Contacts of the strand formed by residues 380 - 390 (chain B) in PDB entry 1NYR
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 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B GLY 3.5 6.1 + - - +
263B LEU* 4.1 9.1 - - - +
264B PRO* 5.1 4.2 - - - +
362B THR* 5.7 1.3 - - - -
363B MET 3.5 7.4 - - - -
364B HIS* 3.9 18.2 - - - -
378B VAL* 3.4 12.4 - - - +
379B ARG* 1.3 77.8 - - - +
381B MET* 1.3 59.5 + - - -
525B GLU* 3.7 9.7 - - - +
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Residues in contact with MET 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B THR* 3.2 6.4 - - - +
363B MET* 3.0 60.4 + - + +
365B ARG* 3.8 26.2 - - + +
378B VAL* 3.7 31.4 - - + +
379B ARG 3.7 14.8 - - - +
380B GLY* 1.3 74.4 - - - +
382B THR* 1.3 63.7 + - - +
523B THR* 3.4 16.2 - - - +
525B GLU* 3.3 11.7 - - - +
2003B ATP 3.6 33.7 - - + -
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Residues in contact with THR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.3 29.7 + - - +
278B GLU* 4.7 2.5 - - - +
360B LEU* 3.4 34.5 - - + +
361B GLY 3.5 2.9 - - - -
362B THR* 2.5 25.3 + - - +
381B MET* 1.3 72.9 - - - +
383B LEU* 1.3 61.2 + - - +
523B THR* 3.0 3.2 + - - -
524B MET* 2.7 44.7 + - + +
525B GLU* 3.0 10.4 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B LEU* 3.2 7.3 - - - -
361B GLY 2.7 35.9 + - - +
363B MET* 3.7 29.8 - - + -
381B MET 4.1 0.6 - - - -
382B THR* 1.3 73.4 - - - +
384B ASN* 1.3 66.8 + - - +
385B ASP* 2.8 44.3 + - + +
518B ARG 5.5 0.7 - - - +
519B GLY* 5.5 4.0 - - - -
522B SER* 3.8 6.7 - - - -
523B THR* 3.7 21.8 - - - +
524B MET* 5.4 0.9 - - - -
2003B ATP 3.8 22.0 - - - +
2004B THR* 4.0 20.2 - - + +
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 3.3 23.3 - - + +
285B GLU* 2.9 27.3 + - - +
359B GLU 3.9 2.0 - - - -
360B LEU* 4.3 10.7 - - + +
382B THR 4.2 0.2 + - - -
383B LEU* 1.3 72.2 - - - +
385B ASP* 1.3 59.9 + - - +
518B ARG* 4.3 1.3 + - - +
519B GLY* 3.3 17.2 - - - -
520B VAL* 3.1 21.6 - - - +
521B VAL* 3.0 33.5 - - + +
522B SER 3.3 23.6 + - - +
524B MET* 4.4 9.1 - - + +
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 4.6 3.8 - - - +
335B ASN* 2.7 48.0 + - - +
339B HIS* 4.7 4.7 - - + -
358B ALA* 3.7 3.3 - - - +
359B GLU 2.9 37.3 + - - +
383B LEU* 2.8 22.5 + - + +
384B ASN* 1.3 72.7 - - - +
386B SER* 1.3 70.3 + - - +
387B HIS* 3.6 13.2 + - - -
518B ARG 3.7 4.7 - - - +
2004B THR* 3.3 28.9 + - - -
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B TYR* 3.1 27.9 - - - -
339B HIS* 5.1 0.7 - - - -
357B ILE 3.5 10.1 + - - -
358B ALA* 4.3 1.7 - - - +
385B ASP* 1.3 78.7 + - - +
387B HIS* 1.3 80.4 + - - +
388B ILE* 4.0 4.1 - - - +
518B ARG* 2.8 59.9 + - - +
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Residues in contact with HIS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B CYS* 2.9 36.2 - - + -
339B HIS* 2.5 41.9 + - + +
340B MET* 5.6 1.8 - - + -
357B ILE 2.6 25.6 + - - +
385B ASP* 3.6 12.1 - - - -
386B SER* 1.3 88.4 + - - +
388B ILE* 1.3 60.9 + - - +
389B PHE* 3.0 28.5 - + + -
515B VAL* 4.9 6.5 - - + -
516B ILE 3.7 2.2 - - - -
517B HIS* 3.6 19.1 - + - -
2001B ZN 2.2 31.8 - - - -
2004B THR* 3.3 1.8 + - - -
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B TYR* 3.6 21.8 - - + +
354B PRO 3.6 15.9 - - - +
355B ILE 3.5 4.5 - - - +
356B ARG* 3.8 20.6 - - + +
386B SER* 4.0 9.2 - - - +
387B HIS* 1.3 73.6 - - - +
389B PHE* 1.3 63.1 + - - +
390B VAL* 3.5 21.8 - - + +
398B GLU* 3.1 32.1 - - + +
402B VAL* 4.5 3.8 - - + -
515B VAL* 3.4 3.0 - - - +
516B ILE* 2.8 49.5 + - + +
518B ARG* 4.5 11.0 - - + -
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Residues in contact with PHE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B HIS 4.0 11.4 - - - -
340B MET* 3.7 28.3 - - + -
343B TYR* 3.2 55.6 - + + -
353B LEU* 2.9 19.8 - - + +
354B PRO 3.2 14.6 - - - +
355B ILE* 2.8 22.5 + - + +
357B ILE* 3.7 17.5 - - + -
387B HIS* 3.0 34.1 - - + -
388B ILE* 1.3 68.9 - - - +
390B VAL* 1.3 61.5 + - - +
501B LEU* 3.9 7.0 - - + -
513B PRO* 4.5 5.8 - - + -
514B VAL 3.4 6.3 - - - +
515B VAL* 3.6 20.2 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.4 9.9 - - - -
354B PRO* 4.6 6.1 - - + +
388B ILE* 3.5 28.5 - - + +
389B PHE* 1.3 79.9 - - - +
391B ARG* 1.3 71.3 + - - +
394B GLN* 3.1 33.7 - - + +
395B ILE* 4.0 15.0 - - + +
398B GLU* 4.4 7.6 - - + +
513B PRO* 3.1 10.1 - - - +
514B VAL* 2.6 41.8 + - + +
516B ILE* 3.9 20.9 - - + -
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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