Contacts of the helix formed by residues 529 - 535 (chain B) in PDB entry 1ED8
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 GLN 529 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A ALA* 4.1 16.6 - - - +
428A ASN* 2.8 23.3 + - - +
430A VAL 5.8 0.4 - - - +
507B LEU* 4.7 5.2 - - - +
510B ARG* 3.0 31.6 + - - +
525B LEU* 4.1 16.9 - - + +
526B THR* 4.7 6.3 + - - +
527B GLY 2.9 28.1 + - - +
528B ASP* 1.3 75.8 + - - +
530B THR* 1.3 66.3 + - - +
531B ALA 3.3 2.5 - - - -
532B ALA* 3.1 21.0 + - + +
533B LEU* 2.9 28.5 + - + +
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Residues in contact with THR 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.3 8.4 - - + +
38A SER 4.0 15.5 + - - +
39A ASP* 3.7 23.4 - - + +
425A HIS* 4.7 3.3 - - - -
427A ALA* 3.8 19.3 - - + +
428A ASN* 5.1 0.2 + - - -
528B ASP* 2.9 24.0 + - - -
529B GLN* 1.3 77.7 - - - +
531B ALA* 1.3 62.3 + - - +
533B LEU* 3.3 2.9 + - - +
534B ARG* 3.1 57.3 + - - +
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Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP* 5.6 1.7 + - - +
528B ASP* 4.5 3.7 + - - +
529B GLN 3.3 0.6 - - - -
530B THR* 1.3 80.3 - - - +
532B ALA* 1.3 61.9 + - - +
534B ARG* 3.3 18.0 + - - +
535B ASP* 3.1 30.2 + - - +
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B PRO* 4.1 10.6 - - + +
507B LEU* 6.2 2.7 - - + -
528B ASP 5.3 1.9 + - - +
529B GLN* 3.1 29.7 + - + +
531B ALA* 1.3 77.9 - - - +
533B LEU* 1.3 63.3 + - + +
535B ASP* 3.4 10.2 + - - +
536B SER* 2.9 26.4 + - - -
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 5.5 2.5 - - + -
37A LEU* 4.0 27.4 - - + -
80A LEU* 4.6 6.5 - - + -
427A ALA* 4.4 9.2 - - + +
430A VAL* 4.1 29.8 - - + +
507B LEU* 6.3 1.6 - - + -
510B ARG* 6.0 3.8 - - - +
529B GLN* 2.9 20.1 + - + +
530B THR 3.8 3.1 - - - +
532B ALA* 1.3 78.1 - - + +
534B ARG* 1.3 58.2 + - - +
536B SER* 2.7 27.5 + - - +
537B LEU* 3.4 12.2 + - + +
579B PRO* 4.1 29.6 - - + +
580B LEU* 3.9 24.2 - - + -
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Residues in contact with ARG 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 5.3 8.1 + - + +
37A LEU* 3.2 51.3 + - + +
38A SER* 4.0 6.3 - - - +
39A ASP* 4.1 19.4 + - - +
40A LYS* 5.5 4.6 - - - +
530B THR* 3.1 33.6 + - - +
531B ALA* 3.5 18.9 - - - +
533B LEU* 1.3 75.1 - - - +
535B ASP* 1.3 61.0 - - - +
537B LEU* 3.1 29.5 + - + +
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Residues in contact with ASP 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B GLU* 3.6 11.7 - - - +
504B MET* 3.2 21.1 - - - +
505B PRO* 3.7 10.6 - - + +
531B ALA* 3.1 15.8 + - - +
532B ALA* 3.5 13.1 - - - +
534B ARG* 1.3 78.8 - - - +
536B SER* 1.3 59.0 + - - +
537B LEU 3.3 2.3 + - - -
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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