Contacts of the strand formed by residues 373 - 382 (chain A) in PDB entry 4RUH
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 GLU 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLU* 3.5 1.4 - - - +
220A VAL* 3.1 6.1 - - - -
221A GLU* 2.6 70.9 + - + +
371A PRO 3.6 1.9 + - - +
372A ASN* 1.3 71.7 - - - +
374A PHE* 1.3 59.7 + - - +
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Residues in contact with PHE 374 (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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218A ILE* 3.7 16.2 - - + -
219A GLU 3.2 9.9 - - - -
220A VAL* 4.5 4.0 - - + -
246A LEU* 3.4 31.6 - - + -
361A LEU* 3.9 19.7 - - + -
362A THR* 3.6 32.8 - - + -
365A PHE* 3.4 44.8 - + + -
372A ASN 3.3 2.2 + - - -
373A GLU* 1.3 74.3 - - - +
375A LYS* 1.3 76.1 + - - +
376A VAL* 3.8 23.8 - - + -
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Residues in contact with LYS 375 (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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70A PRO* 4.7 12.5 + - - +
217A PHE 3.4 1.1 - - - +
218A ILE* 3.4 4.0 - - - +
219A GLU* 2.6 68.3 + - + +
374A PHE* 1.3 84.8 - - - +
376A VAL* 1.3 62.1 + - - +
377A TYR* 3.6 32.7 - - - -
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Residues in contact with VAL 376 (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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216A PHE* 4.4 7.6 - - + -
217A PHE 3.4 8.3 - - - +
218A ILE* 4.4 6.1 - - + -
357A VAL* 4.4 11.0 - - + -
358A THR* 3.6 42.2 + - + +
361A LEU* 3.6 26.5 - - + -
362A THR* 4.2 4.5 - - + -
374A PHE* 3.8 24.1 - - + -
375A LYS* 1.3 76.9 - - - +
377A TYR* 1.3 72.8 + - - +
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Residues in contact with TYR 377 (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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70A PRO* 3.8 22.0 - - + +
216A PHE* 3.4 10.1 - - - +
217A PHE* 2.9 72.0 + + + +
219A GLU* 3.5 24.2 + - + +
337A VAL* 5.3 1.2 - - - +
358A THR* 5.5 2.0 - - - -
375A LYS* 3.6 37.0 - - + -
376A VAL* 1.3 80.0 - - - +
378A MET* 1.3 69.1 + - - +
379A GLY* 3.9 3.8 + - - -
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Residues in contact with MET 378 (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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214A CYS* 3.7 22.7 - - - -
215A TYR 3.5 10.8 - - - +
216A PHE* 4.2 13.9 - - + -
350A PRO* 3.6 36.6 - - + +
351A GLU* 5.4 1.8 - - - -
354A GLY* 4.5 10.8 - - - -
377A TYR* 1.3 79.0 - - - +
379A GLY* 1.3 67.5 + - - +
380A HIS* 3.6 22.8 - - - +
381A GLY 5.0 3.6 - - - +
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Residues in contact with GLY 379 (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 TYR 3.0 9.1 + - - -
217A PHE* 3.5 28.0 - - - -
377A TYR* 4.7 6.1 - - - -
378A MET* 1.3 75.9 - - - +
380A HIS* 1.3 67.0 + - - +
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Residues in contact with HIS 380 (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 SER* 3.6 20.7 - - - +
169A GLY* 3.6 23.2 - - - +
213A ILE* 4.3 9.5 - - + +
214A CYS* 3.8 0.2 - - - -
215A TYR* 3.1 56.8 + + + +
217A PHE* 5.2 1.3 - + - -
378A MET* 3.2 11.1 - - - +
379A GLY* 1.3 87.8 - - - +
381A GLY* 1.3 62.2 + - - +
419A PRO* 5.9 0.2 - - - +
501A BES 3.3 38.1 - - + +
328B ALA* 4.2 15.3 - - + +
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Residues in contact with GLY 381 (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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169A GLY* 5.2 3.9 - - - +
213A ILE* 3.1 11.9 - - - -
214A CYS* 4.5 1.8 - - - -
350A PRO* 4.0 22.0 - - - +
378A MET* 4.5 5.0 - - - +
380A HIS* 1.3 79.7 - - - +
382A GLY* 1.3 59.2 + - - -
419A PRO* 4.4 9.4 - - - +
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Residues in contact with GLY 382 (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 GLY* 3.1 3.6 - - - -
213A ILE* 2.9 36.5 + - - +
344A LEU* 3.8 3.8 - - - +
350A PRO* 3.7 9.5 - - - +
381A GLY* 1.3 74.3 - - - -
383A LYS* 1.3 62.6 + - - -
417A SER* 6.0 0.4 - - - -
419A PRO* 3.7 27.1 - - - -
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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