Contacts of the helix formed by residues 350 - 364 (chain A) in PDB entry 5U03
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 GLU 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A THR* 2.6 17.3 + - - +
349A GLU* 1.3 76.3 - - - +
351A PRO* 1.3 69.4 - - + +
352A VAL* 3.0 28.0 - - + +
353A ARG* 2.8 55.4 + - - +
354A TYR 3.1 7.8 + - - -
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Residues in contact with PRO 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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347A SER* 3.3 29.4 - - - +
348A GLN 4.5 1.6 - - - +
349A GLU 3.6 5.6 - - - +
350A GLU* 1.3 84.1 - - + +
352A VAL* 1.3 69.7 + - + +
354A TYR* 3.6 9.6 - - + -
355A HIS* 2.9 44.6 + - + +
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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
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350A GLU* 3.0 21.7 - - + +
351A PRO* 1.3 82.9 - - + +
353A ARG* 1.3 59.0 + - + +
355A HIS* 4.0 1.7 - - - +
356A GLU* 2.8 43.5 + - + +
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Residues in contact with ARG 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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341A ASP* 2.7 40.3 + - - +
346A THR* 3.5 13.2 + - + +
349A GLU* 3.9 20.2 + - - +
350A GLU* 2.8 53.8 + - - +
352A VAL* 1.3 78.4 - - + +
354A TYR* 1.3 61.4 + - - +
356A GLU* 3.6 13.3 - - - +
357A ALA* 2.8 32.7 + - - +
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Residues in contact with TYR 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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341A ASP 3.2 17.3 - - - -
342A LEU 3.2 21.7 + - - -
343A GLU 3.0 28.7 - - - -
344A PRO* 3.8 6.9 - - + +
346A THR* 3.7 3.7 - - + +
347A SER* 3.6 37.0 - - - +
350A GLU 3.1 5.3 + - - -
351A PRO* 3.5 8.3 - - + +
352A VAL 3.2 0.2 - - - -
353A ARG* 1.3 78.7 - - - +
355A HIS* 1.3 93.8 + + - +
357A ALA* 3.2 8.7 + - - +
358A TRP* 3.2 41.4 + + - -
383A GLN* 5.6 2.3 + - - -
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Residues in contact with HIS 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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347A SER* 5.0 2.6 + - - -
351A PRO* 2.9 37.3 + - + +
352A VAL* 4.2 1.8 - - - +
354A TYR* 1.3 99.7 - + - +
356A GLU* 1.3 56.2 + - - +
358A TRP* 3.3 6.8 + - - +
359A GLN* 2.7 36.3 + - - +
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Residues in contact with GLU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 2.8 32.4 + - + +
353A ARG* 3.6 12.6 - - - +
355A HIS* 1.3 77.8 - - - +
357A ALA* 1.3 56.3 + - - +
359A GLN* 3.2 9.0 + - - +
360A LYS* 2.9 62.8 + - + +
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Residues in contact with ALA 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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337A ILE* 3.6 15.8 - - + +
341A ASP* 3.7 21.5 - - + +
342A LEU* 3.6 19.5 - - + -
353A ARG 2.8 17.9 + - - +
354A TYR 3.5 5.2 - - - +
356A GLU* 1.3 77.2 - - - +
358A TRP* 1.3 56.3 + - - +
360A LYS* 3.1 11.5 + - - +
361A LEU* 2.8 27.2 + - - +
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Residues in contact with TRP 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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342A LEU* 2.9 48.3 + - + +
354A TYR* 3.2 48.6 + + - -
355A HIS* 3.9 8.5 - - - +
357A ALA* 1.3 75.8 - - - +
359A GLN* 1.3 66.6 + - - +
361A LEU* 3.2 35.1 + - + +
362A CYS* 3.0 23.2 + - - +
383A GLN* 3.9 37.2 - - + -
384A ALA* 4.3 2.0 - - - -
387A TRP* 3.8 28.4 - + + -
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Residues in contact with GLN 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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355A HIS 2.7 23.2 + - - +
356A GLU* 3.5 10.2 - - - +
358A TRP* 1.3 73.2 - - - +
360A LYS* 1.3 75.8 + - - +
362A CYS* 3.2 6.6 + - - +
363A SER* 3.0 33.2 + - - -
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Residues in contact with LYS 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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335A LYS* 3.7 24.7 - - + +
336A TYR 5.4 6.6 + - - +
337A ILE* 3.9 20.4 - - + -
356A GLU* 2.9 48.9 + - + +
357A ALA* 3.4 8.1 - - - +
359A GLN* 1.3 85.5 - - - +
361A LEU* 1.3 64.2 + - - +
363A SER* 2.5 24.5 + - - +
364A ALA 2.9 8.3 + - - -
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Residues in contact with LEU 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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302A ALA* 3.6 25.8 - - + -
304A VAL* 4.2 12.8 - - + -
337A ILE* 3.8 8.7 - - + -
342A LEU* 4.4 8.1 - - + -
357A ALA 2.8 15.3 + - - +
358A TRP* 3.5 43.3 - - + +
359A GLN 3.2 0.2 - - - -
360A LYS* 1.3 75.9 - - - +
362A CYS* 1.3 63.5 + - - +
364A ALA* 3.1 17.5 + - - +
367A VAL* 3.6 20.3 - - + +
384A ALA* 4.2 15.9 - - + -
387A TRP* 3.5 28.8 - - + -
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Residues in contact with CYS 362 (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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358A TRP 3.0 12.9 + - - +
359A GLN* 3.7 8.7 - - - +
361A LEU* 1.3 75.0 - - - +
363A SER* 1.3 62.8 + - - +
364A ALA 3.1 10.4 - - - +
387A TRP* 3.6 28.5 - - + +
393A LYS* 5.0 11.3 + - - -
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Residues in contact with SER 363 (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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300A SER* 3.6 7.9 + - - -
335A LYS* 3.4 15.2 + - - -
359A GLN* 3.0 25.3 + - - -
360A LYS* 2.5 28.4 + - - -
362A CYS* 1.3 75.3 - - - +
364A ALA* 1.3 61.3 + - - +
365A HIS* 3.6 9.4 + - - -
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Residues in contact with ALA 364 (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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300A SER* 3.3 12.3 - - - +
301A ILE 4.1 1.6 - - - -
302A ALA* 3.7 22.9 - - + +
335A LYS* 4.2 3.8 - - + +
360A LYS 2.9 10.4 + - - +
361A LEU 3.4 14.0 - - - +
362A CYS 3.1 14.7 - - - +
363A SER* 1.3 76.9 + - - +
365A HIS* 1.3 62.5 + - - +
366A GLY 3.4 20.0 - - - +
367A VAL* 4.9 1.4 - - + +
387A TRP* 5.1 1.2 - - - -
393A LYS* 5.1 8.3 + - - +
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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