Contacts of the helix formed by residues 443 - 457 (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 GLY 443 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441C GLY 3.8 1.0 - - - -
442C SER* 1.3 76.1 - - - +
444C ALA* 1.3 58.9 + - - +
445C ILE 3.5 2.0 - - - -
446C GLY* 4.2 2.4 - - - +
447C CYS* 2.8 35.2 + - - -
470C ASP* 3.9 3.6 + - - -
482C GLN* 3.3 24.0 - - - -
494C LYS* 3.8 10.1 - - - -
542C ALA 4.8 3.8 + - - -
76D GLY* 4.3 4.9 - - - -
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Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLY* 1.3 73.7 - - - +
445C ILE* 1.3 63.1 + - - +
447C CYS* 3.6 2.8 + - - +
448C GLU* 3.3 16.5 + - - +
481C ARG* 3.9 36.2 - - + +
482C GLN* 3.2 15.6 - - - +
568C THR* 6.1 0.2 - - - +
870C THR* 3.5 29.8 - - + +
76D GLY* 3.6 20.0 + - - +
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Residues in contact with ILE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ALA* 1.3 75.5 - - - +
446C GLY* 1.3 53.8 + - - +
448C GLU* 3.1 4.2 + - - +
449C MET* 2.8 42.6 + - + +
541C ASN 3.9 20.0 - - - +
542C ALA* 3.9 8.1 - - + -
543C LEU 4.8 3.4 - - - +
566C SER* 3.4 39.7 - - - +
567C GLY* 4.1 7.0 - - - -
568C THR* 4.5 10.8 - - + -
870C THR* 4.1 15.7 - - + +
873C VAL* 4.9 2.0 - - + -
874C THR* 3.9 15.6 + - - +
75D GLY 4.4 0.4 - - - +
76D GLY* 3.0 34.5 + - - +
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Residues in contact with GLY 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 4.0 7.8 - - - +
441C GLY 3.9 11.4 - - - -
442C SER* 4.0 7.0 - - - -
443C GLY 3.3 6.3 + - - -
444C ALA 3.3 0.6 - - - -
445C ILE* 1.3 77.7 - - - +
447C CYS* 1.3 62.6 + - - +
449C MET* 3.1 3.9 + - - +
450C LEU* 2.9 30.0 + - - +
542C ALA* 3.5 21.6 - - - +
76D GLY* 4.5 0.2 + - - -
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Residues in contact with CYS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C SER 3.6 3.0 + - - -
443C GLY 2.8 22.8 + - - +
444C ALA 4.0 3.1 - - - +
446C GLY* 1.3 70.2 - - - +
448C GLU* 1.3 65.2 + - + +
450C LEU* 3.1 5.6 + - - +
451C LYS* 3.0 24.1 + - - +
481C ARG 5.3 0.2 - - - +
482C GLN* 3.9 17.3 - - - -
483C PHE* 4.6 7.6 - - + +
484C LEU* 3.8 36.7 - - + +
485C PHE* 3.6 35.9 - - - -
498C ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 2.6 26.2 + - - -
54C ASN* 5.0 0.3 - - - +
57C LEU* 6.1 0.2 - - - +
444C ALA 3.3 12.2 + - - +
445C ILE 3.1 9.2 + - - +
447C CYS* 1.3 79.0 - - + +
449C MET* 1.3 61.9 + - - +
451C LYS* 2.9 32.9 + - - +
452C ASN* 3.0 28.8 + - - -
481C ARG 5.0 5.1 - - - +
483C PHE* 3.2 19.3 - - - -
867C ALA* 5.3 4.0 - - - +
870C THR* 3.7 18.6 - - + -
871C SER* 3.3 20.2 - - - -
874C THR* 3.5 19.7 - - + +
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Residues in contact with MET 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 4.4 9.6 - - + -
445C ILE* 2.8 30.4 + - + +
446C GLY* 3.1 7.4 + - - +
448C GLU* 1.3 74.9 - - - +
450C LEU* 1.3 56.6 + - - +
452C ASN* 3.1 2.5 + - - +
453C TRP* 2.9 68.2 + - + +
540C THR* 3.6 19.7 - - + -
874C THR* 3.6 13.0 - - - +
877C VAL* 3.4 26.2 - - + -
878C ASN* 2.9 44.2 - - - +
881C LEU* 4.7 1.6 - - + -
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Residues in contact with LEU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 4.0 17.0 - - + -
442C SER* 4.5 2.7 - - - +
446C GLY 2.9 18.5 + - - +
447C CYS 3.5 3.8 - - - +
449C MET* 1.3 73.4 - - - +
451C LYS* 1.3 61.4 + - - +
453C TRP* 3.3 18.6 + - + +
454C ALA* 2.9 31.4 + - - +
466C ILE* 4.4 11.0 - - + -
468C VAL* 4.2 32.5 - - + -
484C LEU* 4.3 2.2 - - + -
498C ALA* 3.7 34.3 - - + +
499C ALA* 4.6 2.2 - - - +
502C VAL* 3.4 25.1 - - + +
513C ILE* 5.2 4.5 - - + -
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Residues in contact with LYS 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 2.6 34.9 + - - +
