A GLU* 3.7 23.1 - - + -
288A PRO* 3.2 47.2 + - + +
289A THR* 4.5 1.2 - - - +
290A THR* 3.2 41.3 + - - +
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Residues in contact with ILE 258 (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* 5.4 6.1 - - + -
170A ILE* 4.3 15.9 - - + +
187A ILE* 3.7 33.9 - - + -
210A PHE* 3.5 34.3 - - + -
211A SER 3.7 3.8 - - - +
212A ILE* 4.0 14.6 - - + +
257A TRP* 1.3 73.2 - - - +
259A ARG* 1.3 62.4 + - - +
275A SER* 3.2 8.7 - - - -
276A ALA* 2.8 38.6 + - + +
277A ILE 3.7 4.3 - - - +
278A LEU* 3.7 37.5 - - + +
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Residues in contact with ARG 259 (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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170A ILE* 4.9 0.4 - - - -
209A VAL 4.0 2.5 - - - +
210A PHE* 3.2 9.7 - - - -
211A SER* 2.8 42.8 + - - +
213A ASP* 2.7 42.5 + - - +
257A TRP* 3.5 20.4 - - + +
258A ILE* 1.3 80.3 - - - +
260A ALA* 1.3 61.6 + - - +
269A PHE* 3.4 54.7 - - + +
274A ASN 3.6 3.6 - - - -
275A SER* 4.8 1.9 + - - +
290A THR 3.4 15.2 + - - -
291A SER* 4.1 0.6 - - - +
292A GLN* 3.6 40.5 + - - +
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Residues in contact with ALA 260 (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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148A LEU* 4.0 29.2 - - + -
168A THR* 4.1 11.6 + - + -
170A ILE* 4.1 11.9 - - + -
208A HIS* 3.8 16.5 - - + -
209A VAL 3.4 6.7 - - - -
210A PHE* 4.4 2.2 - - + +
259A ARG* 1.3 75.3 - - - +
261A LEU* 1.3 62.7 + - - +
262A PRO* 3.3 9.9 - - - +
269A PHE* 4.0 0.2 - - - -
274A ASN* 3.0 23.8 + - - +
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Residues in contact with LEU 261 (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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207A ASN* 3.8 0.7 + - - +
208A HIS* 3.2 2.8 - - - -
209A VAL* 2.8 53.2 + - + +
259A ARG 4.0 0.2 - - - -
260A ALA* 1.3 71.3 - - - +
262A PRO* 1.3 73.1 - - + +
267A ARG* 3.5 59.3 + - - +
268A ASN* 3.8 5.4 - - - +
269A PHE* 3.7 35.1 - - + -
292A GLN* 6.2 0.9 - - - +
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Residues in contact with PRO 262 (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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168A THR* 4.0 4.7 - - - +
206A PRO* 4.2 8.7 - - + -
207A ASN* 3.2 9.9 - - - +
208A HIS* 3.7 17.5 - - + +
260A ALA 3.3 9.6 - - - +
261A LEU* 1.3 89.7 - - + +
263A ASN* 1.3 57.7 + - - +
264A SER 3.2 23.1 - - - +
266A THR 3.5 16.8 - - - +
267A ARG* 2.8 25.7 + - - +
274A ASN* 3.5 25.6 - - - +
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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