Contacts of the helix formed by residues 567 - 578 (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 VAL 567 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B GLU* 4.2 15.0 - - - +
564B GLN* 3.3 28.0 - - + +
566B GLY* 1.3 78.7 - - - +
568B GLU* 1.3 68.7 + - + +
569B LEU 3.6 0.4 - - - -
570B GLY* 3.8 4.6 + - - -
571B LYS* 3.4 44.8 + - - +
5002B G6Q 6.1 1.1 - - - +
441C GLN* 3.3 26.5 - - + +
442C HIS* 5.2 1.8 - - - +
445C TYR* 5.4 1.8 - - + -
446C GLN* 4.6 15.7 - - + +
449C HIS* 5.7 1.3 - - - -
483C GLN* 5.2 3.1 + - - +
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Residues in contact with GLU 568 (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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564B GLN 4.9 0.9 - - - +
565B TRP* 3.3 43.8 + - + +
567B VAL* 1.3 81.4 - - + +
569B LEU* 1.3 65.1 + - - +
571B LYS* 3.2 11.3 + - + +
572B VAL* 3.0 33.8 + - + +
518C LYS* 3.3 32.4 + - - +
520C PHE* 4.8 3.4 - - + -
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Residues in contact with LEU 569 (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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567B VAL 3.6 0.4 - - - -
568B GLU* 1.3 75.9 - - - +
570B GLY* 1.3 57.7 + - - +
572B VAL* 3.3 6.0 + - + +
573B LEU* 3.0 47.2 + - + +
449C HIS* 5.5 0.7 - - + -
486C ALA* 3.6 37.7 - - + +
489C ILE* 5.5 1.1 - - + -
490C GLY* 3.6 29.6 - - - +
491C LYS* 3.7 33.4 - - + +
520C PHE* 3.7 40.1 - - + -
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Residues in contact with GLY 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLY 5.4 0.6 + - - -
567B VAL 3.8 4.7 + - - -
568B GLU 3.4 0.6 - - - -
569B LEU* 1.3 78.1 - - - +
571B LYS* 1.3 56.5 + - - +
573B LEU* 3.7 0.4 + - - -
574B ALA* 3.1 29.6 + - - +
441C GLN* 6.0 0.2 - - - -
449C HIS* 5.2 4.1 + - - -
479C ASN* 5.0 1.4 - - - +
482C ALA* 3.7 8.0 - - - +
483C GLN* 3.5 32.1 + - - -
486C ALA* 4.2 12.4 - - - +
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Residues in contact with LYS 571 (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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263B THR* 5.3 9.3 + - - +
265B GLU* 5.9 0.2 - - - -
567B VAL* 3.4 37.8 + - + +
568B GLU* 3.2 12.8 + - + +
570B GLY* 1.3 74.3 - - - +
572B VAL* 1.3 60.3 + - + +
574B ALA* 3.4 6.5 + - - +
575B LYS* 3.1 26.9 + - - +
5002B G6Q 4.8 6.5 + - - -
441C GLN* 5.8 4.5 - - - +
442C HIS* 4.3 24.5 - - - -
479C ASN* 5.5 4.0 - - - +
483C GLN* 6.0 0.9 - - - +
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Residues in contact with VAL 572 (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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568B GLU* 3.0 24.4 + - + +
569B LEU* 3.8 6.7 - - + +
571B LYS* 1.3 75.3 - - + +
573B LEU* 1.3 68.2 + - + +
575B LYS* 3.3 14.9 + - + +
576B SER* 3.3 20.1 + - - -
491C LYS* 4.4 19.1 - - - +
499C GLU* 5.3 4.7 - - - +
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Residues in contact with LEU 573 (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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569B LEU* 3.0 29.6 + - + +
570B GLY 4.2 0.2 - - - +
572B VAL* 1.3 80.8 - - + +
574B ALA* 1.3 57.1 + - - +
576B SER* 3.5 9.8 + - - -
577B ILE* 3.1 32.1 + - - +
590B HIS* 6.2 1.3 - - + -
482C ALA* 3.7 12.6 - - + +
485C GLU* 3.6 26.1 - - - +
486C ALA* 3.7 36.8 - - + +
489C ILE* 3.9 21.3 - - + -
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Residues in contact with ALA 574 (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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264B GLN* 5.5 5.8 - - - +
570B GLY 3.1 19.5 + - - +
571B LYS* 3.6 7.2 - - - +
572B VAL 3.2 0.2 - - - -
573B LEU* 1.3 73.6 - - - +
575B LYS* 1.3 60.4 + - - +
577B ILE 3.2 0.6 + - - +
578B LEU* 2.9 28.3 + - - +
478C SER* 3.5 35.6 - - - +
479C ASN* 4.0 15.3 - - - +
482C ALA* 3.5 9.1 - - + +
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Residues in contact with LYS 575 (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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264B GLN* 6.1 2.0 - - - +
571B LYS 3.1 13.7 + - - +
572B VAL* 3.4 16.6 - - - +
574B ALA* 1.3 75.7 - - - +
576B SER* 1.3 64.6 + - - +
578B LEU* 3.8 7.9 + - - +
579B PRO* 3.2 23.4 - - - +
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Residues in contact with SER 576 (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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572B VAL 3.3 9.2 + - - -
573B LEU* 3.7 16.2 - - - -
574B ALA 3.2 0.2 - - - -
575B LYS* 1.3 92.2 - - - +
577B ILE* 1.3 61.1 + - - +
579B PRO* 3.6 15.0 - - - +
580B GLN* 3.8 13.8 + - - +
589B ASN* 5.0 9.4 + - - -
590B HIS* 5.1 4.7 - - - -
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Residues in contact with ILE 577 (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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573B LEU 3.1 15.4 + - - +
574B ALA 3.2 3.6 + - - +
576B SER* 1.3 78.3 - - - +
578B LEU* 1.3 65.2 + - - +
580B GLN* 2.9 22.7 + - + +
581B LEU* 3.4 21.1 + - + +
590B HIS* 3.6 24.0 - - + -
594B THR* 4.3 2.2 - - + -
598B ILE* 3.8 21.5 - - + -
478C SER* 4.2 15.3 - - - +
481C PHE* 4.1 12.3 - - + -
482C ALA* 3.8 24.2 - - - +
485C GLU* 3.6 21.8 - - - +
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Residues in contact with LEU 578 (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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264B GLN* 3.8 24.9 - - - +
574B ALA 2.9 15.9 + - - +
575B LYS* 4.0 7.0 - - - +
577B ILE* 1.3 74.5 - - - +
579B PRO* 1.4 68.0 - - + +
580B GLN 3.1 1.4 + - - -
581B LEU* 3.2 18.0 + - - +
582B ARG* 5.5 0.2 - - - +
474C LYS* 3.5 52.2 + - + +
475C ILE* 3.7 20.9 - - + +
478C SER* 3.9 7.8 - - - +
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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