53C LYS* 4.0 3.6 - - - +
80C PHE* 3.7 37.2 - - + +
364C ALA* 4.5 5.7 - - - +
447C CYS 3.0 12.6 + - - +
448C GLU* 2.9 27.6 + - - +
450C LEU* 1.3 76.8 - - - +
452C ASN* 1.3 80.5 + - - +
454C ALA* 3.2 5.2 + - - +
455C LEU* 3.0 38.3 + - + +
483C PHE* 3.6 23.1 - - + -
484C LEU* 5.1 0.7 - - + -
502C VAL* 3.8 10.2 - - + +
505C MET* 4.4 6.6 - - - +
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Residues in contact with ASN 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C PRO* 3.6 33.9 - - + +
361C GLY* 3.9 2.4 + - - -
364C ALA* 4.1 11.7 - - - +
448C GLU* 3.0 24.0 + - - +
449C MET 3.1 5.6 + - - +
451C LYS* 1.3 96.6 + - - +
453C TRP* 1.3 58.5 + - - +
455C LEU* 3.3 9.6 + - - +
456C LEU* 2.9 32.0 + - - +
874C THR* 3.5 16.1 - - - +
878C ASN* 3.3 30.1 + - - +
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Residues in contact with TRP 453 (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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437C VAL* 3.4 30.1 - - + -
439C LEU* 3.8 26.5 - - + -
449C MET* 2.9 37.2 + - + +
450C LEU* 3.8 12.8 - - + +
452C ASN* 1.3 74.5 - - - +
454C ALA* 1.3 61.9 + - - +
456C LEU* 3.3 12.9 + - + -
457C GLY* 2.8 24.6 + - - -
458C LEU* 3.0 36.0 + - + +
466C ILE* 3.9 24.9 - - + -
509C LEU* 4.4 2.2 - - - +
538C PHE* 4.7 2.2 - + - -
540C THR* 3.4 33.7 - - - -
878C ASN* 3.0 27.6 + - - -
881C LEU* 3.4 15.2 - - + +
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Residues in contact with ALA 454 (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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416C ARG* 5.5 0.2 - - - -
450C LEU 2.9 18.4 + - - +
451C LYS* 3.5 5.2 - - - +
453C TRP* 1.3 77.2 - - - +
455C LEU* 1.3 61.0 + - + +
457C GLY* 3.2 5.2 + - - -
502C VAL* 3.9 26.2 - - + +
505C MET* 5.0 6.5 - - + -
506C ASN* 2.7 38.1 + - + +
509C LEU* 3.5 22.8 - - + +
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Residues in contact with LEU 455 (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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76C LEU 3.6 15.3 - - - +
77C SER* 3.5 19.1 - - - +
78C THR* 3.4 34.1 - - + +
80C PHE* 4.0 18.4 - - + +
360C PRO* 4.1 17.5 - - + -
363C VAL* 6.4 0.2 - - + -
416C ARG* 4.1 13.7 + - - +
417C TYR* 3.7 10.7 - - - -
420C GLN* 3.0 19.4 + - - -
451C LYS* 3.0 35.4 + - + +
452C ASN* 3.4 10.3 - - - +
454C ALA* 1.3 77.0 - - - +
456C LEU* 1.3 59.8 + - - +
457C GLY 3.5 0.3 + - - -
505C MET* 6.4 0.9 - - + -
506C ASN* 5.0 0.2 + - - -
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Residues in contact with LEU 456 (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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360C PRO* 3.7 20.0 - - + -
361C GLY 5.5 0.2 - - - +
417C TYR* 3.8 5.0 - - - -
420C GLN* 3.5 14.8 - - - +
429C GLN* 3.4 20.1 - - - +
432C ILE* 3.8 18.0 - - + +
452C ASN* 2.9 16.1 + - + +
453C TRP* 3.5 14.6 - - + +
455C LEU* 1.3 76.9 - - - +
457C GLY* 1.3 60.8 + - - +
458C LEU* 3.4 8.4 + - + +
878C ASN* 4.0 26.0 - - + +
881C LEU* 4.1 21.5 - - + -
882C TYR* 3.3 33.7 - - + +
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Residues in contact with GLY 457 (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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417C TYR* 3.5 25.8 - - - -
433C ALA* 3.4 10.3 - - - +
453C TRP 2.8 7.2 + - - -
454C ALA* 3.2 9.9 + - - -
455C LEU 3.2 1.0 + - - -
456C LEU* 1.3 78.3 - - - +
458C LEU* 1.3 58.9 + - - +
459C GLY 3.4 0.5 + - - -
460C SER* 2.4 34.0 + - - -
506C ASN* 4.3 1.8 - - - -
509C LEU* 5.3 1.8 - - - -
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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