Contacts of the helix formed by residues 417 - 425 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C SER* 5.3 0.2 - - - -
415C SER* 3.0 15.9 + - - +
416C ARG* 1.3 95.0 - - + +
418C ASP* 1.3 53.8 + - - +
419C ASN 3.2 2.7 - - - -
420C GLN* 2.7 33.4 + - + +
421C ILE* 2.8 23.8 + - + +
429C GLN* 4.2 19.3 - - + +
455C LEU 3.7 17.5 - - - -
456C LEU 3.8 8.3 - - - -
457C GLY* 3.5 31.7 - - - -
460C SER* 4.2 4.5 + - - -
506C ASN* 2.9 18.8 + - - -
508C ASP* 2.6 33.9 + - - +
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Residues in contact with ASP 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 5.7 0.7 - - - +
74C ALA* 4.5 13.1 + - + +
410C THR 4.8 1.4 - - - +
412C PRO* 3.5 23.0 - - + +
413C VAL 2.5 44.4 + - - +
414C ASN* 4.2 1.7 - - - +
415C SER* 3.0 29.6 + - - +
416C ARG 3.4 1.4 + - - -
417C TYR* 1.3 75.9 - - - +
419C ASN* 1.3 65.7 + - - +
421C ILE* 3.4 11.7 + - - +
422C ALA* 2.8 27.4 + - - +
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Residues in contact with ASN 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 4.5 12.7 - - - +
74C ALA* 3.6 35.9 + - - +
77C SER* 3.9 9.7 - - - +
356C ARG* 3.7 19.9 + - - +
357C GLY* 3.3 8.0 - - - -
358C ASP* 2.9 51.5 + - + +
359C ILE* 4.0 1.7 - - - +
416C ARG 5.0 0.2 + - - -
417C TYR 3.2 1.0 - - - -
418C ASP* 1.3 80.7 - - - +
420C GLN* 1.3 60.1 + - - +
422C ALA* 4.0 10.5 - - - +
423C VAL 4.5 0.3 + - - -
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Residues in contact with GLN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C SER* 2.9 43.0 + - - +
358C ASP 3.5 9.9 - - - +
359C ILE* 3.8 11.4 - - + -
360C PRO* 3.5 18.1 - - + +
417C TYR* 2.7 15.4 + - - +
419C ASN* 1.3 74.9 - - - +
421C ILE* 1.3 68.5 + - - +
422C ALA 3.0 1.1 - - - -
423C VAL* 2.9 12.1 + - - -
424C PHE* 2.9 20.1 + - + +
429C GLN* 3.1 32.9 + - - +
455C LEU 3.0 15.5 + - - -
456C LEU* 3.5 21.7 - - - +
882C TYR* 4.5 1.1 + - - +
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Residues in contact with ILE 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C THR 4.2 1.1 - - - +
410C THR* 3.4 26.2 - - - +
411C GLN 3.6 13.7 - - - +
413C VAL* 4.8 7.0 - - + -
415C SER* 4.4 7.0 - - - +
417C TYR* 2.8 30.8 + - + +
418C ASP* 3.5 19.3 - - - +
420C GLN* 1.3 76.4 - - - +
422C ALA* 1.3 59.7 + - - +
425C GLY 2.9 30.4 + - - +
426C LEU* 4.1 35.7 - - + +
429C GLN* 3.8 24.4 - - + +
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C THR* 3.1 37.1 - - + +
314C MET* 4.7 2.3 - - - +
353C TYR 4.5 4.8 - - - +
354C GLN* 5.9 0.7 - - - -
356C ARG* 4.9 4.0 - - + -
357C GLY* 4.5 12.1 - - - +
405C ARG* 4.7 1.0 + - - -
410C THR* 3.5 19.8 - - - +
418C ASP 2.8 17.6 + - - +
419C ASN* 4.0 16.6 - - - +
420C GLN 3.0 0.4 - - - -
421C ILE* 1.3 77.0 - - - +
423C VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY* 3.9 27.4 - - - -
159C LEU* 4.0 6.3 - - + -
354C GLN* 3.9 29.4 - - + +
357C GLY* 4.0 14.4 - - - -
359C ILE* 4.0 8.1 - - + -
397C LEU* 3.9 17.2 - - + +
405C ARG* 2.6 41.4 + - - +
410C THR* 4.4 0.6 - - - +
419C ASN 4.6 0.2 - - - +
420C GLN 2.9 6.9 + - - +
422C ALA* 1.3 81.9 - - - +
424C PHE* 1.3 74.4 - - + +
425C GLY 3.7 0.4 - - - -
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Residues in contact with PHE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C LEU* 4.1 12.1 - - + -
359C ILE* 3.5 25.4 - - + -
396C SER 3.9 22.7 - - - -
397C LEU* 4.6 2.2 - - + -
398C PRO* 3.7 15.8 - - + +
403C PHE* 4.5 9.2 - - - +
404C PRO 5.1 0.2 - - - +
405C ARG* 4.2 13.9 - - - +
420C GLN* 2.9 20.5 + - + +
423C VAL* 1.3 93.7 - - + +
425C GLY* 1.3 60.8 + - - +
428C PHE* 3.7 43.5 - + + +
429C GLN* 4.2 14.8 - - - +
882C TYR* 3.5 43.5 - + - -
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Residues in contact with GLY 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C PRO 5.1 0.4 - - - -
409C THR* 3.5 26.5 - - - -
410C THR* 3.9 1.6 - - - +
421C ILE* 2.9 21.5 + - - -
423C VAL 3.7 0.4 - - - -
424C PHE* 1.3 80.8 - - - +
426C LEU* 1.3 64.6 + - - -
427C ASP 3.5 2.2 - - - -
428C PHE 3.6 1.1 + - - -
429C GLN* 3.3 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