Contacts of the strand formed by residues 353 - 361 (chain A) in PDB entry 3H13
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 LYS 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A PHE* 3.5 11.7 - - + -
340A PHE* 3.1 37.5 - - + +
341A MET* 4.9 1.3 - - - +
342A GLY 5.1 2.9 - - - +
348A LEU* 3.0 42.4 + - + -
349A ALA* 4.6 1.4 - - - +
350A GLY 4.4 3.6 - - - +
351A LYS 2.7 29.9 + - - +
352A PRO* 1.3 71.7 - - - +
354A MET* 1.3 62.3 + - - +
355A PHE* 3.8 20.3 - - + -
397A ARG 5.5 0.4 - - - -
399A ALA 4.1 4.0 + - - -
400A ASP* 2.8 17.8 + - - +
401A PHE* 3.5 27.6 - - + -
402A PHE* 2.9 26.2 + - - +
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Residues in contact with MET 354 (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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276A TYR* 3.6 23.3 - - - +
307A SER* 4.0 14.8 - - - -
308A PHE* 2.8 19.5 + - - +
309A VAL* 3.3 17.3 - - + +
310A CYS* 2.7 32.6 + - - +
352A PRO* 4.2 8.7 - - + +
353A LYS* 1.3 76.1 - - - +
355A PHE* 1.3 58.6 + - - +
356A PHE* 3.9 18.4 - - + -
402A PHE* 3.4 21.5 - - + -
439A LEU* 3.7 19.3 - - + -
475A LEU* 3.9 9.2 - - + -
477A LEU* 3.6 31.2 - - + -
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Residues in contact with PHE 355 (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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308A PHE* 4.2 7.6 - + - -
310A CYS* 3.2 31.9 - - + +
336A ILE* 4.0 22.7 - - + -
337A ARG* 4.7 1.8 - - - -
340A PHE* 3.8 31.6 - + - -
353A LYS* 3.8 19.7 - - + -
354A MET* 1.3 76.5 - - - +
356A PHE* 1.3 62.4 + - - +
357A ILE* 4.1 10.1 - - + -
401A PHE* 3.6 28.9 - + - -
402A PHE* 2.8 13.5 + - - +
403A TRP* 3.4 40.8 - + + -
404A SER* 2.9 30.5 + - - +
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Residues in contact with PHE 356 (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 LEU* 4.8 0.2 - - + -
271A PHE* 3.6 30.1 - + - -
309A VAL* 4.0 16.4 - - + -
310A CYS 2.9 7.9 + - - +
311A VAL* 3.2 18.1 - - + +
312A LEU 3.0 24.3 + - - +
354A MET* 3.9 21.8 - - + -
355A PHE* 1.3 72.1 - - - +
357A ILE* 1.3 60.9 + - - +
358A GLN 4.3 0.2 + - - -
402A PHE* 3.8 21.1 - + - -
404A SER* 3.5 11.9 - - - -
423A TYR* 3.7 15.9 - - + +
424A LEU* 5.9 0.7 - - + -
427A LEU* 3.5 39.3 - - + -
431A LEU* 4.5 2.2 - - + -
439A LEU* 4.1 28.5 - - + -
443A HIS* 5.0 1.6 - + - -
477A LEU* 5.4 0.2 - - + -
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Residues in contact with ILE 357 (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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310A CYS* 5.4 0.9 - - - +
312A LEU* 3.3 33.4 - - + +
321A VAL* 4.8 4.0 - - + -
333A LEU* 4.1 13.9 - - + -
336A ILE* 5.7 0.4 - - + -
355A PHE* 4.4 6.7 - - + -
356A PHE* 1.3 82.0 - - - +
358A GLN* 1.3 62.9 + - - +
359A ASN* 4.4 4.0 - - + +
403A TRP* 3.3 50.3 - - + +
404A SER 2.8 12.7 + - - +
405A LEU* 3.6 21.3 - - + -
406A CYS* 2.7 34.5 + - - +
423A TYR* 3.8 5.8 + - - -
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Residues in contact with GLN 358 (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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312A LEU 2.8 9.7 + - - +
313A VAL* 3.4 15.3 - - + +
314A SER 3.0 26.0 + - - +
356A PHE 4.3 0.2 + - - -
357A ILE* 1.3 72.6 - - - +
359A ASN* 1.3 82.4 + - - +
360A TYR* 3.5 22.8 - - + +
406A CYS* 3.3 34.4 + - - -
408A ALA* 3.8 15.0 - - - +
421A SER* 2.6 34.1 + - - +
423A TYR* 3.5 6.9 - - + +
424A LEU* 4.2 19.2 - - + +
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Residues in contact with ASN 359 (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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314A SER 3.1 6.3 - - - +
315A ARG 3.4 0.7 - - - +
316A GLY* 3.1 28.2 + - - -
317A GLY 2.7 29.1 + - - -
318A SER* 4.8 0.6 - - - +
319A GLN 4.6 3.4 - - - +
320A SER 3.4 11.3 + - - +
321A VAL* 4.3 7.1 - - - +
333A LEU* 5.3 2.0 - - - +
357A ILE* 3.9 3.8 - - + -
358A GLN* 1.3 82.4 + - - +
360A TYR* 1.3 62.2 + - - +
361A VAL* 3.6 10.6 - - - +
405A LEU* 4.0 18.4 - - + +
406A CYS 2.7 12.6 + - - +
407A THR* 4.4 8.7 + - - +
408A ALA 3.0 23.3 + - - -
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Residues in contact with TYR 360 (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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260A ILE* 3.3 32.5 - - + -
262A ASN* 3.1 24.8 + - - -
313A VAL* 4.3 1.6 - - + -
314A SER 3.0 7.9 + - - -
315A ARG* 3.3 4.7 - - - -
316A GLY 2.8 25.6 + - - +
358A GLN* 3.5 23.5 - - + +
359A ASN* 1.3 75.4 + - - +
361A VAL* 1.3 60.4 + - - +
408A ALA* 3.3 22.9 - - + +
409A ASP 3.8 15.5 - - - -
410A MET* 3.8 14.9 - - - +
412A LEU* 4.3 14.1 - - + -
413A LEU* 3.7 36.6 - - + -
419A SER 4.5 0.9 + - - -
421A SER* 3.4 24.1 + - - -
424A LEU* 5.8 0.2 - - - +
463A TYR* 5.2 0.4 + - - -
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Residues in contact with VAL 361 (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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316A GLY 3.5 18.4 - - - +
317A GLY* 3.6 15.7 - - - +
318A SER* 4.7 6.5 - - - +
359A ASN* 3.6 22.4 - - - +
360A TYR* 1.3 78.5 - - - +
362A VAL* 1.3 75.7 + - + +
363A SER* 3.6 0.7 + - - -
407A THR* 3.8 25.4 - - + -
408A ALA 2.9 7.2 + - - +
409A ASP* 3.5 6.6 - - - -
410A MET* 2.7 32.7 + - - -
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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