Contacts of the helix formed by residues 441 - 452 (chain B) in PDB entry 2C0O
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 SER 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B LYS* 5.1 0.9 - - - +
439B GLY 4.0 0.2 + - - -
440B MET* 1.3 72.9 - - - +
442B ASN* 1.3 54.9 + - - +
443B PRO* 4.0 8.4 - - - +
444B GLU* 2.8 44.5 + - - +
445B VAL* 2.8 38.0 + - - +
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Residues in contact with ASN 442 (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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400B ILE* 3.2 40.3 - - + +
401B LYS* 3.7 24.0 - - - +
441B SER* 1.3 71.7 - - - +
443B PRO* 1.4 74.7 - - + +
445B VAL* 2.8 17.0 + - - +
446B ILE* 2.9 20.1 + - + +
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Residues in contact with PRO 443 (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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441B SER* 4.2 7.4 - - - +
442B ASN* 1.4 93.0 - - + +
444B GLU* 1.3 64.4 + - - +
446B ILE* 3.2 24.5 + - + +
447B ARG* 3.3 34.4 + - - +
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Residues in contact with GLU 444 (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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439B GLY 3.9 5.2 - - - +
440B MET* 3.4 20.9 - - + +
441B SER* 2.8 48.2 + - - +
443B PRO* 1.3 78.5 - - - +
445B VAL* 1.3 62.7 + - - +
447B ARG* 3.6 24.3 + - - +
448B ALA* 3.5 18.4 + - - +
451B ARG* 5.0 1.4 + - - -
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Residues in contact with VAL 445 (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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400B ILE* 5.3 2.9 - - + -
401B LYS* 4.3 15.0 - - + +
437B TYR* 3.5 52.7 - - + -
440B MET* 3.5 25.1 - - + -
441B SER 2.8 31.8 + - - +
442B ASN* 2.8 11.3 + - - +
444B GLU* 1.3 69.6 - - - +
446B ILE* 1.3 64.7 + - - +
448B ALA* 3.0 17.8 + - + +
449B LEU* 3.1 19.9 + - + +
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Residues in contact with ILE 446 (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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400B ILE* 4.1 21.1 - - + -
408B ILE* 4.9 26.2 - - + -
409B ASN* 5.3 7.2 - - - +
442B ASN* 2.9 31.8 + - + +
443B PRO* 3.6 16.4 - - + +
445B VAL* 1.3 73.8 - - - +
447B ARG* 1.3 68.0 + - + +
449B LEU* 3.3 12.4 + - + +
450B GLU* 3.3 18.2 + - + +
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Residues in contact with ARG 447 (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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443B PRO* 3.3 25.7 + - - +
444B GLU* 3.6 36.3 + - - +
446B ILE* 1.3 80.3 - - + +
448B ALA* 1.3 57.2 + - - +
450B GLU* 3.0 13.4 + - - +
451B ARG* 2.9 51.8 + - - +
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Residues in contact with ALA 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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440B MET* 5.0 10.8 - - + -
444B GLU 3.5 9.9 + - - +
445B VAL* 3.0 12.7 + - + +
447B ARG* 1.3 75.2 - - - +
449B LEU* 1.3 61.2 + - + +
451B ARG* 3.3 18.8 - - + +
452B GLY 2.9 8.0 + - - -
453B TYR* 2.9 52.8 + - + +
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Residues in contact with LEU 449 (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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401B LYS 6.2 0.2 - - - +
403B THR 4.9 2.7 - - - +
405B PRO* 4.9 14.1 - - + -
408B ILE* 4.6 20.2 - - + -
420B TRP* 4.1 25.8 - - + -
437B TYR* 3.3 32.3 - - + +
445B VAL* 3.1 23.7 + - + +
446B ILE* 3.5 11.4 - - - +
447B ARG 3.2 0.2 - - - -
448B ALA* 1.3 72.5 - - - +
450B GLU* 1.3 61.9 + - - +
452B GLY* 2.7 25.3 + - - +
453B TYR* 3.7 19.3 - - + +
454B ARG* 3.9 10.9 + - - +
475B ASN* 5.1 4.7 + - - +
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Residues in contact with GLU 450 (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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409B ASN* 6.1 2.2 - - - +
446B ILE* 3.3 7.1 + - + +
447B ARG* 3.0 14.0 + - - +
449B LEU* 1.3 80.5 - - - +
451B ARG* 1.3 62.1 + - - +
452B GLY* 3.1 1.7 + - - -
475B ASN* 5.2 7.6 + - - -
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Residues in contact with ARG 451 (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 GLU 5.0 1.2 + - - -
447B ARG* 2.9 51.7 + - - +
448B ALA* 3.3 21.3 - - - +
450B GLU* 1.3 75.5 - - - +
452B GLY* 1.3 56.1 + - - +
453B TYR* 3.6 3.4 - - + +
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Residues in contact with GLY 452 (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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448B ALA 2.9 0.4 + - - -
449B LEU 2.7 20.9 + - - -
450B GLU 3.9 1.6 - - - -
451B ARG* 1.3 73.7 - - - +
453B TYR* 1.3 64.4 + - - +
454B ARG* 3.6 15.9 + - - +
475B ASN* 5.5 2.2 - - - -
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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