Contacts of the helix formed by residues 417 - 425 (chain A) in PDB entry 3CMM
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 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A SER* 2.8 22.3 + - - +
416A ARG* 1.3 102.0 - - + +
418A ASP* 1.3 58.3 + - - +
419A ASN 3.3 2.7 - - - -
420A GLN* 2.9 15.5 + - - +
421A ILE* 2.9 30.8 + - + +
429A GLN* 4.3 19.5 - - + +
430A LYS* 6.4 0.4 - - - -
455A LEU 3.8 16.2 - - - -
456A LEU 4.1 7.0 - - - -
457A GLY* 3.6 31.7 - - - -
460A SER* 4.3 5.3 + - - -
506A ASN* 2.9 15.3 + - - -
508A ASP* 2.7 33.3 + - - +
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Residues in contact with ASP 418 (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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74A ALA* 3.9 16.5 - - - +
410A THR 4.8 1.2 - - - +
412A PRO* 3.3 33.8 - - + +
413A VAL 3.3 7.8 + - - +
414A ASN* 3.1 27.5 + - - -
415A SER* 2.9 23.5 + - - +
416A ARG 3.4 1.6 - - - -
417A TYR* 1.3 78.8 - - - +
419A ASN* 1.3 64.1 + - - +
420A GLN 3.2 0.2 - - - -
421A ILE* 3.6 16.2 - - + +
422A ALA* 2.8 26.3 + - - +
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Residues in contact with ASN 419 (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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45A LYS* 5.1 7.6 + - - -
74A ALA* 3.5 30.5 - - - +
77A SER* 3.9 8.8 - - - +
356A ARG* 3.5 24.4 + - - +
357A GLY* 3.3 8.5 - - - -
358A ASP* 3.0 43.8 + - + +
359A ILE* 4.2 1.7 - - - +
417A TYR 3.3 0.4 - - - -
418A ASP* 1.3 85.0 + - - +
420A GLN* 1.3 61.6 + - - +
422A ALA* 3.6 9.2 - - - +
423A VAL* 4.3 0.3 - - - +
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Residues in contact with GLN 420 (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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77A SER* 3.1 26.0 + - - +
358A ASP 3.6 16.6 - - - +
359A ILE* 4.1 9.4 - - + -
360A PRO* 3.8 14.3 - - + +
417A TYR* 2.9 17.2 + - - +
419A ASN* 1.3 77.0 - - - +
421A ILE* 1.3 64.6 + - - +
422A ALA 3.1 1.6 - - - -
423A VAL* 3.0 11.8 + - - -
424A PHE* 3.1 19.6 + - + -
429A GLN* 2.8 40.4 + - - +
455A LEU 3.0 26.9 + - - +
456A LEU* 3.5 21.0 + - - +
882A TYR* 4.7 2.4 + - - +
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Residues in contact with ILE 421 (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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409A THR 4.1 1.3 - - - +
410A THR* 3.1 18.2 + - - +
411A GLN 3.6 21.8 - - - +
413A VAL* 4.1 11.9 - - + -
415A SER* 4.7 2.2 - - - +
417A TYR* 2.9 27.0 + - + +
418A ASP* 3.4 20.6 + - + +
420A GLN* 1.3 72.3 - - - +
422A ALA* 1.3 67.0 + - - +
423A VAL 3.0 1.2 + - - -
425A GLY 3.0 24.5 + - - +
426A LEU* 3.8 43.5 - - + +
429A GLN* 4.0 22.4 - - + +
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Residues in contact with ALA 422 (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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313A THR* 3.1 35.9 - - + +
314A MET* 4.6 0.3 - - - +
353A TYR 4.5 3.6 - - - +
354A GLN* 5.4 1.1 - - - -
356A ARG* 4.5 3.6 - - + +
357A GLY* 4.2 14.1 - - - +
405A ARG* 4.5 4.3 + - - -
410A THR* 3.2 19.8 + - - +
418A ASP 2.8 17.3 + - - +
419A ASN* 3.6 20.4 - - - +
421A ILE* 1.3 76.1 - - - +
423A VAL* 1.3 57.4 + - - +
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Residues in contact with VAL 423 (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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158A GLY* 3.9 12.8 - - - -
159A LEU* 4.1 16.4 - - + -
354A GLN* 4.0 24.9 - - + +
357A GLY* 3.7 26.7 - - - -
359A ILE* 3.8 14.6 - - + -
397A LEU* 4.1 8.0 - - + +
405A ARG* 2.9 36.6 + - - +
410A THR* 4.4 0.7 - - - -
419A ASN 4.3 0.4 - - - +
420A GLN 3.0 6.6 + - - +
422A ALA* 1.3 79.4 - - - +
424A PHE* 1.3 79.9 + - + +
425A GLY 3.7 0.9 - - - -
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Residues in contact with PHE 424 (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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159A LEU* 4.2 11.9 - - + -
359A ILE* 3.5 21.5 - - + -
396A SER 3.7 24.0 - - - -
397A LEU* 4.4 2.7 - - + -
398A PRO* 3.6 22.6 - - + +
403A PHE* 4.5 8.7 - - - +
405A ARG* 4.7 6.6 - - - +
409A THR* 5.2 0.5 - - - +
420A GLN* 3.1 18.0 + - + +
423A VAL* 1.3 92.7 - - + +
425A GLY* 1.3 60.1 + - - +
428A PHE* 3.3 51.3 - + + +
429A GLN* 4.1 14.4 - - - +
882A TYR* 3.5 43.7 - + - -
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Residues in contact with GLY 425 (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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409A THR* 3.4 28.5 - - - -
410A THR* 4.0 2.2 + - - -
421A ILE* 3.0 19.4 + - - -
423A VAL 3.7 0.6 - - - -
424A PHE* 1.3 82.9 - - - +
426A LEU* 1.3 67.0 + - - -
427A ASP 3.4 2.5 - - - -
428A PHE 3.6 0.6 + - - -
429A GLN* 3.2 20.4 + - - +
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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