Contacts of the helix formed by residues 443 - 457 (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 GLY 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A GLY 3.8 1.6 - - - -
442A SER* 1.3 77.2 - - - +
444A ALA* 1.3 56.1 + - - -
445A ILE 3.4 2.2 - - - -
446A GLY* 4.1 2.8 - - - +
447A CYS* 2.8 37.1 + - - -
470A ASP* 3.8 2.4 + - - -
482A GLN* 3.8 9.6 - - - -
494A LYS* 3.7 21.8 - - - -
542A ALA 4.7 4.0 + - - -
76B GLY* 4.4 6.5 - - - -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLY* 1.3 71.5 - - - +
445A ILE* 1.3 63.5 + - - +
447A CYS* 3.9 2.4 - - - +
448A GLU* 3.1 20.4 + - - +
481A ARG* 3.7 40.3 - - + +
482A GLN* 3.7 13.5 - - - +
870A THR* 3.4 25.7 - - + +
76B GLY* 3.2 19.7 + - - +
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Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA* 1.3 69.9 - - - +
446A GLY* 1.3 54.6 + - - +
448A GLU* 3.3 1.6 + - - +
449A MET* 2.7 47.8 + - + +
541A ASN 4.2 2.5 - - - +
542A ALA* 3.8 20.4 - - + -
543A LEU 5.1 1.6 - - - +
566A SER* 3.8 28.3 - - - +
567A GLY* 4.2 8.7 - - - +
568A THR* 4.1 20.0 - - + -
870A THR* 3.7 19.3 - - + +
873A VAL* 4.6 3.6 - - + -
874A THR* 4.0 14.5 + - - +
877A VAL* 6.1 0.2 - - + -
75B GLY 4.2 3.1 - - - +
76B GLY* 2.7 39.5 + - - +
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 4.0 9.5 - - - +
441A GLY 3.8 13.0 - - - -
442A SER* 4.0 5.6 - - - -
443A GLY 3.3 7.9 + - - +
444A ALA 3.3 0.6 - - - -
445A ILE* 1.3 76.5 - - - +
447A CYS* 1.3 58.0 + - - +
449A MET* 2.9 3.4 + - - +
450A LEU* 2.8 35.1 + - - +
542A ALA* 3.5 21.3 - - - +
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Residues in contact with CYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER 4.1 2.8 - - - -
443A GLY 2.8 23.0 + - - +
444A ALA 3.9 3.4 - - - +
446A GLY* 1.3 70.9 - - - +
448A GLU* 1.3 63.3 + - - +
450A LEU* 4.8 1.8 - - - -
451A LYS* 3.1 23.9 + - - +
481A ARG 5.3 0.2 - - - +
482A GLN* 4.0 11.4 - - - -
483A PHE* 4.2 15.4 - - + +
484A LEU* 3.8 38.2 - - + +
485A PHE* 3.5 35.4 - - - -
498A ALA* 4.7 2.7 - - - -
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 3.8 0.5 - - - +
53A LYS* 2.8 36.3 + - - -
54A ASN* 4.9 0.2 - - - +
57A LEU* 5.9 0.2 - - - +
364A ALA* 5.5 0.2 - - - +
444A ALA 3.1 18.7 + - - +
445A ILE 3.8 0.2 - - - +
447A CYS* 1.3 77.2 - - - +
449A MET* 1.3 57.7 + - - +
451A LYS* 3.2 21.4 + - - +
452A ASN* 2.9 35.2 + - - -
481A ARG 5.0 6.2 - - - +
483A PHE* 3.3 22.0 - - + +
867A ALA* 5.2 3.4 - - - +
870A THR* 3.8 15.3 - - + -
871A SER* 3.3 19.7 + - - +
874A THR* 3.4 24.5 - - - +
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Residues in contact with MET 449 (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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439A LEU* 4.3 8.7 - - + -
445A ILE* 2.7 30.8 + - + +
446A GLY* 3.3 6.7 - - - +
448A GLU* 1.3 68.7 - - - +
450A LEU* 1.3 67.7 + - - +
451A LYS 3.0 1.1 - - - -
452A ASN* 2.9 5.7 + - - +
453A TRP* 2.8 58.9 + - + +
540A THR* 3.7 22.0 - - + -
874A THR* 3.5 13.6 - - - +
877A VAL* 3.9 21.5 - - + -
878A ASN* 2.7 46.0 - - - +
881A LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 3.8 28.0 - - + -
442A SER* 4.5 3.1 - - - +
446A GLY 2.8 16.2 + - - +
447A CYS 4.1 2.9 - - - +
449A MET* 1.3 72.9 - - - +
451A LYS* 1.3 56.7 + - - +
453A TRP* 3.2 21.3 + - + +
454A ALA* 2.9 29.6 + - - +
466A ILE* 4.0 22.8 - - + +
468A VAL* 3.9 22.2 - - + -
484A LEU* 4.6 2.5 - - + -
495A SER 5.5 0.2 - - - +
498A ALA* 4.0 28.3 - - + +
499A ALA* 4.9 2.2 - - - +
502A VAL* 3.6 25.8 - - + +
509A LEU* 5.3 0.2 - - - +
513A ILE* 5.2 2.9 - - + -
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 2.6 31.2 + - - -
53A LYS* 4.1 0.2 - - - +
80A PHE* 3.6 34.9 - - + -
364A ALA* 4.8 4.0 - - - +
447A CYS 3.1 18.7 + - - +
448A GLU* 3.2 22.8 + - - +
