Contacts of the helix formed by residues 444 - 451 (chain C) in PDB entry 2O2C
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 PHE 444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B GLN* 3.7 31.0 - - + +
410B MET* 3.7 31.7 - - + +
411B GLU* 4.9 1.3 - - - +
392C LEU* 3.8 14.6 - - + -
433C PHE* 3.8 25.4 - + - -
434C GLY* 4.0 3.4 - - - -
435C GLU* 3.7 33.2 - - + -
440C GLY* 3.0 21.9 + - - -
443C ALA* 1.3 87.3 - - + +
445C TYR* 1.3 80.9 + + - +
446C GLN 3.1 7.2 - - - +
447C LEU* 3.2 16.5 + - - +
448C ILE* 3.5 16.8 + - + +
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Residues in contact with TYR 445 (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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566B GLY 5.2 0.4 - - - -
567B VAL* 5.4 1.8 - - + -
392C LEU* 3.2 32.9 - - + +
394C TYR* 3.0 36.2 + - - -
435C GLU 5.2 0.2 + - - -
437C GLY* 4.7 3.9 - - - -
440C GLY* 3.0 33.8 + - - +
441C GLN* 3.4 29.3 + - + +
443C ALA 3.9 0.4 - - - -
444C PHE* 1.3 97.6 - + - +
446C GLN* 1.3 60.7 + - - +
448C ILE* 3.1 12.7 + - + -
449C HIS* 2.9 44.9 + + + -
459C PHE* 3.8 9.8 - + - -
483C GLN* 3.3 28.0 - - + +
487C LEU* 6.5 0.4 - - + -
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Residues in contact with GLN 446 (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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410B MET 4.1 0.4 - - - +
411B GLU* 3.5 47.5 + - + +
414B GLY 3.1 23.2 + - - +
415B LYS* 3.5 19.4 - - - +
564B GLN* 3.3 14.5 - - - +
565B TRP 4.7 0.4 - - - +
566B GLY* 2.7 34.7 + - - +
567B VAL* 4.0 9.4 + - + +
444C PHE 4.7 0.4 - - - -
445C TYR* 1.3 77.8 - - - +
447C LEU* 1.3 56.5 + - - +
449C HIS* 4.0 0.9 - - - +
450C GLN* 2.8 50.9 + - - +
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Residues in contact with LEU 447 (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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410B MET* 3.7 37.4 + - + +
414B GLY* 3.8 26.9 - - - -
429B GLY 3.4 24.7 - - - +
430B PRO 3.5 15.9 - - - +
431B ILE* 4.2 2.7 - - + -
444C PHE 3.2 10.1 + - - +
445C TYR 3.1 0.4 - - - -
446C GLN* 1.3 78.8 - - - +
448C ILE* 1.3 61.2 + - - +
451C GLY* 2.8 30.0 + - - -
453C ASN* 3.8 18.9 - - + +
455C ILE* 3.5 27.1 - - + -
524C ARG* 4.7 1.6 + - - -
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Residues in contact with ILE 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 5.4 0.4 - - + -
390C ALA* 4.6 0.2 - - + -
392C LEU* 4.5 2.9 - - + -
433C PHE* 4.5 10.1 - - + -
444C PHE* 3.7 38.6 - - + +
445C TYR* 3.1 23.6 + - + +
447C LEU* 1.3 76.1 - - + +
449C HIS* 1.3 58.1 + - + +
453C ASN 5.5 0.2 - - - -
455C ILE* 4.0 32.4 + - + +
457C CYS* 3.9 31.6 - - - -
487C LEU* 3.7 21.1 - - + -
524C ARG* 3.1 34.1 + - + +
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Residues in contact with HIS 449 (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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416B TYR* 3.9 5.9 + - - -
566B GLY 3.7 25.1 - - - +
567B VAL* 5.7 0.7 - - - -
569B LEU* 5.2 0.2 - - + -
570B GLY 5.2 3.6 + - - -
445C TYR* 2.9 34.7 + + + +
446C GLN 4.0 1.3 - - - +
448C ILE* 1.3 79.1 - - + +
450C GLN* 1.3 63.4 + - + +
451C GLY 3.8 0.2 - - - -
483C GLN* 2.9 27.0 + - - -
486C ALA* 3.6 31.6 + - + -
487C LEU* 3.7 30.9 - - + +
520C PHE* 3.9 23.7 - + + +
521C ILE* 4.8 2.1 + - - +
522C GLY 5.4 0.5 + - - -
524C ARG* 3.1 22.7 + - - +
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Residues in contact with GLN 450 (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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414B GLY 3.6 4.5 - - - +
415B LYS* 3.2 5.9 - - - +
416B TYR* 3.1 53.7 + - + +
565B TRP* 3.8 2.9 + - - +
566B GLY* 3.1 24.8 + - - +
446C GLN* 2.8 38.6 + - - +
449C HIS* 1.3 78.4 - - - +
451C GLY* 1.3 60.8 + - - +
517C HIS 3.0 26.3 + - - +
518C LYS* 4.3 0.2 - - - +
519C THR 3.1 23.8 + - - +
520C PHE* 4.2 14.3 - - + -
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Residues in contact with GLY 451 (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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414B GLY* 3.9 17.0 - - - -
415B LYS 4.2 1.3 - - - -
416B TYR* 3.5 6.6 - - - -
428B THR* 4.8 0.2 - - - -
447C LEU* 2.8 31.3 + - - -
449C HIS 3.8 1.0 - - - -
450C GLN* 1.3 75.4 - - - +
452C THR* 1.3 62.8 + - - -
453C ASN 3.3 6.2 + - - -
524C ARG* 3.1 20.5 + - - +
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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