Contacts of the strand formed by residues 212 - 221 (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 GLY 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ARG* 1.3 73.4 - - - +
213A ILE* 1.3 56.8 + - - -
343A ARG* 3.2 6.6 - - - -
344A LEU* 2.6 42.3 + - - -
382A GLY 3.1 16.4 - - - -
383A LYS 3.7 3.1 - - - -
384A PRO* 3.3 17.8 - - - +
417A SER* 3.2 13.0 + - - -
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Residues in contact with ILE 213 (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* 1.3 74.8 - - - +
214A CYS* 1.3 77.1 + - - +
215A TYR* 4.0 5.8 - - + +
341A SER* 4.0 15.0 - - - -
342A ILE 3.2 10.8 - - - +
343A ARG* 4.0 17.9 - - - +
344A LEU* 4.0 1.5 - - - +
380A HIS* 4.3 11.2 - - + +
381A GLY* 3.1 4.9 - - - -
382A GLY* 2.9 40.0 + - - +
417A SER* 3.7 17.3 - - - +
419A PRO* 4.9 0.7 - - + -
501A BES 3.8 24.7 - - + -
330B THR* 3.8 29.2 - - + -
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Residues in contact with CYS 214 (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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213A ILE* 1.3 81.6 - - - +
215A TYR* 1.3 59.7 + - - +
216A PHE* 3.4 27.3 - - + -
341A SER* 3.1 2.9 - - - -
342A ILE* 2.8 37.5 + - + +
344A LEU* 3.7 8.7 - - + +
350A PRO* 3.5 32.8 - - - -
353A VAL* 3.9 22.7 - - + -
378A MET* 3.7 15.5 - - - -
380A HIS 3.8 3.8 - - - -
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Residues in contact with TYR 215 (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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213A ILE* 4.0 2.1 - - + +
214A CYS* 1.3 72.9 - - - +
216A PHE* 1.3 76.0 + - - +
217A PHE* 3.9 10.3 - + - -
317A HIS* 3.2 38.1 - + - +
339A LYS* 3.6 15.6 - - + +
340A PHE 4.3 1.1 - - - -
341A SER* 3.4 17.0 - - - -
378A MET* 3.5 4.3 - - - +
379A GLY 3.0 26.3 + - - -
380A HIS* 3.1 37.6 + - + +
323B PHE* 4.1 2.6 - - - -
328B ALA* 3.5 26.7 - - + -
329B LYS 3.0 31.6 + - - -
330B THR* 3.6 18.8 - - + -
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Residues in contact with PHE 216 (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* 3.4 38.6 - - + -
215A TYR* 1.3 79.8 - - - +
217A PHE* 1.3 72.1 + - - +
218A ILE 4.3 0.4 - - - -
338A GLY 4.5 0.4 - - - -
339A LYS* 3.7 13.2 - - - -
340A PHE* 2.8 55.0 + + + +
342A ILE* 3.9 12.1 - - + -
353A VAL* 4.1 6.3 - - + -
354A GLY* 4.2 16.4 - - - -
357A VAL* 3.4 46.0 - - + -
358A THR* 5.4 0.9 - - - -
376A VAL* 4.4 8.5 - - + -
377A TYR 3.4 14.1 - - - +
378A MET* 4.2 13.9 - - + -
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Residues in contact with PHE 217 (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* 3.9 13.7 - + - -
216A PHE* 1.3 74.8 - - - +
218A ILE* 1.3 62.5 + - - +
219A GLU 3.8 0.6 + - - -
320A GLU* 5.6 0.4 - - - -
337A VAL* 3.8 11.4 - - + -
338A GLY 3.5 4.0 - - - -
339A LYS* 3.8 26.0 - - + -
375A LYS 3.4 2.1 - - - +
376A VAL* 3.4 4.6 - - - -
377A TYR* 2.9 65.3 + + + +
379A GLY* 3.5 35.2 - - - -
380A HIS* 5.2 1.6 - + - -
327B GLY* 3.6 24.7 - - - -
328B ALA* 3.9 22.0 - - + -
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Residues in contact with ILE 218 (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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217A PHE* 1.3 75.0 - - - +
219A GLU* 1.3 55.8 + - - +
220A VAL* 4.6 1.8 - - + -
243A LEU* 3.5 22.7 - - + +
246A LEU* 4.0 13.5 - - + -
247A MET* 4.4 21.5 - - + +
250A LEU* 5.1 1.1 - - + -
336A VAL 3.5 1.2 - - - +
337A VAL* 3.2 4.8 - - - +
338A GLY 2.9 33.7 + - - +
340A PHE* 3.8 25.6 - - + -
361A LEU* 3.7 33.4 - - + -
374A PHE* 3.7 31.2 - - + -
375A LYS 3.4 2.5 - - - -
376A VAL* 4.4 2.5 - - + -
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Residues in contact with GLU 219 (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* 4.4 10.7 - - - +
218A ILE* 1.3 71.4 - - - +
220A VAL* 1.3 64.3 + - - +
221A GLU* 6.4 0.4 - - + -
335A LYS* 3.6 32.3 + - + -
336A VAL 3.4 4.3 - - - +
337A VAL* 3.5 25.3 - - + +
373A GLU 4.1 1.1 - - - +
374A PHE* 3.2 6.6 - - - -
375A LYS* 2.6 66.0 + - + +
377A TYR* 3.5 32.4 + - + -
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Residues in contact with VAL 220 (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* 4.5 2.2 - - + +
219A GLU* 1.3 78.1 - - - +
221A GLU* 1.3 64.3 + - - +
239A ALA* 3.6 20.6 - - + +
242A ASP* 3.9 20.9 - - + +
243A LEU* 4.2 34.8 - - + +
246A LEU* 4.8 1.6 - - + -
335A LYS* 3.2 4.6 - - - +
336A VAL* 2.9 33.1 + - + +
365A PHE* 4.9 4.3 - - + -
372A ASN* 3.7 24.5 - - + -
373A GLU 3.1 5.8 - - - +
374A PHE* 4.5 12.6 - - + -
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Residues in contact with GLU 221 (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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219A GLU* 6.4 0.4 - - + -
220A VAL* 1.3 76.4 - - - +
222A CYS* 1.3 62.8 + - - +
223A SER 3.9 15.4 - - - +
239A ALA* 4.5 0.2 - - - -
334A ARG 3.3 10.5 - - - +
335A LYS* 4.1 24.8 + - + +
372A ASN* 3.2 7.4 - - - +
373A GLU* 2.6 70.4 + - + +
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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