Contacts of the strand formed by residues 252 - 258 (chain A) in PDB entry 3H11
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 GLY 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A PRO* 3.0 7.9 - - - +
251A LEU* 1.3 82.7 - - - +
253A ILE* 1.3 66.1 + - - -
276A TYR* 3.4 10.4 - - - -
277A GLU 3.0 23.4 + - - -
305A TYR* 3.7 17.5 - - - -
307A SER 3.3 14.6 - - - -
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Residues in contact with ILE 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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252A GLY* 1.3 75.0 - - - -
254A CYS* 1.3 69.9 + - - +
255A LEU* 4.0 3.1 - - - +
276A TYR* 4.0 2.3 - - - -
277A GLU* 3.4 28.5 - - - +
279A GLN* 4.6 8.1 - - + +
296A PHE* 4.0 24.5 - - + -
299A MET* 3.5 34.1 - - + -
301A GLU* 5.1 1.1 - - + -
302A HIS* 3.9 15.8 - - + -
305A TYR* 3.6 26.1 - - + +
307A SER 4.0 3.4 + - - -
308A PHE* 3.4 14.3 - - + -
309A VAL 3.1 24.8 + - - +
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Residues in contact with CYS 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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252A GLY 3.9 0.6 + - - -
253A ILE* 1.3 72.3 - - - +
255A LEU* 1.3 59.0 + - - +
256A ILE* 3.5 20.8 + - - -
271A PHE* 3.8 29.4 - - - -
276A TYR* 3.8 25.8 - - + -
277A GLU 2.8 9.1 + - - -
278A VAL* 3.3 13.2 - - + +
279A GLN 3.0 24.1 + - - -
309A VAL* 3.3 20.0 - - + -
311A VAL* 4.6 4.5 - - - -
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Residues in contact with LEU 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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253A ILE* 3.8 2.3 - - + -
254A CYS* 1.3 70.0 - - - +
256A ILE* 1.3 61.9 + - - +
257A ILE* 4.4 12.8 - - + -
279A GLN 3.7 4.7 - - - +
281A PHE* 3.4 39.3 - - + -
292A ILE* 4.6 1.6 - - + +
293A LEU* 4.1 26.5 - - + -
296A PHE* 3.8 42.4 - - + -
308A PHE* 4.0 20.0 - - + -
309A VAL 2.8 14.4 + - - +
310A CYS* 3.2 6.5 - - - -
311A VAL 2.8 27.5 + - - +
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Residues in contact with ILE 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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254A CYS* 3.9 16.8 - - - -
255A LEU* 1.3 75.0 - - - +
257A ILE* 1.3 70.1 + - - +
258A ASP* 4.4 8.7 - - + +
267A LEU* 3.9 21.8 - - + -
268A ARG* 3.9 17.5 - - + +
278A VAL* 3.6 25.8 - - + -
279A GLN 2.9 13.3 + - - +
280A LYS* 3.3 24.0 - - + -
281A PHE* 2.9 26.7 + - - -
311A VAL* 3.4 20.4 - - + +
313A VAL* 5.8 1.6 - - + -
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Residues in contact with ILE 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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255A LEU* 4.4 13.9 - - + -
256A ILE* 1.3 78.7 - - - +
258A ASP* 1.3 59.6 + - - +
259A CYS* 3.8 23.8 - - - -
281A PHE* 3.4 9.4 - - + +
284A LEU* 4.2 17.9 - - + -
289A ILE* 4.3 10.8 - - + -
292A ILE* 3.4 33.0 - - + -
293A LEU* 4.1 22.0 - - + -
310A CYS* 4.7 4.5 - - - -
311A VAL 2.8 12.3 + - - +
312A LEU* 3.4 17.3 - - + -
313A VAL* 2.8 26.7 + - - +
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Residues in contact with ASP 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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256A ILE* 4.0 12.4 - - + +
257A ILE* 1.3 71.2 - - - +
259A CYS* 1.3 60.6 + - - +
260A ILE* 3.0 8.7 + - - +
261A GLY* 2.7 39.0 + - - -
262A ASN 4.2 0.3 + - - -
263A GLU* 3.4 29.9 + - + +
280A LYS* 4.8 4.3 + - - -
281A PHE 3.1 8.4 + - - -
282A LEU* 3.3 24.2 - - + +
283A HIS 3.0 17.9 + - - -
313A VAL* 3.6 23.1 - - + +
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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