Contacts of the helix formed by residues 503 - 510 (chain A) in PDB entry 3EDY
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 LEU 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A THR* 4.7 4.9 - - + +
386A THR* 3.7 22.5 + - + +
481A PHE* 4.9 5.2 - - + -
485A LEU* 3.8 34.3 - - + -
500A LEU* 4.3 23.3 - - + +
501A GLY 3.1 9.1 + - - +
502A PHE* 1.3 77.2 - - - +
504A ASN* 1.3 65.3 + - - +
505A PRO* 3.4 0.9 - - - -
506A ARG* 3.1 12.4 + - + +
507A LEU* 3.0 44.4 + - + +
556A LEU* 6.5 0.2 - - + -
560A LEU* 4.1 27.4 - - + -
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Residues in contact with ASN 504 (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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383A PRO 4.2 0.2 + - - -
385A VAL 2.9 23.7 + - - -
386A THR* 2.7 31.0 + - - +
421A TYR* 3.1 30.3 + - + -
447A ARG* 3.6 0.8 - - - +
451A ASP* 3.2 24.4 + - - +
502A PHE* 3.5 16.7 - - + -
503A LEU* 1.3 78.0 - - - +
505A PRO* 1.3 72.3 - - + +
507A LEU* 3.2 5.1 + - - +
508A TYR* 2.9 34.3 + - + +
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Residues in contact with PRO 505 (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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66A GLN* 5.8 2.7 - - - +
69A SER* 3.4 39.5 - - - +
70A ASP* 4.5 7.2 - - + -
71A PRO* 4.5 0.2 - - - -
421A TYR* 4.0 25.8 - - + +
502A PHE* 3.5 23.1 - - + +
503A LEU 3.4 3.6 - - - -
504A ASN* 1.3 97.1 - - + +
506A ARG* 1.3 56.8 + - - +
508A TYR* 4.2 0.7 - - - +
509A GLN* 3.0 40.5 + - - +
701A EDO 4.6 3.8 - - - -
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 4.2 4.2 + - - +
71A PRO* 4.0 24.7 - - + +
76A TYR* 2.8 43.6 + - + +
492A ARG* 3.7 8.3 - - - +
500A LEU* 4.4 4.1 - - - +
502A PHE 5.6 0.4 - - - +
503A LEU* 3.1 14.5 + - + +
505A PRO* 1.3 77.4 - - - +
507A LEU* 1.3 61.7 + - - +
509A GLN* 3.3 1.3 + - - +
510A GLN* 2.9 59.9 + - - +
559A THR 3.4 18.1 + - - -
560A LEU* 3.6 28.3 - - + +
562A ASN 3.3 20.4 + - - -
563A PRO* 2.9 36.6 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 5.5 0.7 - - + -
451A ASP* 4.0 9.9 - - + +
452A VAL* 3.4 31.2 - - + -
481A PHE* 6.0 0.9 - - + -
503A LEU* 3.0 35.1 + - + +
504A ASN* 3.7 10.8 - - - +
506A ARG* 1.3 76.5 - - - +
508A TYR* 1.3 63.3 + - + +
510A GLN* 3.4 9.3 + - + +
511A HIS 3.3 3.1 + - - -
512A GLY* 3.0 35.7 + - - -
513A ALA 5.1 0.9 - - - +
515A LEU* 3.8 21.8 - - + -
548A TRP* 3.8 21.7 + - + +
556A LEU* 4.8 12.1 - - + -
560A LEU* 6.0 3.4 - - + -
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Residues in contact with TYR 508 (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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421A TYR* 2.8 41.7 - + + +
422A GLN* 3.3 31.8 + - + -
425A ALA* 4.0 6.5 - - + -
448A ALA 4.3 0.2 + - - -
450A PRO 3.7 1.4 + - - -
451A ASP* 2.6 41.3 + - + -
504A ASN* 2.9 31.2 + - + +
505A PRO 4.3 1.1 - - - +
507A LEU* 1.3 77.3 - - + +
509A GLN* 1.3 66.4 + - - +
511A HIS* 2.9 20.3 + - - -
542A TRP* 2.8 33.4 + + - -
548A TRP* 3.2 38.9 - + - +
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Residues in contact with GLN 509 (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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70A ASP* 2.9 27.9 + - - +
71A PRO* 3.1 29.1 - - + +
72A SER* 3.3 16.5 + - - -
421A TYR* 5.9 6.3 - - + +
505A PRO* 3.0 26.7 + - - +
506A ARG* 3.6 5.8 - - - +
508A TYR* 1.3 77.1 - - + +
510A GLN* 1.3 59.1 + - + +
511A HIS* 3.4 20.7 + - - -
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Residues in contact with GLN 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 5.3 3.8 - - + +
506A ARG* 2.9 56.1 + - + +
507A LEU* 4.0 8.0 - - + +
508A TYR 3.1 0.4 - - - -
509A GLN* 1.3 78.2 - - + +
511A HIS* 1.3 71.5 + - - +
512A GLY 3.2 2.0 - - - -
513A ALA* 3.0 25.2 + - + +
559A THR* 3.1 39.7 + - - +
560A LEU* 4.1 4.2 - - - +
563A PRO* 5.7 0.5 - - - +
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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