Contacts of the strand formed by residues 275 - 278 (chain A) in PDB entry 1HS6
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 LEU 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.3 38.8 - - + -
170A MET 3.5 25.6 - - - +
171A SER* 4.3 4.7 - - - -
205A VAL* 4.5 3.4 - - + -
221A TRP* 4.2 10.1 - - + +
256A TYR* 5.8 0.2 - - - -
257A ASP* 3.4 30.1 - - + +
258A LEU 4.1 2.5 - - - -
259A LEU* 4.1 17.5 - - + -
272A ASN* 3.0 17.7 + - - +
273A PRO 3.0 1.6 - - - -
274A CYS* 1.3 79.0 - - - +
276A THR* 1.3 64.5 + - - +
277A PHE* 3.2 31.9 - - + -
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Residues in contact with THR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 2.9 40.8 + - - +
257A ASP 3.0 7.3 + - - -
258A LEU* 3.4 18.9 - - + +
259A LEU* 2.8 27.2 + - - +
270A MET 3.4 6.7 - - - +
271A GLU* 3.8 9.9 - - - -
272A ASN 3.3 4.2 + - - -
275A LEU* 1.3 72.6 - - - +
277A PHE* 1.3 69.8 + - - +
278A VAL* 3.8 7.9 - - + -
293A ILE* 5.3 1.1 - - + -
296A GLU* 3.6 26.9 + - + +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 4.6 0.9 - - + -
133A SER 3.6 20.6 - - - -
134A GLN* 5.2 0.7 - - - -
203A ALA* 3.7 21.3 - - + -
204A LEU* 4.2 18.6 - - - -
205A VAL* 4.5 2.2 - - + -
259A LEU* 3.4 30.1 - - + -
261A LEU* 3.4 27.1 - - + -
265A PHE* 3.7 25.6 - + + -
269A GLY* 3.2 4.2 - - - -
270A MET* 3.0 28.3 + - + +
272A ASN* 3.2 17.9 - - - +
275A LEU* 3.2 31.4 - - + -
276A THR* 1.3 75.1 - - - +
278A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 4.0 16.4 - - + -
258A LEU* 4.2 6.3 - - + -
259A LEU 2.8 17.6 + - - +
260A VAL* 3.9 21.3 - - + -
261A LEU* 3.1 27.7 + - - +
265A PHE* 4.0 6.1 - - - -
268A GLY 3.4 11.7 - - - +
269A GLY* 4.3 3.6 - - - -
276A THR* 3.8 18.4 - - + -
277A PHE* 1.3 80.8 - - - +
279A THR* 1.3 67.7 + - - +
282A LEU* 3.8 7.6 - - + -
292A VAL* 4.8 2.5 - - + -
293A ILE* 3.8 21.1 - - + -
296A GLU* 5.3 0.2 - - + -
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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