Contacts of the strand formed by residues 367 - 379 (chain A) in PDB entry 4NTX
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 ASN 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LEU 3.6 1.6 - - - -
282A ILE* 3.8 14.6 - - - +
304A TYR 4.9 4.2 - - - +
305A SER* 5.9 0.7 - - - -
365A PRO* 3.9 9.6 - - - +
366A CYS* 1.3 89.7 - - - +
368A VAL* 1.3 66.6 + - - +
369A THR* 6.2 0.2 - - - +
501A NAG 1.4 86.0 + - + +
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Residues in contact with VAL 368 (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 GLU* 5.7 2.9 - - - +
279A GLN 3.8 0.9 - - - +
280A ARG* 3.6 1.9 - - - +
281A LEU* 2.7 58.4 + - + +
283A TYR* 4.4 1.6 - - + -
306A ILE* 5.6 2.0 - - + -
364A MET* 3.6 23.1 - - + -
365A PRO* 3.4 34.8 - - + +
367A ASN* 1.3 73.5 - - - +
369A THR* 1.3 72.5 + - - +
370A ARG* 4.6 5.4 - - + +
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Residues in contact with THR 369 (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 SER* 4.5 17.2 + - - -
255A GLU* 4.2 14.7 + - - +
278A GLU* 3.9 24.0 - - + +
279A GLN 3.6 3.4 - - - +
280A ARG* 4.2 12.4 - - + +
367A ASN 4.3 0.8 + - - -
368A VAL* 1.3 78.6 - - - +
370A ARG* 1.3 63.1 + - - +
371A TYR* 3.5 37.5 - - + +
501A NAG 5.7 0.9 + - - -
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Residues in contact with ARG 370 (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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277A GLN 3.6 0.7 - - - +
278A GLU* 3.6 2.6 - - - -
279A GLN* 2.9 71.8 + - + +
281A LEU* 4.2 13.9 - - + -
368A VAL* 4.0 5.8 + - + -
369A THR* 1.3 74.5 - - - +
371A TYR* 1.3 72.0 + - - +
372A GLY* 3.9 28.2 - - - +
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Residues in contact with TYR 371 (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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87A THR 4.9 3.3 + - - -
89A PRO* 3.6 23.5 - - + +
250A ILE* 4.0 32.8 - - + +
251A HIS* 4.0 3.8 - - - -
252A SER* 3.9 28.3 - - - -
276A CYS* 4.9 5.6 - - + -
277A GLN 3.4 3.4 - - - +
278A GLU* 4.1 21.6 + - + -
369A THR* 3.5 27.4 - - + +
370A ARG* 1.3 87.1 + - - +
372A GLY* 1.3 65.9 + - - +
373A LYS* 3.4 27.1 + - + +
411A PHE* 3.9 34.3 - + - -
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Residues in contact with GLY 372 (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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275A SER 3.8 0.6 - - - +
276A CYS* 3.1 6.1 - - - -
277A GLN* 2.7 45.8 + - - -
370A ARG* 3.9 27.0 - - - +
371A TYR* 1.3 74.1 - - - +
373A LYS* 1.3 58.9 + - - +
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Residues in contact with LYS 373 (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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250A ILE* 4.0 15.3 + - + +
262A LEU 5.8 1.6 + - - -
264A PHE* 3.8 36.6 - - + -
274A VAL* 3.8 27.4 - - + -
275A SER 3.4 4.7 - - - -
276A CYS* 4.2 8.7 - - - -
371A TYR* 3.4 20.5 + - + +
372A GLY* 1.3 77.1 - - - +
374A GLU* 1.3 66.7 + - - +
375A LEU* 4.1 11.6 + - + +
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Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A PHE* 3.3 3.5 - - - +
275A SER* 2.8 47.6 + - - +
373A LYS* 1.3 78.3 - - - +
375A LEU* 1.3 63.0 + - - +
376A SER* 5.2 0.5 + - - -
412A GLU* 5.0 9.3 - - - +
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Residues in contact with LEU 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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264A PHE* 3.7 31.9 - - + -
265A GLY 4.2 9.2 - - - +
272A THR* 4.0 18.8 - - + -
273A PHE 3.1 3.8 - - - +
274A VAL* 4.0 28.0 - - + -
373A LYS* 4.1 17.9 + - + +
374A GLU* 1.3 77.2 - - - +
376A SER* 1.3 63.9 + - - +
377A MET* 6.3 0.2 - - + -
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Residues in contact with SER 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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272A THR* 3.4 5.7 - - - +
273A PHE* 2.8 51.2 + - - +
374A GLU 5.2 0.5 + - - -
375A LEU* 1.3 77.6 - - - +
377A MET* 1.3 65.4 + - - +
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Residues in contact with MET 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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267A ALA* 4.6 11.2 - - + +
270A PHE* 3.3 58.8 - - + -
271A GLN 3.2 5.8 - - - +
272A THR* 3.7 20.9 - - + +
273A PHE* 4.9 1.8 - - - -
375A LEU* 6.3 0.2 - - + -
376A SER* 1.3 83.1 + - - +
378A VAL* 1.3 68.0 + - - +
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Residues in contact with VAL 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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270A PHE* 3.2 13.1 - - - +
271A GLN* 2.8 62.5 + - + +
273A PHE* 4.1 14.4 - - + -
377A MET* 1.3 80.4 - - - +
379A LYS* 1.3 64.0 + - - +
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Residues in contact with LYS 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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269A GLY 3.8 11.4 - - - +
270A PHE* 4.3 9.6 - - + -
271A GLN 4.6 0.4 - - - -
378A VAL* 1.3 81.4 - - - +
380A ILE* 1.3 67.8 + - - +
381A PRO* 4.1 24.6 - - - +
382A SER* 4.5 3.7 + - - -
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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