Contacts of the helix formed by residues 547 - 556 (chain A) in PDB entry 2JY5
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 PHE 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A PHE* 3.9 37.0 - + + -
545A VAL* 3.1 9.0 - - - +
546A ARG* 1.3 77.6 - - - +
548A GLN* 1.3 53.3 + - - +
549A GLN* 2.5 21.2 + - - +
550A GLN* 2.5 52.8 + - + +
551A LEU 4.0 0.7 - - - +
566A LEU* 2.9 27.5 - - + +
569A LEU* 3.2 32.1 - - + -
570A ILE* 3.4 33.7 - - + -
573A GLY* 6.1 0.9 - - - -
574A GLY* 5.7 3.1 - - - -
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Residues in contact with GLN 548 (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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540A PHE* 6.3 0.7 - - + -
545A VAL* 2.7 43.1 + - + +
546A ARG 2.9 1.2 - - - -
547A PHE* 1.3 74.6 - - - +
549A GLN* 1.3 77.8 + - + +
551A LEU* 3.2 13.6 - - + +
552A GLU* 3.0 24.8 + - - +
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Residues in contact with GLN 549 (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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547A PHE 2.5 6.0 + - - +
548A GLN* 1.3 92.0 + - + +
550A GLN* 1.3 55.8 + - + +
551A LEU 3.0 1.6 - - - -
552A GLU* 2.7 37.4 + - - +
553A GLN* 2.6 27.5 + - - +
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Residues in contact with GLN 550 (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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547A PHE* 2.5 49.5 + - + +
549A GLN* 1.3 78.0 - - + +
551A LEU* 1.3 61.6 + - - +
553A GLN* 3.1 20.9 + - - +
554A LEU 3.3 10.0 + - - -
569A LEU* 2.9 35.4 - - + +
574A GLY* 3.3 24.4 + - - -
576A ILE* 3.0 27.0 - - - +
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Residues in contact with LEU 551 (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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545A VAL 3.6 7.4 - - - +
546A ARG* 2.6 49.0 + - + +
547A PHE* 3.3 2.0 + - - +
548A GLN* 3.2 15.9 - - + +
549A GLN 3.0 0.2 - - - -
550A GLN* 1.3 76.3 - - - +
552A GLU* 1.3 59.0 + - - +
553A GLN 3.0 2.0 - - - -
554A LEU 3.3 0.3 + - - -
555A SER* 2.7 49.4 + - - -
562A ARG* 4.0 20.2 - - - +
565A ASN* 3.6 31.8 + - + +
569A LEU* 5.3 0.2 - - - -
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Residues in contact with GLU 552 (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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548A GLN 3.0 13.4 + - - +
549A GLN* 2.7 30.5 + - - +
551A LEU* 1.3 75.7 - - - +
553A GLN* 1.3 65.7 + - + +
555A SER* 3.8 5.4 - - - -
556A ALA* 2.8 30.7 + - - +
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Residues in contact with GLN 553 (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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549A GLN* 2.6 36.5 + - - +
550A GLN* 3.1 18.5 + - - +
551A LEU 3.0 1.6 - - - -
552A GLU* 1.3 83.3 - - + +
554A LEU* 1.4 66.3 + - - +
555A SER 3.0 0.9 - - - -
556A ALA* 2.8 22.2 + - + +
557A MET* 3.2 9.2 + - - +
576A ILE* 3.0 39.1 - - + +
577A ASN* 6.3 0.4 - - - +
580A ILE* 5.1 3.4 - - + +
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Residues in contact with LEU 554 (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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550A GLN 3.3 2.6 + - - -
551A LEU 3.3 2.0 + - - -
553A GLN* 1.4 75.9 - - - +
555A SER* 1.3 61.8 + - - +
557A MET* 3.3 6.9 + - - +
559A PHE* 3.1 31.3 - - + +
565A ASN* 3.5 24.7 - - + +
568A ALA* 3.3 26.7 - - + -
569A LEU* 3.2 23.8 - - + -
576A ILE* 3.6 12.5 - - + +
579A ALA* 3.9 2.9 - - + -
580A ILE* 3.4 46.2 - - + +
583A LEU* 3.4 20.9 - - + -
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Residues in contact with SER 555 (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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551A LEU* 2.7 35.1 + - - -
552A GLU* 3.9 6.1 - - - -
554A LEU* 1.3 77.3 - - - +
556A ALA* 1.3 58.9 + - - +
558A GLY* 2.8 21.5 + - - -
559A PHE* 3.3 17.6 + - - +
562A ARG* 2.8 27.0 + - - -
565A ASN* 4.1 2.8 - - - +
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Residues in contact with ALA 556 (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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552A GLU* 2.8 31.5 + - + +
553A GLN* 2.8 13.6 + - + +
555A SER* 1.3 76.7 - - - +
557A MET* 1.3 58.7 + - + +
558A GLY 3.1 4.3 + - - -
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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