Contacts of the helix formed by residues 444 - 451 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LEU* 3.8 15.7 - - + -
433B PHE* 3.9 17.9 - + - -
434B GLY* 4.0 4.7 - - - -
435B GLU* 3.8 37.5 - - + -
440B GLY* 3.0 16.0 + - - -
443B ALA* 1.3 84.6 - - + +
445B TYR* 1.3 85.4 + + - +
446B GLN 3.1 6.5 - - - +
447B LEU* 3.2 15.4 + - - +
448B ILE* 3.5 19.6 + - + +
406C GLN* 3.6 33.0 - - + +
410C MET* 3.7 33.1 - - + +
411C GLU 4.9 1.3 - - - +
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Residues in contact with TYR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.3 33.1 - - + +
394B TYR* 3.0 37.1 + - - -
435B GLU 5.3 0.3 + - - -
437B GLY* 4.9 3.0 - - - -
440B GLY* 3.0 27.9 + - - -
441B GLN* 3.5 33.9 + - + +
443B ALA 3.9 0.2 - - - -
444B PHE* 1.3 98.4 - + - +
446B GLN* 1.3 63.6 + - - +
447B LEU 3.2 0.2 - - - -
448B ILE* 3.1 12.9 + - + +
449B HIS* 2.9 39.5 + - + -
459B PHE* 3.8 8.7 - + - -
483B GLN* 3.2 28.0 - - + +
487B LEU* 6.4 0.7 - - + -
566C GLY 5.1 0.4 - - - -
567C VAL* 5.5 2.0 - - + -
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B PHE 4.7 0.2 - - - -
445B TYR* 1.3 77.8 - - - +
447B LEU* 1.3 53.4 + - - +
449B HIS* 3.9 0.7 - - - +
450B GLN* 2.8 56.7 + - - +
410C MET 4.2 0.2 - - - +
411C GLU* 3.5 47.7 + - + +
414C GLY 3.1 23.5 + - - +
415C LYS* 3.5 17.7 - - - +
564C GLN* 3.2 15.3 - - - +
565C TRP 4.7 0.2 - - - +
566C GLY* 2.7 34.2 + - - -
567C VAL* 4.0 8.7 + - + +
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Residues in contact with LEU 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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444B PHE 3.2 10.5 + - - +
445B TYR 3.2 0.2 - - - -
446B GLN* 1.3 78.4 - - - +
448B ILE* 1.3 61.9 + - - +
451B GLY* 2.8 30.5 + - - -
453B ASN* 4.5 10.8 - - + +
455B ILE* 3.5 27.1 - - + -
524B ARG* 4.6 1.0 + - - -
410C MET* 3.7 37.0 + - + +
414C GLY* 3.8 24.9 - - - -
429C GLY* 3.4 25.1 - - - +
430C PRO 3.5 16.4 - - - +
431C ILE* 4.2 10.3 - - + -
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Residues in contact with ILE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA* 4.6 2.7 - - + -
392B LEU* 4.6 0.9 - - + -
433B PHE* 4.5 10.5 - - + -
444B PHE* 3.8 36.6 - - + +
445B TYR* 3.1 22.9 + - + +
447B LEU* 1.3 76.1 - - + +
449B HIS* 1.3 57.4 + - + +
453B ASN 4.7 0.2 - - - +
455B ILE* 4.0 34.3 + - + +
457B CYS* 3.8 31.9 - - - -
487B LEU* 3.7 21.8 - - + -
524B ARG* 3.0 33.6 + - + +
410C MET* 5.5 0.2 - - + -
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Residues in contact with HIS 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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445B TYR* 2.9 37.3 + + + +
446B GLN 4.0 1.3 - - - +
448B ILE* 1.3 78.6 - - + +
450B GLN* 1.3 62.5 + - + +
483B GLN* 2.9 28.7 + - - -
486B ALA* 3.8 26.9 + - + -
487B LEU* 3.6 31.9 + - + +
520B PHE* 4.0 23.7 - + + +
521B ILE* 4.8 1.7 + - - +
522B GLY 5.5 0.3 + - - -
524B ARG* 2.9 25.4 + - - +
416C TYR* 4.1 5.9 + - - -
566C GLY 3.6 24.7 - - - +
567C VAL* 5.6 0.9 - - - -
570C GLY 5.3 3.8 + - - -
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Residues in contact with GLN 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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446B GLN* 2.8 38.5 + - - +
449B HIS* 1.3 77.3 - - - +
451B GLY* 1.3 59.7 + - - +
517B HIS 3.0 27.1 + - - +
518B LYS 4.2 2.6 - - - -
519B THR 3.0 23.6 + - - +
520B PHE* 4.2 11.9 - - + -
414C GLY 3.6 4.7 - - - +
415C LYS* 3.2 7.6 - - - +
416C TYR* 3.1 51.8 + - + +
565C TRP* 3.8 3.3 + - - +
566C GLY* 3.1 24.2 + - - +
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Residues in contact with GLY 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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447B LEU* 2.8 31.5 + - - -
449B HIS 3.8 1.2 - - - -
450B GLN* 1.3 73.9 - - - +
452B THR* 1.3 60.7 + - - -
453B ASN 3.3 8.5 + - - -
521B ILE* 5.4 0.2 - - - +
524B ARG* 3.2 19.6 + - - +
414C GLY* 3.9 17.5 - - - -
415C LYS 4.2 1.6 - - - -
416C TYR* 3.6 7.0 - - - -
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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