Contacts of the helix formed by residues 438 - 452 (chain B) in PDB entry 2C2Z
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 ASP 438 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B GLY 3.6 2.0 + - - -
437B ASP* 1.3 77.0 - - - +
439B ILE* 1.3 64.1 + - - +
440B LEU* 3.2 33.8 + - - +
441B THR* 2.6 27.3 + - - -
442B ILE* 3.1 21.3 + - - +
473B LYS* 3.6 40.2 + - + +
474B LEU 3.2 18.1 + - - +
475B VAL* 3.8 9.9 - - + -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.6 12.1 - - + -
400B LEU* 3.5 34.8 - - + -
425B LEU* 5.1 0.2 - - + -
429B LEU* 3.8 28.9 - - + -
438B ASP* 1.3 73.2 - - - +
440B LEU* 1.3 65.7 + - + +
442B ILE* 3.2 8.4 + - + +
443B LEU* 2.8 42.9 + - + +
470B LEU* 4.1 9.2 - - + -
474B LEU* 2.8 41.5 + - + +
475B VAL* 5.0 0.2 - - - +
476B PHE* 4.2 14.8 - - + -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.3 17.7 - - + -
438B ASP* 3.2 13.7 + - - +
439B ILE* 1.3 89.5 - - + +
441B THR* 1.3 57.8 + - - +
443B LEU* 3.5 7.2 + - + +
444B THR* 2.8 32.3 + - - -
466B PRO* 5.4 4.0 - - + -
468B PHE* 3.8 54.3 - - + -
470B LEU* 4.6 8.1 - - + -
472B LYS 6.0 1.1 - - - +
473B LYS* 6.4 1.1 - - + -
474B LEU 6.4 0.2 - - - +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ARG* 3.6 33.7 + - - +
437B ASP* 4.5 5.8 - - + +
438B ASP* 2.6 33.4 + - - -
440B LEU* 1.3 78.3 - - - +
442B ILE* 1.3 63.1 + - - +
444B THR* 3.3 9.3 + - - -
445B GLU 3.2 16.3 + - - -
473B LYS* 5.0 1.9 + - - -
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 4.9 2.7 - - + +
428B SER* 3.6 28.7 - - - +
429B LEU* 4.0 19.3 - - + +
432B ARG* 3.7 32.3 - - + +
433B CYS* 3.8 29.6 - - - +
437B ASP* 4.0 13.9 - - + +
438B ASP 3.1 15.5 + - - +
439B ILE* 3.6 12.3 - - + +
441B THR* 1.3 76.1 - - - +
443B LEU* 1.3 60.6 + - - +
445B GLU* 3.1 9.8 + - - +
446B VAL* 3.0 27.6 + - + +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.3 8.1 - - + -
400B LEU* 4.0 25.8 - - + -
402B GLY* 5.1 2.7 - - - -
421B TYR* 4.0 18.2 - - + +
425B LEU* 3.7 29.2 - - + -
439B ILE* 2.8 42.4 + - + +
440B LEU* 4.0 7.6 - - + +
442B ILE* 1.3 70.4 - - - +
444B THR* 1.3 60.8 + - - +
446B VAL* 3.3 10.8 + - + +
447B ASN* 3.0 33.1 + - - +
466B PRO* 3.9 26.7 - - + -
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B LEU 2.8 18.8 + - - -
441B THR* 3.4 13.3 - - - -
443B LEU* 1.3 76.5 - - - +
445B GLU* 1.3 64.4 + - - +
447B ASN* 3.2 13.8 + - + +
448B TYR* 3.0 20.7 + - + +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER* 3.3 21.3 + - - +
431B GLU* 3.4 16.6 - - - +
432B ARG* 3.1 47.8 + - - +
435B ARG* 5.8 0.3 + - - -
441B THR 3.2 2.0 + - - -
442B ILE* 3.1 9.8 + - - +
444B THR* 1.3 79.4 - - - +
446B VAL* 1.3 60.4 + - - +
448B TYR* 3.1 8.4 + - + +
449B GLU* 2.9 40.6 + - + +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 3.8 35.2 - - + +
424B SER* 3.7 20.2 - - - +
425B LEU* 3.9 26.7 - - + +
428B SER* 3.8 17.5 - - - +
442B ILE* 3.0 20.1 + - + +
443B LEU* 3.5 15.7 - - + +
445B GLU* 1.3 74.7 - - - +
447B ASN* 1.3 64.6 + - - +
450B VAL* 2.9 31.1 + - + +
464B PRO* 4.6 2.7 - - + -
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Residues in contact with ASN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU 3.0 17.5 + - - +
444B THR* 3.3 15.8 + - + +
446B VAL* 1.3 77.3 - - - +
448B TYR* 1.3 54.7 + - - +
450B VAL* 4.2 0.3 - - - +
451B SER* 2.7 38.3 + - - -
463B MET* 3.8 20.4 - - + +
464B PRO* 3.1 34.0 + - - +
466B PRO* 3.8 23.5 - - - +
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Residues in contact with TYR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B THR* 3.0 13.2 + - + +
445B GLU* 3.1 13.4 + - + +
447B ASN* 1.3 79.8 - - - +
449B GLU* 1.3 79.8 + - - +
451B SER* 3.4 11.0 + - - -
452B ASN* 3.1 44.1 + - - +
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER* 3.7 20.6 - - - +
428B SER* 5.1 2.5 - - - +
445B GLU* 2.9 37.7 + - + +
446B VAL 3.9 0.2 - - - +
448B TYR* 1.3 95.7 - - - +
450B VAL* 1.3 62.3 + - - +
452B ASN* 3.1 18.2 + - - +
453B LYS* 3.6 14.2 - - - +
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Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TRP* 4.1 19.1 - - + +
421B TYR* 4.3 4.5 - - - -
424B SER* 4.0 16.8 - - - -
446B VAL* 2.9 34.5 + - + +
449B GLU* 1.3 72.7 - - - +
451B SER* 1.3 63.1 + - - +
452B ASN 3.1 0.2 - - - -
453B LYS* 3.1 27.0 + - + +
462B GLN* 3.4 41.7 + - + +
464B PRO* 3.6 27.6 - - + -
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Residues in contact with SER 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ASN 2.7 24.2 + - - -
448B TYR* 3.6 7.6 - - - -
449B GLU 3.2 0.2 - - - -
450B VAL* 1.3 77.0 - - - +
452B ASN* 1.3 61.5 + - - +
453B LYS 3.3 0.2 - - - -
461B LYS* 2.9 26.9 + - - +
462B GLN 4.0 7.9 + - - -
463B MET* 3.4 28.6 - - - +
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Residues in contact with ASN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TYR* 3.1 49.4 + - - +
449B GLU* 3.1 13.4 + - - +
450B VAL 3.1 0.8 - - - -
451B SER* 1.3 82.0 - - - +
453B LYS* 1.3 62.9 + - + +
454B ASP* 4.0 6.8 - - - +
461B LYS* 3.8 5.2 + - - +
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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