Contacts of the helix formed by residues 569 - 578 (chain A) in PDB entry 5I0H
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 ARG 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ALA 2.8 23.6 + - - -
375A GLN 2.9 26.0 + - - -
376A ARG* 3.7 9.2 - - - +
389A LEU* 3.5 15.7 - - - +
397A SER* 2.8 40.1 + - - +
400A SER* 5.3 0.2 + - - -
567A THR* 4.3 8.7 - - + +
568A PHE* 1.3 79.9 - - - +
570A ASP* 1.3 59.0 + - - +
571A ASP* 2.9 34.2 + - + +
572A LEU* 3.0 36.2 + - + +
573A LEU* 3.1 9.4 + - - -
595A ASN* 3.5 10.8 - - - +
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Residues in contact with ASP 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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568A PHE 3.5 0.9 + - - +
569A ARG* 1.3 67.9 - - - +
571A ASP* 1.4 61.0 + - - +
573A LEU* 3.6 12.8 - - + +
574A ASN* 2.8 42.7 + - - +
593A SER* 2.7 38.4 + - - -
594A ARG 4.4 0.7 + - - -
595A ASN* 2.9 32.0 + - - +
476B ARG 5.1 5.9 - - - +
477B GLU* 4.9 6.7 - - - +
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Residues in contact with ASP 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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372A ALA* 4.6 10.0 - - + +
375A GLN 4.1 1.2 - - - +
376A ARG* 3.4 4.2 - - - +
377A SER* 2.9 48.3 + - - +
569A ARG* 2.9 35.2 + - - +
570A ASP* 1.4 80.2 - - - +
572A LEU* 1.3 58.2 + - + +
574A ASN* 3.7 10.7 + - - +
575A LEU* 3.1 25.1 + - - +
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Residues in contact with LEU 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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372A ALA* 4.0 34.5 - - + +
373A LEU* 4.5 13.5 - - + -
397A SER* 3.5 20.2 - - - +
400A SER* 3.3 26.5 - - - +
401A LEU* 4.4 9.9 - - + +
568A PHE* 3.6 21.5 - - + -
569A ARG* 3.0 30.6 + - + +
571A ASP* 1.3 75.5 - - - +
573A LEU* 1.3 61.4 + - - +
575A LEU* 3.5 11.1 - - + +
576A LEU* 2.9 32.7 + - - +
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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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568A PHE* 3.6 18.8 - - + +
569A ARG 3.1 9.4 + - - +
570A ASP* 3.2 15.7 + - - +
572A LEU* 1.3 76.1 - - - +
574A ASN* 1.3 63.3 + - - +
576A LEU* 3.3 3.6 + - - +
577A ARG* 3.1 71.6 + - - +
588A PHE* 4.0 28.9 - - + +
591A VAL* 4.1 17.7 - - + +
592A SER 4.6 2.7 - - - +
593A SER* 4.4 21.1 - - - -
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Residues in contact with ASN 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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570A ASP* 2.8 28.7 + - - +
571A ASP* 3.8 11.5 + - - +
573A LEU* 1.3 75.3 - - - +
575A LEU* 1.3 64.0 + - - +
577A ARG* 3.2 28.2 + - - +
578A GLU* 3.4 16.6 + - - +
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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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364A LEU* 3.4 29.5 - - + +
368A GLN* 3.9 42.4 - - + +
369A LEU* 3.6 31.2 - - + +
372A ALA* 3.8 18.4 - - + -
401A LEU* 4.5 7.4 - - + -
571A ASP 3.1 18.6 + - - +
572A LEU* 3.5 14.8 - - + +
573A LEU 3.3 0.2 - - - -
574A ASN* 1.3 75.5 - - - +
576A LEU* 1.4 57.6 + - - +
578A GLU* 2.9 29.9 + - - +
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Residues in contact with LEU 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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362A LEU* 5.7 1.8 - - + -
364A LEU* 4.4 17.5 - - + -
401A LEU* 3.6 31.9 - - + -
404A ALA* 5.1 0.4 - - + -
405A LEU* 3.9 23.1 - - + -
568A PHE* 3.8 10.8 - - + -
572A LEU 2.9 18.9 + - - +
573A LEU 3.3 4.5 + - - +
575A LEU* 1.4 75.0 - - + +
577A ARG* 1.3 58.2 + - - +
579A SER* 3.0 26.9 + - - -
584A ILE* 3.9 16.5 - - + +
585A TYR* 4.5 4.3 - - - -
588A PHE* 3.7 49.1 - - + -
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Residues in contact with ARG 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 39.1 + - - +
574A ASN* 3.6 19.7 + - - +
575A LEU 3.2 0.4 - - - -
576A LEU* 1.3 75.8 - - - +
578A GLU* 1.3 63.3 + - - +
579A SER 3.3 1.0 - - - +
585A TYR* 3.3 39.2 - - + +
588A PHE* 2.9 34.5 + - + +
589A GLU 3.5 16.8 + - - -
590A HIS 4.0 1.2 - - - -
591A VAL 2.9 28.7 + - - +
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Residues in contact with GLU 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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363A GLY 4.2 2.4 - - - +
364A LEU* 4.5 4.4 - - + -
368A GLN* 3.8 28.4 + - - +
574A ASN 3.6 14.1 - - - +
575A LEU* 2.9 15.0 + - - +
577A ARG* 1.3 80.0 - - - +
579A SER* 1.3 66.1 + - - +
580A ARG* 3.4 3.3 + - - +
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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