Contacts of the helix formed by residues 529 - 534 (chain D) in PDB entry 5ED1
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D ARG* 4.0 0.7 - - - -
404D LEU* 3.6 23.4 - - - +
407D LEU* 4.3 14.1 - - + -
526D VAL 3.3 18.1 + - - +
527D GLY* 3.4 3.6 - - - -
528D ILE* 1.3 88.7 + - - +
530D GLY* 1.3 77.2 + - - +
533D LEU* 3.5 24.9 + - + +
534D SER* 3.6 27.1 - - - +
537D VAL* 4.1 14.4 - - + -
539D PRO* 4.0 14.2 - - - +
540D ILE* 3.2 24.9 + - + +
574D TYR* 4.6 1.2 + - - -
668D TYR* 3.6 7.5 - - - -
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Residues in contact with GLY 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D ARG* 4.0 7.1 - - - +
404D LEU* 5.8 0.2 - - - -
527D GLY 4.5 1.4 + - - -
528D ILE 3.4 3.2 + - - -
529D GLN* 1.3 91.7 + - - +
531D SER* 1.3 67.2 + - - -
532D LEU 3.3 1.6 - - - -
534D SER* 3.1 18.7 + - - -
668D TYR* 3.5 24.4 + - - -
801D IHP 3.6 11.2 - - - -
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Residues in contact with SER 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D GLY* 1.3 71.1 - - - -
532D LEU* 1.3 70.2 + - - +
534D SER* 2.9 18.4 + - - -
535D ILE* 3.7 1.2 - - - +
662D LYS* 3.2 37.1 - - - +
665D ALA* 3.2 12.3 - - - +
668D TYR* 3.4 32.8 - - - -
669D GLN* 4.2 2.9 - - - -
801D IHP 2.6 30.5 + - - -
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Residues in contact with LEU 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D TYR* 3.9 8.5 - - - +
530D GLY 3.3 1.0 - - - -
531D SER* 1.3 84.9 + - - +
533D LEU* 1.3 62.9 + - - +
535D ILE* 3.1 15.3 + - + +
536D PHE 4.4 0.2 + - - -
632D LEU* 5.5 3.1 - - + -
633D TYR* 4.0 15.7 - - + +
636D TRP* 3.1 44.9 + - + -
658D TYR* 3.5 34.3 - - + +
661D SER* 3.8 42.0 - - - +
662D LYS* 3.8 14.6 - - + +
801D IHP 5.0 0.4 + - - -
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D LEU* 3.9 12.1 - - + +
407D LEU* 3.8 35.9 - - + -
408D TYR* 3.7 43.7 + - + +
411D LEU* 4.0 25.1 - - + -
529D GLN* 3.5 31.1 + - + +
530D GLY 3.6 1.6 + - - -
531D SER 3.5 0.2 - - - -
532D LEU* 1.3 72.9 - - - +
534D SER* 1.3 57.9 + - - +
535D ILE 2.8 11.9 + - - -
536D PHE* 2.8 20.1 + - + +
537D VAL* 3.0 21.6 + - + +
636D TRP* 4.7 1.6 - - - +
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Residues in contact with SER 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D GLN* 3.6 19.2 - - - +
530D GLY 3.1 16.9 + - - -
531D SER 2.9 14.6 + - - -
532D LEU 3.2 0.4 - - - -
533D LEU* 1.3 75.5 - - - +
535D ILE* 1.3 58.6 + - - +
536D PHE 3.3 0.4 - - - -
537D VAL 3.0 23.7 - - - +
539D PRO 5.7 0.4 - - - -
574D TYR* 4.2 12.6 + - - -
649D ARG* 3.2 19.8 + - - +
650D SER* 5.8 0.3 - - - -
665D ALA* 3.5 14.2 - - - +
668D TYR* 3.7 9.2 + - - +
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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