449A MET 3.0 0.8 - - - -
450A LEU* 1.3 75.3 - - - +
452A ASN* 1.3 83.4 + - - +
454A ALA* 3.2 6.9 + - - +
455A LEU* 3.2 36.1 + - + +
483A PHE* 3.6 25.8 - - + -
484A LEU* 5.1 0.4 - - + -
502A VAL* 3.9 10.7 - - + +
505A MET* 4.2 7.4 - - - -
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Residues in contact with ASN 452 (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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360A PRO* 3.8 28.6 - - + +
361A GLY* 3.9 1.9 + - - -
364A ALA* 4.3 11.8 - - - +
448A GLU* 2.9 24.8 + - - +
449A MET 2.9 7.8 + - - +
451A LYS* 1.3 95.4 - - - +
453A TRP* 1.3 59.7 + - - +
455A LEU* 3.1 11.6 + - - +
456A LEU* 2.8 32.2 + - + +
874A THR* 3.9 10.0 - - - +
878A ASN* 3.3 39.0 + - - +
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Residues in contact with TRP 453 (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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437A VAL* 3.4 35.0 - - + -
438A PHE 4.6 0.7 - - - -
439A LEU* 3.8 27.6 - - + -
449A MET* 2.8 35.0 + - + +
450A LEU* 3.5 25.1 - - + +
452A ASN* 1.3 77.9 - - - +
454A ALA* 1.3 61.8 + - - +
456A LEU* 3.1 11.5 + - + -
457A GLY* 3.0 18.4 + - - -
458A LEU* 3.0 31.6 + - + +
466A ILE* 4.0 15.7 - - + -
509A LEU* 4.8 2.5 - - - -
538A PHE* 4.7 2.5 - + - -
540A THR* 3.3 35.7 - - - -
878A ASN* 3.1 26.7 + - - -
881A LEU* 3.5 16.2 - - + +
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Residues in contact with ALA 454 (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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450A LEU 2.9 13.1 + - - +
451A LYS* 3.3 11.4 - - - +
453A TRP* 1.3 75.2 - - - +
455A LEU* 1.3 64.4 + - + +
457A GLY* 3.3 5.7 + - - -
502A VAL* 4.0 31.4 - - + +
505A MET* 4.7 7.9 - - + -
506A ASN* 2.8 35.9 - - + +
509A LEU* 3.9 14.2 - - + +
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Residues in contact with LEU 455 (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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76A LEU 3.8 20.9 - - - +
77A SER* 3.7 9.2 - - - +
78A THR* 3.9 32.5 - - - +
79A GLN 4.7 0.2 - - - +
80A PHE* 4.0 21.3 - - + -
360A PRO* 4.0 14.8 - - + -
416A ARG* 4.6 11.0 + - - +
417A TYR* 3.8 9.7 - - - -
420A GLN* 3.0 19.9 + - - +
451A LYS* 3.4 35.2 - - + +
452A ASN* 3.1 12.4 + - - +
454A ALA* 1.3 74.8 - - + +
456A LEU* 1.3 66.4 + - - +
457A GLY 3.1 2.5 + - - -
505A MET* 6.1 2.0 - - + -
506A ASN* 6.4 0.2 - - + -
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Residues in contact with LEU 456 (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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360A PRO* 3.5 31.6 - - + -
361A GLY 5.5 0.2 - - - +
417A TYR* 4.0 4.4 - - - -
420A GLN* 3.5 11.6 + - - +
429A GLN* 3.2 21.2 - - - +
432A ILE* 3.7 20.4 - - + +
433A ALA* 5.9 0.2 - - - +
452A ASN* 2.8 14.3 + - + +
453A TRP* 3.1 18.8 + - + +
455A LEU* 1.3 78.1 - - - +
457A GLY* 1.3 58.1 + - - +
458A LEU* 3.5 11.4 + - + +
878A ASN* 3.5 31.4 - - + +
881A LEU* 4.5 15.5 - - + -
882A TYR* 3.6 20.4 - - + +
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Residues in contact with GLY 457 (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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417A TYR* 3.6 27.1 - - - -
433A ALA* 3.3 10.4 - - - +
453A TRP 3.0 5.2 + - - -
454A ALA 3.3 6.3 + - - -
455A LEU 3.1 4.8 + - - -
456A LEU* 1.3 77.6 - - - +
458A LEU* 1.3 63.4 + - - +
459A GLY 3.3 0.7 + - - -
460A SER* 2.5 28.5 + - - -
506A ASN* 4.4 0.7 - - - -
509A LEU* 4.6 3.8 - - - -
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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
------------------------------------------------------------
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