Contacts of the helix formed by residues 514 - 521 (chain B) in PDB entry 1EQR
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 514 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PRO 5.5 1.3 - - - -
196B LEU* 3.6 29.4 - - + -
450B PRO* 3.8 32.5 - - + -
451B PHE* 3.7 19.5 - + + -
500B PHE* 3.3 30.3 - + - -
505B ILE* 4.7 4.0 - - + -
510B GLN* 3.0 24.7 + - - -
512B GLU 3.4 0.4 - - - -
513B LYS* 1.3 113.1 - - + +
515B GLY* 1.3 61.5 + - - +
516B PHE* 3.6 7.9 - - - -
517B LEU* 4.0 9.4 - - + -
518B LEU* 3.1 28.3 + - + +
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Residues in contact with GLY 515 (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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511B ARG* 3.4 46.4 + - - -
512B GLU 4.8 0.6 - - - -
514B PHE* 1.3 72.1 - - - +
516B PHE* 1.3 63.0 + - - +
517B LEU 3.1 1.8 - - - -
518B LEU* 3.2 5.1 + - - +
519B ASP* 2.8 35.3 + - - +
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Residues in contact with PHE 516 (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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123A LYS* 4.6 7.6 - - - +
126A TYR* 4.1 6.7 - - + -
564A MET* 3.2 32.5 - - + +
565A THR* 3.3 38.6 - - + -
167B LYS* 5.4 7.9 - - + -
196B LEU* 3.7 40.2 - - + -
197B PHE* 5.0 5.2 - + - -
200B LEU* 3.7 31.9 - - + -
513B LYS 5.1 2.0 - - - -
514B PHE* 4.4 8.1 - - - -
515B GLY* 1.3 77.9 - - - +
517B LEU* 1.3 69.0 + - + +
519B ASP* 3.2 11.1 + - - +
520B ALA* 2.8 27.6 + - - +
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Residues in contact with LEU 517 (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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196B LEU* 3.7 24.9 - - + +
199B GLN* 4.3 25.4 - - + +
200B LEU* 3.2 29.4 - - + +
203B MET* 5.3 1.1 - - + -
451B PHE* 3.4 44.2 - - + -
514B PHE* 3.7 13.6 + - + +
515B GLY 3.1 0.4 - - - -
516B PHE* 1.3 83.6 - - + +
518B LEU* 1.3 60.2 + - - +
520B ALA* 2.6 33.0 + - + +
521B LEU* 3.0 20.5 + - + +
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Residues in contact with LEU 518 (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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451B PHE* 3.5 33.0 - - + -
496B GLN* 4.3 4.9 - - + -
500B PHE* 3.8 14.8 - - + -
510B GLN* 3.6 45.1 - - + +
511B ARG* 4.7 9.2 - - - +
514B PHE 3.1 21.0 + - - +
515B GLY* 3.6 6.3 - - - +
517B LEU* 1.3 78.5 - - - +
519B ASP* 1.3 65.6 + - - +
521B LEU* 3.4 23.2 + - + +
522B LYS* 4.0 10.7 - - - +
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Residues in contact with ASP 519 (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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123A LYS* 4.8 12.5 + - - -
124A TYR* 5.7 1.9 - - + -
126A TYR* 3.7 15.6 + - - +
511B ARG* 2.5 35.1 + - - -
515B GLY 2.8 12.3 + - - +
516B PHE* 3.3 12.5 - - - +
517B LEU 2.9 0.2 - - - -
518B LEU* 1.3 78.3 - - - +
520B ALA* 1.3 62.7 + - - +
522B LYS* 3.1 49.6 + - + +
523B TYR* 3.6 8.2 - - + +
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Residues in contact with ALA 520 (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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126A TYR* 3.6 29.6 - - + -
130A ARG* 5.1 1.4 + - - -
200B LEU* 4.0 20.2 - - + -
203B MET* 4.1 22.2 - - + +
516B PHE 2.8 13.5 + - - +
517B LEU* 2.6 18.7 + - + +
519B ASP* 1.3 72.4 - - - +
521B LEU* 1.3 56.3 + - - -
522B LYS 3.1 5.0 + - - -
523B TYR* 3.6 16.2 + - - +
525B THR* 5.1 0.9 - - - -
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Residues in contact with LEU 521 (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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203B MET* 3.7 20.2 - - + -
451B PHE* 3.9 31.0 - - + -
490B ILE 5.0 7.0 - - - +
491B HIS* 5.7 1.1 - - - +
493B GLY* 6.4 1.8 - - - -
496B GLN* 5.0 7.2 - - + +
517B LEU* 3.0 15.9 + - + +
518B LEU* 3.7 24.5 - - + +
519B ASP 3.1 1.0 - - - -
520B ALA* 1.3 74.4 - - - +
522B LYS* 1.3 61.8 + - - +
523B TYR 3.4 1.3 + - - -
524B GLY 4.8 0.3 + - - -
525B THR* 3.7 43.3 + - + +
528B HIS* 4.9 5.8 - - + +
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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