Contacts of the strand formed by residues 350 - 359 (chain A) in PDB entry 5C7Z
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 ALA 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A ARG* 4.2 31.4 - - + +
324A ILE 3.2 15.5 - - - +
325A PRO* 4.2 2.0 - - + -
326A THR* 3.7 4.1 + - - -
344A TYR* 3.4 7.3 - - - -
345A LYS* 2.8 38.5 + - - +
348A GLU* 3.9 7.6 - - + +
349A ASN* 1.3 79.5 - - - +
351A ILE* 1.3 63.1 + - - +
352A VAL* 4.6 1.3 - - + -
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Residues in contact with ILE 351 (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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303A VAL* 6.1 0.2 - - + -
322A VAL 3.5 1.7 - - - +
323A ARG* 3.4 4.3 - - - -
324A ILE* 2.7 65.0 + - + +
326A THR* 4.1 17.9 - - + -
333A VAL* 3.9 25.8 - - + -
335A VAL* 4.1 15.9 - - + -
342A ALA* 4.4 13.0 - - + -
343A LYS 3.5 10.3 - - - +
344A TYR* 4.2 4.9 - - + -
350A ALA* 1.3 74.3 - - - +
352A VAL* 1.3 65.2 + - - +
353A TRP 4.9 0.2 - - - +
366A ILE* 4.7 4.7 - - + -
368A ALA* 3.8 26.5 - - + -
370A ILE* 4.6 8.3 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLU* 4.0 26.9 - - + +
322A VAL 3.5 2.5 - - - +
323A ARG* 3.6 32.8 - - + +
341A LYS 3.9 1.0 - - - +
342A ALA* 3.2 5.9 - - - -
343A LYS* 2.9 34.9 + - + +
345A LYS* 4.0 27.1 - - + -
348A GLU* 4.5 0.7 - - - +
350A ALA* 4.5 7.9 - - + +
351A ILE* 1.3 78.2 - - - +
353A TRP* 1.3 60.4 + - - +
354A LYS* 4.0 24.4 + - + +
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Residues in contact with TRP 353 (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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305A VAL* 4.2 5.8 - - + -
307A ILE* 4.1 20.2 - - + -
320A ILE 3.9 0.2 - - - +
321A GLU* 3.2 5.2 - - - +
322A VAL* 2.8 59.1 + - + +
324A ILE* 5.6 1.6 - - + -
337A CYS* 3.7 15.3 - - + -
339A LYS* 3.0 27.5 + - + -
341A LYS 3.5 12.8 - - - -
342A ALA* 3.8 1.3 - - - -
351A ILE* 4.1 2.0 - - + -
352A VAL* 1.3 72.5 - - - +
354A LYS* 1.3 69.8 + - - +
355A ILE* 3.6 24.2 - - + +
364A SER* 3.8 17.3 - - - -
365A GLN* 3.6 36.3 - - - -
366A ILE* 3.5 41.7 - - + -
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Residues in contact with LYS 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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320A ILE 3.3 7.4 - - - +
321A GLU* 3.7 23.6 - - + +
340A GLY* 3.3 3.5 - - - -
341A LYS* 2.8 38.2 + - + +
345A LYS* 4.6 13.8 - - - +
352A VAL* 4.0 19.3 - - + +
353A TRP* 1.3 78.2 - - - +
355A ILE* 1.3 63.6 + - - +
356A LYS 4.3 0.6 + - - -
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Residues in contact with ILE 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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307A ILE* 3.9 23.8 - - + -
319A LYS* 3.8 0.7 + - - -
320A ILE* 2.8 50.7 + - + +
322A VAL* 5.3 1.6 - - + -
339A LYS* 4.7 11.0 - - + -
340A GLY* 4.1 12.8 - - - +
353A TRP* 3.6 41.5 - - + +
354A LYS* 1.3 79.2 - - - +
356A LYS* 1.3 64.8 + - - +
357A ARG 3.2 26.5 - - - +
358A MET* 4.4 5.8 - - + -
364A SER* 5.2 3.1 - - - +
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Residues in contact with LYS 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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318A GLN* 3.4 9.5 - - - +
319A LYS* 3.2 23.7 + - - +
340A GLY* 5.7 0.4 - - - -
354A LYS 4.3 0.6 + - - -
355A ILE* 1.3 72.9 - - - +
357A ARG* 1.3 91.7 + - - +
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Residues in contact with ARG 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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316A LEU* 3.9 31.6 - - + -
317A ALA 3.3 7.6 - - - +
318A GLN* 3.2 27.7 + - - +
320A ILE* 4.2 1.6 - - - -
355A ILE* 3.2 14.2 - - - +
356A LYS* 1.3 109.5 + - - +
358A MET* 1.3 65.8 + - - +
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Residues in contact with MET 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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287A PHE* 3.9 21.8 - - - -
307A ILE* 4.0 22.9 - - + +
309A SER* 3.4 21.1 - - - +
311A PHE* 4.0 1.7 - - - -
316A LEU* 3.7 5.7 - - - +
317A ALA* 2.8 41.6 + - + +
320A ILE* 3.6 15.3 - - + -
355A ILE* 4.4 6.3 - - + -
357A ARG* 1.3 77.7 - - - +
359A ALA* 1.3 67.4 - - - +
362A LYS* 3.6 31.2 - - + +
363A GLU 3.8 3.4 - - - +
364A SER* 3.5 24.0 - - - +
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Residues in contact with ALA 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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309A SER* 2.5 28.5 + - - -
311A PHE* 4.0 1.6 - - - -
313A PRO* 3.8 15.9 - - + +
315A LEU 3.4 7.0 - - - +
316A LEU* 3.5 18.9 - - + +
358A MET* 1.3 76.9 - - - +
360A GLY* 1.3 60.6 - - - +
362A LYS* 3.1 24.0 - - + +
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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