Contacts of the helix formed by residues 567 - 578 (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 VAL 567 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B GLN 3.5 24.9 - - - +
442B HIS* 5.3 1.3 - - - +
445B TYR* 5.4 1.8 - - + -
446B GLN* 4.5 15.5 - - + +
449B HIS* 5.6 1.6 - - - -
483B GLN* 5.2 3.1 + - - +
411C GLU* 4.0 16.4 - - - +
564C GLN* 3.3 26.5 - - + +
566C GLY* 1.3 79.9 - - - +
568C GLU* 1.3 64.1 + - + +
569C LEU 3.6 1.1 + - - -
570C GLY* 3.7 4.7 + - - -
571C LYS* 3.4 47.5 + - + +
5003C G6Q 6.0 3.1 - - - +
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Residues in contact with GLU 568 (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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491B LYS* 5.9 2.9 - - - +
499B GLU* 4.0 11.4 - - - +
518B LYS* 2.9 38.8 + - - +
520B PHE* 4.7 4.0 - - + -
565C TRP* 3.3 27.4 + - + +
567C VAL* 1.3 81.0 - - + +
569C LEU* 1.3 66.1 + - - +
571C LYS* 3.2 10.5 + - + +
572C VAL* 3.0 36.2 + - + +
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Residues in contact with LEU 569 (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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449B HIS* 5.6 0.4 - - + -
486B ALA* 3.6 32.5 - - + +
489B ILE* 5.6 0.7 - - + -
490B GLY* 3.5 34.5 - - - +
491B LYS* 3.8 34.5 - - + +
520B PHE* 3.7 37.7 - - + -
567C VAL 3.6 0.6 - - - -
568C GLU* 1.3 77.4 - - - +
570C GLY* 1.3 57.8 + - - +
572C VAL* 3.4 5.1 + - + -
573C LEU* 3.0 48.3 + - + +
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Residues in contact with GLY 570 (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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449B HIS* 5.3 3.9 + - - -
479B ASN* 4.9 1.4 - - - +
482B ALA* 3.8 9.0 - - - +
483B GLN* 3.4 33.2 + - - -
486B ALA* 4.3 12.1 - - - +
566C GLY 5.3 0.4 + - - -
567C VAL 3.7 5.3 + - - -
568C GLU 3.3 0.8 - - - -
569C LEU* 1.3 77.8 - - - +
571C LYS* 1.3 56.8 + - - +
574C ALA* 3.1 28.8 + - - +
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Residues in contact with LYS 571 (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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441B GLN* 6.0 2.0 - - - +
442B HIS* 4.5 20.1 - - - -
479B ASN* 5.4 3.6 - - - +
483B GLN* 6.0 0.7 - - - +
263C THR* 5.4 8.6 + - - +
567C VAL* 3.4 40.3 + - + +
568C GLU* 3.2 11.5 + - + +
570C GLY* 1.3 75.4 - - - +
572C VAL* 1.3 60.3 + - + +
574C ALA* 3.4 6.6 + - - +
575C LYS* 3.1 37.5 + - + +
5003C G6Q 4.8 9.9 + - - -
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Residues in contact with VAL 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LYS* 4.5 19.3 - - - +
568C GLU* 3.0 32.8 + - + +
569C LEU* 3.9 5.2 - - - +
571C LYS* 1.3 76.6 - - + +
573C LEU* 1.3 68.6 + - + +
575C LYS* 3.3 14.0 + - + +
576C SER* 3.1 29.6 + - - +
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Residues in contact with LEU 573 (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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482B ALA* 3.7 15.7 - - + +
485B GLU* 3.8 23.6 - - - +
486B ALA* 3.8 34.1 - - + +
489B ILE* 3.9 23.8 - - + -
491B LYS* 6.2 0.2 - - - +
569C LEU* 3.0 29.8 + - + +
572C VAL* 1.3 82.1 - - + +
574C ALA* 1.3 55.9 + - - +
576C SER* 3.4 12.0 + - - +
577C ILE* 3.1 32.7 + - - +
590C HIS* 6.3 1.1 - - + -
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Residues in contact with ALA 574 (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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478B SER* 3.5 34.2 - - - +
479B ASN* 3.9 17.0 - - - +
482B ALA* 3.5 9.3 - - + +
264C GLN* 5.5 6.1 - - - +
570C GLY 3.1 19.8 + - - +
571C LYS* 3.6 6.5 - - - +
572C VAL 3.2 0.2 - - - -
573C LEU* 1.3 73.6 - - - +
575C LYS* 1.3 60.2 + - + +
577C ILE 3.3 0.6 + - - +
578C LEU* 3.0 28.0 + - - +
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Residues in contact with LYS 575 (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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264C GLN* 5.2 12.6 - - - +
571C LYS* 3.1 23.8 + - + +
572C VAL* 3.5 13.9 - - + +
574C ALA* 1.3 75.8 - - - +
576C SER* 1.3 58.7 + - - +
578C LEU* 4.2 7.3 - - - +
579C PRO* 3.2 23.7 - - - +
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Residues in contact with SER 576 (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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572C VAL* 3.1 18.7 + - - +
573C LEU* 3.6 18.2 - - - +
574C ALA 3.2 0.4 - - - -
575C LYS* 1.3 79.2 - - - +
577C ILE* 1.3 63.2 + - - +
579C PRO* 3.6 9.7 - - - +
580C GLN* 3.7 15.7 - - - +
590C HIS* 5.5 5.8 - - - -
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Residues in contact with ILE 577 (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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478B SER* 4.2 15.3 - - - +
481B PHE* 4.1 12.6 - - + -
482B ALA* 3.9 23.1 - - - +
485B GLU* 3.5 23.8 - - - +
573C LEU 3.1 15.2 + - - +
574C ALA 3.3 3.3 + - - +
576C SER* 1.3 77.7 - - - +
578C LEU* 1.3 65.4 + - - +
580C GLN* 2.9 22.9 + - + +
581C LEU* 3.5 19.8 + - + +
590C HIS* 3.6 24.7 - - + +
594C THR* 4.2 2.0 - - + -
598C ILE* 3.9 22.0 - - + -
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Residues in contact with LEU 578 (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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474B LYS* 3.6 56.6 + - + +
475B ILE* 3.9 19.1 - - + -
478B SER* 4.0 9.2 - - - +
264C GLN* 3.8 22.9 - - - +
574C ALA 3.0 18.1 + - - +
575C LYS* 4.2 6.7 - - + +
577C ILE* 1.3 75.0 - - - +
579C PRO* 1.4 69.0 - - + +
580C GLN 3.2 0.7 + - - -
581C LEU* 3.2 17.9 + - - +
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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