Contacts of the helix formed by residues 348 - 362 (chain A) in PDB entry 3ZRH
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 CYS 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A PRO 4.4 3.4 + - - -
345A ALA 4.5 0.4 + - - -
346A MET 3.4 0.2 - - - -
347A VAL* 1.3 84.7 - - + +
349A PRO* 1.3 60.1 - - - +
350A GLU* 3.1 11.7 - - - -
351A LEU* 2.8 52.2 + - + +
352A THR* 3.0 14.1 + - - +
679A MET* 6.0 1.9 - - + +
682A LYS* 3.9 33.9 - - + -
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Residues in contact with PRO 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER 3.3 22.0 - - - +
287A SER* 3.2 29.8 - - - +
288A GLY* 3.7 10.3 - - - +
345A ALA 4.7 1.8 - - - +
346A MET* 3.7 14.4 - - - +
347A VAL 3.8 2.0 - - - +
348A CYS* 1.3 87.0 - - - +
350A GLU* 1.3 62.6 + - - +
352A THR* 3.9 12.2 + - + +
353A GLU* 3.0 24.3 + - - +
458A LYS* 5.2 2.6 - - - -
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A CYS* 3.0 9.5 + - - -
349A PRO* 1.3 79.3 - - - +
351A LEU* 1.3 61.5 + - - +
353A GLU* 3.3 9.6 + - + +
354A GLN* 3.0 50.5 + - + +
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Residues in contact with LEU 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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348A CYS* 2.8 26.9 + - + +
350A GLU* 1.3 73.5 - - - +
352A THR* 1.3 65.0 + - + +
354A GLN* 3.0 20.3 + - - +
355A ILE* 2.9 22.5 + - + +
675A LEU* 3.8 31.6 - - + +
678A GLN* 3.2 39.7 - - + +
679A MET* 3.4 45.1 - - + +
682A LYS* 4.2 9.2 - - + -
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Residues in contact with THR 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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344A PRO 4.7 0.7 - - - +
345A ALA* 2.7 39.0 + - - +
348A CYS 3.0 18.5 + - - +
349A PRO* 3.9 6.6 + - + +
351A LEU* 1.3 75.7 - - - +
353A GLU* 1.3 56.6 + - - +
355A ILE* 3.3 11.4 + - - +
356A ARG* 2.9 26.5 + - - +
455A ILE* 4.1 22.9 - - - +
456A TYR* 4.4 12.8 + - - -
458A LYS* 4.4 13.0 - - - +
679A MET* 4.6 6.7 - - + -
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PRO 3.0 18.1 + - - +
350A GLU* 3.5 8.5 - - + +
351A LEU 3.1 0.2 - - - -
352A THR* 1.3 74.9 + - - +
354A GLN* 1.3 58.9 + - - +
356A ARG* 3.2 25.0 + - - -
357A ARG* 3.0 70.6 + - - +
458A LYS* 2.9 33.7 + - - +
459A ASP* 4.0 0.8 - - - +
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Residues in contact with GLN 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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350A GLU* 3.0 41.4 + - - +
351A LEU* 3.0 29.3 + - - +
353A GLU* 1.3 73.4 - - + +
355A ILE* 1.3 67.8 + - - +
357A ARG* 3.2 15.4 + - - +
358A GLU* 2.9 23.6 + - - +
675A LEU* 3.6 31.5 - - + +
678A GLN* 5.1 3.2 - - - +
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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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351A LEU* 2.9 17.1 + - + +
352A THR* 3.5 9.0 - - - +
354A GLN* 1.3 75.0 - - - +
356A ARG* 1.3 64.4 + - - +
358A GLU* 3.1 5.3 + - - +
359A ILE* 2.9 31.8 + - + +
453A TRP* 4.0 18.4 - - + -
455A ILE* 3.6 26.0 - - + -
675A LEU* 3.7 46.2 - - + +
676A VAL* 4.1 6.3 - - + +
679A MET* 3.9 35.0 - - + -
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Residues in contact with ARG 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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352A THR 2.9 13.4 + - - +
353A GLU* 3.2 39.0 + - - +
354A GLN 3.3 0.2 - - - -
355A ILE* 1.3 74.6 - - - +
357A ARG* 1.3 74.3 + - - +
359A ILE* 3.1 7.7 + - + +
360A ALA* 2.9 52.4 + - - +
455A ILE* 4.2 11.8 - - + +
458A LYS* 3.5 39.3 - - + +
459A ASP* 3.5 25.0 + - - +
461A VAL* 4.4 18.7 - - + +
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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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353A GLU* 3.0 57.3 + - - +
354A GLN* 3.6 14.0 - - - +
356A ARG* 1.3 93.8 - - - +
358A GLU* 1.3 56.7 + - - +
360A ALA* 3.4 5.4 + - - +
361A ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 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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354A GLN 2.9 11.7 + - - +
355A ILE* 3.1 10.3 + - - +
357A ARG* 1.3 72.7 - - - +
359A ILE* 1.3 65.0 + - - +
361A ALA* 3.3 11.5 + - - +
362A SER* 3.2 24.0 + - - -
377A ASP* 5.6 1.6 - - - +
453A TRP* 4.2 10.1 - - + -
673A HIS* 3.6 28.6 + - + +
675A LEU* 3.5 22.2 - - + +
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Residues in contact with ILE 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 ILE* 2.9 20.3 + - + +
356A ARG* 3.5 7.4 - - + +
358A GLU* 1.3 73.4 - - - +
360A ALA* 1.3 66.3 + - - +
362A SER* 3.1 17.5 + - - -
363A LEU* 3.3 15.9 + - + +
375A LEU* 4.2 17.1 - - + +
449A LEU* 4.1 18.2 - - + -
453A TRP* 3.5 48.2 - - + +
455A ILE* 3.9 25.4 - - + -
461A VAL* 4.5 17.0 - - + -
462A LEU* 5.9 4.7 - - + -
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Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 2.9 33.6 + - - +
357A ARG* 3.7 8.7 - - - +
359A ILE* 1.3 76.3 - - - +
361A ALA* 1.3 61.3 + - - +
362A SER 3.1 1.4 + - - -
363A LEU* 3.1 24.4 + - - +
461A VAL* 4.4 16.1 - - + +
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Residues in contact with ALA 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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357A ARG 3.0 18.4 + - - +
358A GLU* 3.7 13.9 - - - +
359A ILE 3.2 0.4 - - - -
360A ALA* 1.3 75.3 - - - +
362A SER* 1.3 56.4 + - - +
363A LEU 3.3 1.1 - - - -
364A HIS* 3.5 22.3 + - - -
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Residues in contact with SER 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 GLU 3.2 16.1 + - - -
359A ILE* 3.4 9.2 - - - -
360A ALA 3.1 0.4 - - - -
361A ALA* 1.3 76.6 - - - +
363A LEU* 1.3 58.2 + - - +
364A HIS* 4.0 3.1 - - - -
374A PHE 3.6 2.1 - - - +
375A LEU* 3.5 10.2 - - - +
376A THR* 3.1 38.0 + - - +
377A ASP* 2.6 40.7 + - - -
453A TRP* 4.5 0.3 - - - -
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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