Contacts of the helix formed by residues 350 - 359 (chain A) in PDB entry 4BQA
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 PRO 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A PHE* 4.7 3.5 - - + -
335A ILE* 6.1 1.1 - - + -
338A ARG* 5.0 8.7 - - - +
346A LYS* 5.6 3.8 - - + -
347A PRO* 4.1 16.8 - - + +
348A VAL 3.5 9.2 - - - +
349A ILE* 1.3 89.5 - - - +
351A ALA* 1.3 59.7 + - - +
352A ALA* 4.4 4.5 - - + +
353A VAL* 3.3 30.0 + - + +
354A LEU* 3.0 25.5 + - - +
371A GLU* 3.8 12.8 - - + +
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Residues in contact with ALA 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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349A ILE 3.5 1.6 + - - -
350A PRO* 1.3 72.3 - - - +
352A ALA* 1.3 52.7 + - - +
354A LEU* 3.3 6.8 + - - +
355A ALA* 2.7 35.7 + - - +
363A ILE* 3.7 29.6 - - + +
367A GLN* 3.6 30.4 - - + +
368A PHE* 4.1 2.9 - - - +
371A GLU* 2.7 22.6 + - - +
406A ARG* 4.2 4.3 - - - +
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Residues in contact with ALA 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 PRO* 3.2 4.6 - - + +
351A ALA* 1.3 78.3 - - - +
353A VAL* 1.3 61.3 + - + +
355A ALA* 3.2 7.3 + - - +
356A GLY* 2.8 25.1 + - - -
363A ILE* 4.4 16.3 - - + +
371A GLU* 4.6 0.6 + - - -
406A ARG* 5.6 0.2 - - - +
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Residues in contact with VAL 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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331A PHE* 3.6 24.2 - - + -
334A TYR* 3.7 21.1 - - + -
335A ILE* 4.5 2.0 - - + -
338A ARG* 4.1 37.9 - - - +
350A PRO* 3.3 29.3 + - + +
352A ALA* 1.3 77.4 - - + +
354A LEU* 1.3 52.3 + - - +
356A GLY* 3.1 3.6 + - - +
357A PHE* 2.7 32.7 + - - +
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Residues in contact with LEU 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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331A PHE* 3.9 24.6 - - + -
349A ILE* 3.9 17.0 - - + -
350A PRO 3.0 16.4 + - - +
351A ALA* 3.6 6.5 - - - +
353A VAL* 1.3 77.1 - - - +
355A ALA* 1.3 51.6 + - - +
357A PHE* 4.1 3.8 - - + -
358A THR* 2.7 40.1 + - + -
366A TRP* 4.0 12.8 - - + -
367A GLN* 4.0 23.6 - - + +
370A LEU* 3.7 30.7 - - + -
449A LEU* 4.2 23.3 - - + -
450A LEU* 4.7 2.5 - - + -
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Residues in contact with ALA 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 ALA 2.7 21.5 + - - +
352A ALA* 3.2 8.3 + - - +
354A LEU* 1.3 71.5 - - - +
356A GLY* 1.3 56.1 + - - +
358A THR* 3.2 7.6 + - - -
359A GLY* 2.6 35.3 + - - -
360A SER* 3.3 8.6 + - - +
361A GLY 3.5 25.5 + - - +
362A PRO 4.6 4.3 - - - +
363A ILE* 4.8 3.1 - - + +
367A GLN* 3.7 13.0 + - - +
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Residues in contact with GLY 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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334A TYR* 4.0 15.0 + - - -
352A ALA 2.8 14.9 + - - -
353A VAL* 3.1 4.7 + - - -
355A ALA* 1.3 76.2 - - - +
357A PHE* 1.3 62.6 + - - +
359A GLY* 3.7 7.9 + - - -
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Residues in contact with PHE 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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329A MET* 3.3 37.9 - - + -
330A SER 3.4 22.0 - - - -
331A PHE* 3.9 22.2 - + + -
334A TYR* 3.4 35.6 + + + -
353A VAL 2.7 19.7 + - - +
354A LEU* 3.5 6.7 - - + +
355A ALA 3.2 0.2 - - - -
356A GLY* 1.3 73.8 - - - +
358A THR* 1.3 69.6 + - + +
359A GLY* 3.3 0.9 + - - -
449A LEU* 3.8 43.7 - - + -
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Residues in contact with THR 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 LEU* 2.7 32.3 + - + +
355A ALA 3.2 7.1 + - - -
357A PHE* 1.3 80.1 - - + +
359A GLY* 1.3 59.4 + - - +
360A SER* 3.3 10.4 + - - -
366A TRP* 4.2 19.7 - - + -
367A GLN* 3.1 23.7 + - - +
449A LEU* 4.8 11.0 - - + -
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Residues in contact with GLY 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 ALA 2.6 18.3 + - - -
356A GLY* 4.1 7.4 - - - -
357A PHE 3.2 3.4 - - - -
358A THR* 1.3 75.8 - - - +
360A SER* 1.3 62.4 + - - +
361A GLY* 3.4 2.4 - - - -
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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