Contacts of the helix formed by residues 573 - 582 (chain A) in PDB entry 2DFS
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 TYR 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A TRP 4.5 0.4 - - - -
377A HIS 4.3 12.8 - - - -
378A ARG* 4.0 30.4 + - + -
391A ILE* 3.6 25.1 - - + +
395A HIS* 2.9 36.4 + - - +
399A ALA* 3.4 22.4 - - + +
571A THR* 3.7 19.1 - - + -
572A VAL* 1.3 75.8 - - - +
574A GLU* 1.4 66.5 + - - +
575A GLU* 3.3 14.6 - - + +
576A GLN* 3.4 44.6 + - - +
577A ILE* 3.6 9.3 - - - +
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Residues in contact with GLU 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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379A LYS* 2.5 36.2 + - - -
572A VAL* 3.9 3.0 + - - -
573A TYR* 1.4 69.2 - - - +
575A GLU* 1.4 72.2 + - - +
577A ILE* 3.0 26.6 + - + +
578A LYS* 3.2 27.7 + - - +
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Residues in contact with GLU 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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374A TRP* 3.3 41.4 - - + -
377A HIS 4.7 3.8 - - - +
378A ARG* 3.8 12.6 - - - +
379A LYS* 2.6 66.6 + - - +
573A TYR* 4.1 15.3 - - + +
574A GLU* 1.4 91.1 + - - +
576A GLN* 1.3 62.7 + - + +
578A LYS* 3.2 18.5 + - - +
579A VAL* 3.2 18.6 + - - +
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Residues in contact with GLN 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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371A MET* 3.9 24.6 - - + +
374A TRP* 2.9 30.1 + - + +
375A LEU* 3.7 25.0 + - - +
396A ALA 5.7 0.2 + - - -
399A ALA* 3.9 23.8 - - - +
400A ARG 5.2 0.2 - - - +
403A LEU* 4.2 23.6 - - + +
572A VAL* 4.6 0.2 - - - +
573A TYR* 3.4 42.3 + - + +
574A GLU 3.3 0.4 - - - -
575A GLU* 1.3 74.6 - - + +
577A ILE* 1.3 60.4 + - - +
579A VAL* 3.4 13.7 + - - +
580A LEU* 3.5 18.2 + - - +
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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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403A LEU* 4.5 6.7 - - + -
406A HIS* 3.7 27.1 - - + +
572A VAL* 3.8 27.6 - - + -
573A TYR 3.6 13.2 - - - +
574A GLU* 3.0 13.2 + - + +
576A GLN* 1.3 73.2 - - - +
578A LYS* 1.4 59.7 + - - +
580A LEU* 3.3 7.2 + - + +
581A LYS* 2.9 28.9 + - + +
593A PHE* 4.4 34.5 - - + -
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Residues in contact with LYS 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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370A GLU* 2.6 39.4 + - - +
374A TRP* 6.3 0.9 - - - +
574A GLU* 3.2 23.8 + - - +
575A GLU* 3.2 13.2 + - - +
577A ILE* 1.4 75.3 - - - +
579A VAL* 1.4 64.4 + - + +
581A LYS* 3.9 7.1 - - - +
582A SER* 2.9 50.6 + - - +
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Residues in contact with VAL 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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366A VAL* 3.2 35.3 - - + +
370A GLU* 3.7 36.6 - - + +
371A MET* 4.0 35.2 - - + +
374A TRP* 4.2 12.1 - - + -
575A GLU 3.2 16.6 + - - +
576A GLN* 3.5 13.0 - - - +
577A ILE 3.3 0.4 - - - -
578A LYS* 1.4 80.7 - - + +
580A LEU* 1.3 61.2 + - + +
582A SER* 3.2 14.6 + - - -
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Residues in contact with LEU 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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360A PHE* 4.3 13.9 - - + -
364A MET* 4.3 22.9 - - + -
366A VAL* 4.2 15.3 - - + -
371A MET* 4.6 11.7 - - - -
403A LEU* 4.1 21.1 - - + -
407A ILE* 3.8 32.3 - - + -
576A GLN 3.5 9.6 + - - +
577A ILE* 3.3 8.4 + - + +
579A VAL* 1.3 73.6 - - - +
581A LYS* 1.4 63.5 + - - +
582A SER 3.2 2.9 + - - -
583A SER* 3.3 19.2 + - - -
589A LEU* 3.9 23.0 - - + +
590A PRO 4.8 2.1 - - - -
593A PHE* 4.7 13.9 - - + -
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Residues in contact with LYS 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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577A ILE* 2.9 24.2 + - + +
578A LYS* 3.3 8.5 + - - +
580A LEU* 1.4 72.1 - - - +
582A SER* 1.3 55.9 + - - +
583A SER 3.3 4.9 + - - +
590A PRO* 2.7 51.7 + - + +
593A PHE* 2.7 40.0 + - + +
594A GLN* 2.9 15.6 + - - +
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Residues in contact with SER 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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366A VAL* 5.6 0.4 - - - -
370A GLU* 4.4 1.9 + - - -
578A LYS* 2.9 42.3 + - - -
579A VAL 3.2 7.5 + - - -
580A LEU 3.2 0.4 - - - -
581A LYS* 1.3 74.3 - - - +
583A SER* 1.3 62.5 + - - +
584A LYS* 4.6 13.2 + - - +
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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