Contacts of the helix formed by residues 572 - 580 (chain A) in PDB entry 2Y48
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 SER 572 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL 6.2 0.4 - - - -
317A VAL* 3.9 16.4 - - - +
319A THR* 2.8 29.0 + - - -
321A ARG* 3.3 21.3 + - - -
570A GLY 3.3 0.6 - - - -
571A TYR* 1.3 76.5 - - - +
573A CYS* 1.3 57.5 + - - +
574A VAL 2.7 12.3 + - - -
575A PRO* 3.2 6.9 - - - +
576A VAL* 3.1 32.4 + - - +
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Residues in contact with CYS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG* 4.1 8.0 - - - +
349A VAL* 4.1 5.8 - - + +
350A ASN 3.9 12.8 - - - +
351A MET* 3.6 33.9 - - - -
567A VAL* 4.4 0.9 - - - -
569A ASN* 4.2 11.2 - - + +
570A GLY 3.4 21.2 + - - +
571A TYR 2.8 1.9 + - - -
572A SER* 1.3 82.4 + - - +
574A VAL* 1.3 61.0 + - - -
576A VAL* 4.3 5.8 - - - +
577A ALA* 3.3 25.2 + - - +
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 5.0 8.1 - - + -
342A MET* 4.3 11.4 - - + -
345A VAL* 4.3 21.8 - - + -
349A VAL* 4.6 4.0 - - + +
351A MET* 3.7 45.8 - - + -
571A TYR* 2.8 15.7 + - + +
572A SER 2.7 5.3 + - - -
573A CYS* 1.3 75.2 - - - +
575A PRO* 1.4 76.8 - - + +
576A VAL 3.2 0.7 - - - -
577A ALA* 3.3 6.8 + - - +
578A LEU* 3.0 34.9 + - + +
811A VAL* 5.9 0.4 - - + -
815A LEU* 6.2 0.7 - - + -
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Residues in contact with PRO 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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288A VAL* 4.0 13.5 - - + -
291A LEU* 3.8 16.7 - - + +
313A VAL* 4.2 7.9 - - + +
314A GLY* 3.6 34.5 - - - +
317A VAL* 3.7 20.0 - - + +
571A TYR* 3.5 8.1 - - + +
572A SER* 3.2 13.5 - - - +
574A VAL* 1.4 89.9 - - + +
576A VAL* 1.3 66.8 + - + +
578A LEU* 2.7 17.1 + - + +
579A ALA* 2.8 13.5 + - - +
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 4.1 21.5 - - + +
572A SER* 3.1 27.6 + - - +
573A CYS* 4.3 6.5 - - - +
575A PRO* 1.3 80.9 - - + +
577A ALA* 1.3 64.5 - - - +
579A ALA* 3.1 14.2 + - + +
580A GLU* 3.5 7.3 + - - +
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Residues in contact with ALA 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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266A ILE* 3.4 26.0 - - + +
295A ARG* 4.0 2.9 + - - -
349A VAL* 3.9 18.8 - - + -
573A CYS 3.3 18.8 + - - +
574A VAL 3.3 5.6 + - - +
575A PRO 3.3 0.4 - - - -
576A VAL* 1.3 80.7 - - - +
578A LEU* 1.3 60.8 + - - +
580A GLU* 3.3 20.1 - - - +
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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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265A GLY* 4.2 17.9 - - - -
266A ILE* 3.8 24.7 - - + -
288A VAL* 4.5 10.1 - - + -
291A LEU* 4.1 27.6 - - + -
292A ALA* 4.4 11.4 - - - +
295A ARG* 3.1 31.7 + - + +
345A VAL* 5.5 9.6 - - + -
574A VAL* 3.0 26.1 + - + +
575A PRO* 2.7 11.4 + - + +
577A ALA* 1.3 69.1 - - - +
579A ALA* 1.3 58.8 + - - +
580A GLU 3.0 9.4 + - - +
582A LEU* 3.8 11.1 - - - +
815A LEU* 4.5 19.7 - - + -
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Residues in contact with ALA 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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291A LEU* 3.9 11.9 - - + +
313A VAL* 3.9 24.0 - - + -
575A PRO 2.8 10.5 + - - +
576A VAL* 3.1 11.4 + - + +
578A LEU* 1.3 75.4 - - - +
580A GLU* 1.3 62.1 + - - +
581A GLY 3.2 3.3 + - - -
582A LEU* 3.3 18.2 + - - +
584A ILE* 3.5 22.0 - - + +
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Residues in contact with GLU 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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266A ILE* 4.8 8.7 - - - +
295A ARG* 2.6 38.1 + - - -
298A GLN* 5.7 0.2 - - - +
576A VAL 3.5 5.9 + - - +
577A ALA* 3.3 15.9 + - - +
578A LEU 3.0 2.1 - - - +
579A ALA* 1.3 78.1 - - - +
581A GLY* 1.3 61.3 + - - +
582A LEU* 4.4 1.8 - - - +
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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