Contacts of the helix formed by residues 576 - 584 (chain A) in PDB entry 5FHH
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 GLY 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A LEU 3.8 17.0 - - - -
346A GLN 3.9 5.6 - - - -
348A PRO* 4.9 1.3 - - - -
574A ALA 2.2 13.7 + - - -
575A SER* 1.3 72.5 - - - +
577A GLN* 1.3 64.1 + - - -
578A ALA* 3.1 4.3 - - - +
579A TYR* 2.9 9.7 + - - +
580A VAL* 2.7 30.0 + - - +
603A CYS 4.0 6.9 + - - +
604A ASP* 5.4 1.3 - - - -
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Residues in contact with GLN 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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347A LEU* 4.0 20.7 - - + +
427A THR* 3.4 29.6 + - - +
428A HIS* 5.2 2.0 + - - -
554A ILE* 3.2 25.0 - - + +
572A VAL* 3.3 19.7 - - + +
573A PHE 2.8 30.9 + - - +
574A ALA* 2.6 37.6 + - + +
576A GLY* 1.3 68.4 - - - -
578A ALA* 1.3 66.2 + - - +
580A VAL* 4.4 4.9 - - - -
581A ALA* 3.1 17.3 + - - +
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Residues in contact with ALA 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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394A VAL* 4.2 10.8 - - + -
567A ILE* 5.8 1.3 - - - -
572A VAL* 5.0 8.3 + - + +
574A ALA 4.3 2.0 + - - +
576A GLY* 2.9 3.3 + - - +
577A GLN* 1.3 81.3 - - - +
579A TYR* 1.3 68.8 + - - +
581A ALA* 3.0 5.8 + - - +
582A LEU* 3.0 25.5 - - + +
601A VAL* 3.3 35.0 + - + +
602A ARG* 4.1 9.4 - - - -
603A CYS 5.1 1.8 - - - +
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Residues in contact with TYR 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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229A SER* 3.8 3.1 - - - -
230A ALA* 2.8 35.1 + - + +
343A ASP* 4.3 2.5 - - - -
345A LEU* 3.6 29.6 - - + +
346A GLN* 4.4 4.5 - - + -
391A LEU* 4.1 22.8 - - + +
392A GLN* 5.0 1.0 + - - -
394A VAL* 4.2 11.4 - - + +
395A ARG* 3.2 64.4 + - + +
576A GLY* 2.9 12.3 + - - +
578A ALA* 1.3 76.6 - - - +
580A VAL* 1.3 58.5 + - + +
582A LEU* 3.4 2.3 + - - +
583A SER* 2.3 55.6 + - - -
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Residues in contact with VAL 580 (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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346A GLN* 3.5 36.8 - - + +
347A LEU* 3.6 24.7 - - + +
554A ILE* 4.4 6.7 - - + +
557A SER* 4.3 11.7 + - - +
558A GLN* 3.4 29.6 - - + -
576A GLY 2.7 28.3 + - - +
577A GLN* 4.1 3.8 - - - +
579A TYR* 1.3 71.4 - - - +
581A ALA* 1.3 64.6 + - - +
583A SER* 3.1 12.2 + - - -
584A ARG* 3.6 13.2 + - - +
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Residues in contact with ALA 581 (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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425A LEU* 3.8 27.0 - - + +
554A ILE* 3.6 16.8 - - + +
557A SER* 5.1 0.2 - - - -
565A VAL* 4.9 4.9 - - - +
567A ILE* 3.7 28.0 - - + -
577A GLN 3.1 17.2 + - - +
578A ALA 3.0 4.6 + - - +
580A VAL* 1.3 81.2 - - - +
582A LEU* 1.3 64.8 + - - +
584A ARG* 3.4 13.3 + - - +
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Residues in contact with LEU 582 (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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387A PHE* 4.4 10.9 - - + -
390A LEU* 4.9 19.3 - - + -
391A LEU* 4.7 12.8 - - + -
394A VAL* 5.2 9.6 - - + -
407A LEU* 4.7 21.1 - - + -
565A VAL* 5.5 3.8 - - - -
567A ILE* 4.1 23.5 - - + +
578A ALA* 3.0 36.6 - - + +
579A TYR* 4.3 2.7 - - - +
581A ALA* 1.3 79.0 - - - +
583A SER* 1.3 64.0 + - - +
585A ALA* 2.9 27.9 + - - +
591A LEU* 5.5 8.1 - - + -
593A VAL* 5.3 9.9 - - + -
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Residues in contact with SER 583 (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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230A ALA* 3.5 15.4 - - - +
346A GLN* 4.8 1.0 + - - -
381A ARG* 2.5 25.4 + - - -
382A GLN* 3.8 13.0 + - - +
387A PHE* 5.8 0.2 - - - -
391A LEU* 3.8 19.2 - - - +
579A TYR* 2.3 58.0 + - - -
580A VAL* 3.1 13.7 + - - -
582A LEU* 1.3 75.3 - - - +
584A ARG* 1.3 48.7 + - - +
585A ALA 3.1 5.5 + - - -
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Residues in contact with ARG 584 (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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381A ARG* 3.5 11.9 - - - +
425A LEU* 5.4 0.7 - - + -
557A SER* 4.0 16.2 - - - +
560A MET 3.4 16.8 - - - +
561A THR* 4.6 0.9 - - - -
562A LEU* 2.6 49.5 + - + +
565A VAL* 5.2 0.9 - - + -
580A VAL 3.6 8.7 + - - +
581A ALA 3.4 12.7 + - - +
582A LEU 2.9 2.0 + - - -
583A SER* 1.3 77.8 + - - +
585A ALA* 1.3 52.7 + - - +
586A ARG 4.1 0.4 - - - -
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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