Contacts of the helix formed by residues 350 - 356 (chain A) in PDB entry 5IVK
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 TYR 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A SER* 1.3 81.3 - - - +
351A GLU* 1.3 65.7 + - - +
353A LEU* 3.1 46.4 + - + +
410A ASP* 2.7 37.7 + - - -
413A MET* 3.4 33.7 - - + +
414A ASP* 4.0 17.5 - - + -
417A SER* 4.0 8.5 - - - -
467A LYS 5.2 1.1 - - - -
468A GLY* 5.1 4.5 - - - -
469A VAL 3.1 29.0 + - - +
470A SER* 3.4 1.6 - - - -
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Residues in contact with GLU 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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244A SER* 2.5 27.4 + - - -
347A ASN* 3.2 12.8 - - + +
348A THR* 2.8 38.4 + - - +
349A SER 4.0 0.6 - - - -
350A TYR* 1.3 75.3 - - - +
352A GLY* 1.3 59.8 + - - +
353A LEU 3.0 5.0 + - - -
354A PHE* 3.3 7.4 + - - +
417A SER* 3.5 12.0 + - - +
421A PHE* 3.6 33.0 - - + -
422A TRP* 4.5 5.8 - - - +
471A HIS* 2.8 58.1 + - - +
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Residues in contact with GLY 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 TYR 3.3 0.2 - - - -
351A GLU* 1.3 72.5 - - - +
353A LEU* 1.3 60.5 + - - +
354A PHE 3.0 6.9 + - - -
355A PHE* 3.0 22.1 + - - +
413A MET* 3.4 37.7 - - - +
416A CYS* 4.2 8.1 - - - -
417A SER* 2.9 18.0 + - - -
421A PHE* 5.7 2.5 - - - -
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Residues in contact with LEU 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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350A TYR* 3.1 47.3 + - + +
351A GLU 3.0 0.8 + - - -
352A GLY* 1.3 76.7 - - - +
354A PHE* 1.3 61.0 + - - +
355A PHE 3.0 0.2 - - - -
356A THR* 2.8 40.5 + - - +
410A ASP* 5.7 0.2 - - - +
413A MET* 3.7 16.2 - - + -
461A ARG* 5.5 0.5 + - - -
466A VAL* 4.0 19.8 - - + +
467A LYS 3.3 24.2 - - - +
468A GLY* 3.6 26.0 - - - +
469A VAL 4.0 2.0 - - - +
470A SER* 4.3 11.2 - - - +
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Residues in contact with PHE 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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351A GLU 3.3 14.6 + - - +
352A GLY 3.0 0.9 - - - +
353A LEU* 1.3 78.1 - - - +
355A PHE* 1.3 87.6 + + + +
356A THR* 3.2 5.0 + - - -
357A SER* 4.8 4.3 + - - -
358A ILE* 5.2 7.5 - - + +
457A TYR* 4.9 9.6 - + - -
460A MET* 5.1 13.0 - - + -
461A ARG* 3.5 58.2 - - + +
470A SER* 3.9 6.4 - - - -
471A HIS* 3.7 33.0 - + + -
472A THR* 4.6 10.1 - - + -
601A DPF 5.6 11.0 - - + -
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Residues in contact with PHE 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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308A MET* 4.2 23.1 - - + -
352A GLY* 3.0 21.5 + - - +
354A PHE* 1.3 101.6 - + + +
356A THR* 1.3 66.4 + - - +
357A SER 3.6 1.1 - - - -
358A ILE* 3.3 35.2 + - + +
359A LEU* 3.3 18.7 + - + +
412A PHE* 5.2 6.5 - + + -
413A MET* 4.3 9.4 - - + -
416A CYS* 4.2 18.2 - - + -
420A TYR* 4.2 24.2 - + - -
421A PHE* 5.9 5.2 - + - -
601A DPF 5.6 6.3 - - + -
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Residues in contact with THR 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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353A LEU* 2.8 32.6 + - - +
354A PHE 3.2 3.2 + - - -
355A PHE* 1.3 77.0 - - - +
357A SER* 1.3 69.3 + - - +
358A ILE 2.8 1.4 + - - -
359A LEU* 3.0 16.1 + - - +
360A LYS* 3.7 3.1 + - - +
413A MET* 3.5 19.1 - - + +
462A SER 5.8 4.0 - - - +
463A GLY* 6.3 2.2 - - - -
466A VAL* 4.4 21.5 - - + +
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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