Contacts of the helix formed by residues 352 - 359 (chain A) in PDB entry 2JFF
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 PHE 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A VAL* 3.6 21.3 - - + -
347A GLY* 3.7 26.5 - - - -
350A ALA* 3.5 14.9 + - + -
351A ASP* 1.3 71.2 + - - +
353A SER* 1.3 58.2 + - - +
354A PRO* 3.3 3.6 - - - -
355A LEU* 3.0 31.3 + - + +
372A ASP* 4.3 6.3 - - + -
375A GLN* 3.6 45.6 - - + +
376A LEU* 3.6 26.5 - - + -
379A LEU* 3.3 24.1 - - + +
412A ALA* 3.9 14.1 - - + -
413A CYS* 3.8 22.9 - - - -
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Residues in contact with SER 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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351A ASP* 2.7 29.4 + - - -
352A PHE* 1.3 73.9 - - - +
354A PRO* 1.4 65.7 - - - +
355A LEU 2.9 6.7 + - - -
356A ALA* 2.9 21.0 + - - +
357A ARG 4.4 0.7 + - - -
379A LEU* 3.8 11.8 - - - +
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Residues in contact with PRO 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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323A VAL* 4.0 17.3 - - + -
327A GLU* 4.0 14.5 - - - +
351A ASP* 3.2 22.0 - - + +
352A PHE* 3.3 2.2 - - - -
353A SER* 1.4 96.1 - - - +
355A LEU* 1.3 60.0 + - - +
356A ALA 3.6 0.2 + - - -
357A ARG* 3.9 10.1 + - - +
358A TYR* 3.6 19.1 - - - -
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Residues in contact with LEU 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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323A VAL* 3.9 31.9 - - + +
326A THR* 3.8 25.4 - - + -
327A GLU* 3.9 14.6 - - + +
330A LEU* 4.4 7.9 - - + -
341A LEU* 6.2 0.4 - - + -
343A LEU* 4.5 10.5 - - + -
352A PHE* 3.0 22.1 + - + +
353A SER 2.9 0.2 + - - -
354A PRO* 1.3 75.8 - - - +
356A ALA* 1.3 65.1 + - - +
357A ARG 3.2 1.1 - - - -
358A TYR* 3.1 19.4 + - + +
359A LEU* 3.3 17.9 - - + +
376A LEU* 4.9 0.7 - - + -
379A LEU* 4.3 18.6 - - + -
412A ALA* 4.1 24.5 - - + -
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Residues in contact with ALA 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 PHE 4.2 1.0 + - - -
353A SER* 2.9 19.0 + - - +
355A LEU* 1.3 78.5 - - - +
357A ARG* 1.3 60.8 + - - +
358A TYR 3.1 0.2 - - - -
359A LEU* 3.1 25.9 + - - +
360A ASN* 4.1 11.0 + - - +
379A LEU* 4.4 23.7 - - + +
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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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327A GLU* 3.9 6.3 + - - -
331A ASN* 4.3 13.9 + - - +
353A SER 4.4 1.0 + - - -
354A PRO 3.9 7.9 + - - +
355A LEU 3.2 1.6 + - - -
356A ALA* 1.3 77.4 - - - +
358A TYR* 1.3 110.9 + - + +
359A LEU 3.4 0.4 - - - -
360A ASN* 3.6 19.9 + - - +
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A GLU* 2.4 49.8 + - + +
330A LEU* 3.9 43.6 - - + +
331A ASN* 3.6 32.1 + - + -
332A GLY 5.5 0.2 - - - -
339A LEU* 5.9 2.4 - - - +
354A PRO 3.6 15.7 - - - -
355A LEU* 3.1 19.2 + - + +
357A ARG* 1.3 113.8 + - + +
359A LEU* 1.3 63.5 + - - +
360A ASN 3.5 6.1 + - - +
364A VAL* 5.2 2.8 - - - +
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Residues in contact with LEU 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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330A LEU* 4.2 11.9 - - + -
339A LEU* 5.5 1.8 - - + -
341A LEU* 3.8 25.6 - - + -
343A LEU* 4.9 3.1 - - + -
355A LEU* 3.3 21.3 - - + +
356A ALA* 3.1 9.6 + - - +
358A TYR* 1.3 85.4 - - - +
360A ASN* 1.3 56.4 + - - +
364A VAL* 3.2 27.9 - - + +
366A LEU* 3.9 27.4 - - + -
379A LEU* 4.3 26.5 - - + +
380A ARG* 2.8 40.8 + - + -
383A VAL* 5.9 0.4 - - + -
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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