Contacts of the strand formed by residues 251 - 257 (chain A) in PDB entry 2HT8
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 GLN 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TRP* 3.2 35.1 + - - +
219A ALA* 4.3 11.5 - - + +
242A THR* 3.5 1.6 - - - -
243A ASP 2.9 44.0 + - - +
244A GLY* 5.4 0.7 - - - -
250A ALA* 1.3 83.5 + - - +
252A TYR* 1.3 63.5 + - - +
267A ASP* 5.1 7.4 - - - +
268A ILE 5.7 0.4 - - - -
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Residues in contact with TYR 252 (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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240A VAL* 5.0 1.8 - - + -
241A MET 3.4 7.6 - - - +
242A THR* 3.9 5.8 - - + +
249A GLN* 3.4 9.2 + - - -
250A ALA* 3.6 33.3 + - + -
251A GLN* 1.3 77.0 - - - +
253A ARG* 1.3 66.2 + - - +
267A ASP* 3.8 3.3 - - - +
268A ILE* 3.0 60.3 + - + +
270A PHE* 3.9 28.9 - - + -
273A GLY 2.5 26.3 + - - -
274A HIS* 3.2 13.0 - + - -
275A ILE* 3.2 52.9 - - + -
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Residues in contact with ARG 253 (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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215A VAL* 5.6 0.2 - - - +
216A ASN 5.3 0.6 + - - -
218A TRP* 3.0 70.3 - - + +
240A VAL* 3.1 7.1 - - - +
241A MET* 3.0 31.1 + - - +
252A TYR* 1.3 79.4 - - - +
254A ILE* 1.3 65.0 + - - +
255A TYR* 3.0 39.5 + - + -
265A GLN* 3.7 18.9 + - - +
266A THR 3.1 13.9 - - - +
267A ASP* 3.6 25.1 + - - +
268A ILE* 4.1 2.2 - - - -
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Residues in contact with ILE 254 (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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238A TYR* 4.8 4.9 - - + -
239A TRP 3.5 10.5 - - - +
240A VAL* 4.4 3.4 - - + +
253A ARG* 1.3 77.2 - - - +
255A TYR* 1.3 68.6 + - - +
265A GLN* 3.3 8.8 - - - +
266A THR* 3.0 33.4 + - + +
268A ILE* 3.6 23.6 - - + -
303A LEU* 5.0 2.2 - - + -
305A ILE* 3.5 42.2 - - + -
310A LEU* 3.8 18.9 - - + +
312A TYR* 3.9 37.7 - - + -
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Residues in contact with TYR 255 (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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215A VAL* 3.7 29.7 - - + +
218A TRP* 3.9 3.3 - + - -
238A TYR* 3.2 6.8 - - - +
239A TRP* 2.8 61.4 + + + +
241A MET* 3.1 42.6 - - + -
253A ARG* 3.0 47.7 + - + -
254A ILE* 1.3 78.5 - - - +
256A LYS* 1.3 60.0 + - - +
262A ILE* 4.2 16.8 - - + -
264A GLY 4.3 0.7 - - - -
265A GLN* 3.0 34.8 + - + -
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Residues in contact with LYS 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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236A ASP* 3.4 37.7 + - + -
237A CYS 3.5 4.5 - - - +
238A TYR* 3.9 23.4 + - + +
239A TRP* 4.5 1.1 - - - -
255A TYR* 1.3 75.0 - - - +
257A ALA* 1.3 66.4 + - - +
262A ILE* 3.7 4.0 - - - +
263A ILE* 2.8 44.5 + - + +
264A GLY 3.3 17.0 + - - +
308A PRO* 2.6 26.9 + - - +
309A ASP* 4.9 0.6 - - - +
310A LEU* 3.7 28.0 - - + +
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Residues in contact with ALA 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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190A MET* 4.3 12.6 - - - -
236A ASP* 3.1 12.1 - - - +
237A CYS* 2.9 31.0 + - - +
239A TRP* 3.8 24.5 - - + -
256A LYS* 1.3 76.1 - - - +
258A ASN* 1.3 62.7 + - - +
259A GLN 5.0 0.2 - - - +
260A GLY 4.5 2.9 - - - +
261A ARG 3.3 24.5 - - - +
262A ILE* 4.1 1.8 - - + +
263A ILE* 3.8 4.9 - - - +
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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