Contacts of the helix formed by residues 567 - 578 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A GLU* 4.1 21.1 - - + +
564A GLN* 3.5 29.8 - - + +
566A GLY* 1.3 79.4 - - - +
568A GLU* 1.3 67.9 + - + +
569A LEU 3.6 0.8 + - - -
570A GLY* 3.8 4.2 + - - -
571A LYS* 3.1 50.0 + - - +
5001A G6Q 5.9 2.0 - - - +
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Residues in contact with GLU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A GLN 4.9 0.4 - - - +
565A TRP* 3.3 49.9 + - - +
567A VAL* 1.3 81.4 - - + +
569A LEU* 1.3 65.5 + - - +
571A LYS* 3.3 9.2 + - + +
572A VAL* 3.0 32.2 + - + +
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Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A TRP 4.8 1.2 + - - -
566A GLY 4.7 4.8 + - - +
567A VAL 3.6 0.6 - - - -
568A GLU* 1.3 75.9 - - - +
570A GLY* 1.3 58.7 + - - +
572A VAL* 3.3 9.1 + - + -
573A LEU* 3.0 55.9 + - + +
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Residues in contact with GLY 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLY 5.3 1.6 + - - -
567A VAL 3.8 6.0 + - - -
568A GLU 3.4 0.2 - - - -
569A LEU* 1.3 78.2 - - - +
571A LYS* 1.3 56.6 + - - +
573A LEU* 4.0 4.6 - - - +
574A ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A THR* 5.4 13.0 + - - +
265A GLU* 5.8 2.7 - - - -
567A VAL* 3.1 39.2 - - + +
568A GLU* 3.3 10.3 + - + +
569A LEU 3.2 0.6 - - - -
570A GLY* 1.3 74.1 - - - +
572A VAL* 1.3 60.5 + - + +
574A ALA* 3.4 5.9 + - - +
575A LYS* 3.1 36.8 + - + +
5001A G6Q 4.3 15.1 + - - -
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Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A GLU* 3.0 24.4 + - + +
569A LEU* 3.8 10.5 - - + +
571A LYS* 1.3 77.7 - - + +
573A LEU* 1.3 68.9 - - + +
575A LYS* 3.3 12.9 + - + +
576A SER* 3.2 22.0 + - - -
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LEU* 3.0 47.2 + - + +
570A GLY* 4.3 4.7 - - - +
572A VAL* 1.3 78.4 - - + +
574A ALA* 1.3 63.5 + - - +
576A SER* 3.4 10.4 + - - -
577A ILE* 3.1 34.7 + - + +
590A HIS* 5.9 7.0 - - + +
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Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLN* 5.5 10.1 - - - +
570A GLY 3.0 19.9 + - - +
571A LYS* 3.7 6.3 - - - +
572A VAL 3.2 0.4 - - - -
573A LEU* 1.3 73.8 - - - +
575A LYS* 1.3 60.5 + - + +
577A ILE* 3.2 7.4 + - - +
578A LEU* 2.9 32.0 + - - +
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Residues in contact with LYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLN* 5.1 15.5 - - - +
571A LYS* 3.1 23.8 + - + +
572A VAL* 3.5 10.5 - - + +
574A ALA* 1.3 76.6 - - + +
576A SER* 1.3 57.1 + - - +
578A LEU* 4.1 7.7 - - + +
579A PRO* 3.3 21.7 - - - +
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Residues in contact with SER 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A VAL* 3.2 15.4 + - - -
573A LEU* 3.7 13.9 - - - -
574A ALA 3.1 0.6 - - - -
575A LYS* 1.3 77.0 - - - +
577A ILE* 1.3 62.1 + - - +
578A LEU 3.5 0.2 - - - -
579A PRO* 3.5 15.3 - - - +
580A GLN* 3.7 13.0 - - - +
589A ASN* 5.1 8.5 + - - -
590A HIS* 5.1 5.3 - - - -
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Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A LEU* 3.1 24.2 + - + +
574A ALA* 3.2 6.5 + - - +
576A SER* 1.3 78.3 - - - +
578A LEU* 1.3 64.5 + - - +
580A GLN* 2.9 22.1 + - - +
581A LEU* 3.4 30.6 + - + +
590A HIS* 3.7 29.2 - - + +
594A THR* 4.2 11.0 - - + -
598A ILE* 3.9 22.9 - - + -
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLN* 3.7 26.7 - - - +
574A ALA 2.9 16.1 + - - +
575A LYS* 4.1 7.0 - - + +
577A ILE* 1.3 76.4 - - - +
579A PRO* 1.4 67.0 - - + +
580A GLN 3.1 1.0 + - - -
581A LEU* 3.2 32.4 + - + +
582A ARG* 5.5 0.2 - - - +
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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