Contacts of the helix formed by residues 571 - 579 (chain A) in PDB entry 3B60
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 571 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ARG* 3.4 31.6 - - - +
550A VAL* 4.2 17.7 - - + -
552A GLU* 3.9 11.7 - - + +
557A VAL* 4.6 18.8 - - + -
558A GLU* 5.8 0.4 - - + -
569A HIS 3.9 3.4 + - - -
570A GLY* 1.3 75.1 - - - +
572A TYR* 1.3 64.6 + - - +
573A ALA 3.5 0.4 - - - -
574A GLN* 3.3 18.3 - - + +
575A LEU* 3.2 27.7 + - + +
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Residues in contact with TYR 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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375A VAL* 5.4 3.4 - - + -
539A LEU* 4.3 26.5 + - + +
542A ILE* 5.4 2.7 - - + +
543A GLU* 5.1 4.7 + - - +
548A ILE* 3.8 19.4 - - + +
550A VAL* 3.6 27.8 - - + +
562A HIS* 2.9 28.8 + - - +
565A LEU* 3.5 50.0 - - + -
566A LEU* 3.4 26.7 - - + -
570A GLY 2.3 24.0 + - - +
571A VAL* 1.3 64.3 - - - +
573A ALA* 1.3 73.2 + - - +
575A LEU* 2.8 24.9 + - + +
576A HIS* 2.8 21.0 + - + -
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Residues in contact with ALA 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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565A LEU 4.7 0.4 + - - -
566A LEU* 3.7 24.4 - - + +
569A HIS* 3.6 40.8 - - + +
570A GLY 4.2 0.6 + - - +
572A TYR* 1.3 86.5 - - - +
574A GLN* 1.3 64.2 + - - +
576A HIS* 2.8 8.0 + - - +
577A LYS* 2.7 23.5 + - - +
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Residues in contact with GLN 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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377A ARG* 4.4 6.5 + - - +
569A HIS 5.5 0.4 - - - -
571A VAL* 3.3 26.0 + - + +
572A TYR 3.1 0.2 - - - -
573A ALA* 1.3 78.1 - - - +
575A LEU* 1.3 61.1 + - - +
577A LYS* 2.9 27.0 + - - +
578A MET* 2.9 42.8 + - - +
514B GLU* 3.6 24.2 + - - +
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Residues in contact with LEU 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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375A VAL* 4.9 12.3 - - + -
376A GLY* 4.8 17.3 - - - +
377A ARG* 5.2 10.5 - - - +
539A LEU* 4.0 12.8 - - + +
550A VAL* 5.5 4.0 - - + -
571A VAL* 3.2 22.2 - - + +
572A TYR* 2.8 17.1 + - + +
574A GLN* 1.3 78.0 - - - +
576A HIS* 1.3 57.3 + - - +
577A LYS 3.0 0.2 - - - -
578A MET* 3.3 5.2 + - - +
579A GLN* 2.9 23.7 + - - +
512B ASP* 4.2 17.7 - - - +
513B THR* 3.4 32.7 - - + +
514B GLU* 4.0 19.1 - - + -
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Residues in contact with HIS 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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539A LEU* 4.2 18.5 - - + +
540A SER* 5.9 0.4 - - - -
543A GLU* 4.0 18.7 + - + -
562A HIS* 3.4 21.1 + + - -
566A LEU* 3.2 40.2 - - + -
572A TYR* 2.8 18.2 + + + +
573A ALA 2.8 8.6 + - - +
575A LEU* 1.3 73.3 - - - +
577A LYS* 1.3 59.9 + - - +
579A GLN* 2.8 41.2 - - + +
580A PHE* 3.9 14.3 - + - -
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Residues in contact with LYS 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 ALA 2.7 9.7 + - - +
574A GLN* 3.1 17.7 - - - +
576A HIS* 1.3 77.7 - - - +
578A MET* 1.3 66.1 + - + +
579A GLN 2.6 14.3 + - - -
580A PHE* 3.2 30.6 + - + +
581A GLY* 5.3 5.3 - - - -
517B ARG* 4.3 16.8 - - - +
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Residues in contact with MET 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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574A GLN* 2.9 44.9 + - - +
575A LEU* 3.5 8.5 - - - +
577A LYS* 1.3 83.0 - - - +
579A GLN* 1.3 53.3 + - - +
580A PHE* 2.7 24.5 + - - +
513B THR* 3.7 21.2 + - + +
514B GLU* 3.7 36.6 - - + +
516B GLU* 5.6 0.3 - - - +
517B ARG* 3.9 41.8 + - + +
518B ALA 5.6 0.2 - - - +
540B SER* 4.8 2.4 + - - -
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Residues in contact with GLN 579 (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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538A ARG* 5.6 7.1 - - - +
539A LEU* 4.4 20.5 - - + +
540A SER* 5.2 7.8 - - - +
575A LEU 2.9 8.0 + - - -
576A HIS* 2.8 49.8 - - + +
577A LYS 2.6 0.6 + - - -
578A MET* 1.3 74.6 - - - +
580A PHE* 1.3 75.6 + - + +
513B THR* 4.2 7.7 + - - -
540B SER* 4.1 11.3 + - - -
579B GLN* 3.7 28.4 + - - +
580B PHE* 5.2 5.3 - - - +
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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