Contacts of the helix formed by residues 441 - 452 (chain A) in PDB entry 6EBT
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 ASN 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A PRO 5.8 1.8 + - - -
354A GLY* 3.3 25.0 + - - +
355A GLU 2.8 13.6 + - - +
357A ILE* 4.1 25.9 - - + +
439A GLN 3.9 1.6 + - - -
440A ALA* 1.3 68.5 - - - +
442A THR* 1.3 57.0 + - - +
443A GLU* 3.7 8.8 + - - +
444A ARG* 3.1 29.8 + - - +
445A ILE* 2.8 31.3 + - - +
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Residues in contact with THR 442 (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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228A ILE* 3.7 37.2 - - + -
440A ALA* 3.0 14.0 + - + +
441A ASN* 1.3 74.8 - - - +
443A GLU* 1.3 63.0 + - - +
445A ILE* 3.7 7.5 - - - +
446A ASN* 2.8 34.7 + - - +
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Residues in contact with GLU 443 (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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441A ASN* 3.2 7.3 + - - +
442A THR* 1.3 82.1 + - - +
444A ARG* 1.3 56.8 + - - +
446A ASN* 3.9 4.9 + - - +
447A LYS* 3.0 29.4 + - - +
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Residues in contact with ARG 444 (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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349A PRO 4.2 16.7 + - - -
350A ARG* 4.0 19.8 + - - +
352A GLY 3.0 27.7 + - - -
353A LEU* 2.8 19.9 + - - +
354A GLY* 3.3 21.2 - - - +
355A GLU* 6.3 0.4 - - + -
441A ASN* 3.1 29.1 + - - +
443A GLU* 1.3 74.5 - - - +
445A ILE* 1.3 66.5 + - + +
447A LYS* 3.4 10.0 + - + +
448A LEU* 3.0 48.7 + - + +
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Residues in contact with ILE 445 (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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228A ILE* 3.9 24.9 - - + -
229A ILE 3.2 26.7 - - - +
230A LYS* 3.8 15.0 - - + -
244A LEU* 4.1 12.6 - - + -
355A GLU* 3.6 51.1 - - + +
440A ALA* 4.4 0.9 - - + -
441A ASN 2.8 21.5 + - - +
442A THR* 3.7 4.5 - - - +
444A ARG* 1.3 78.6 - - + +
446A ASN* 1.3 64.1 + - - +
448A LEU* 3.3 6.2 + - - +
449A MET* 3.0 22.0 + - - +
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Residues in contact with ASN 446 (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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229A ILE 5.6 0.4 - - - -
442A THR 2.8 20.4 + - - +
443A GLU* 4.1 4.7 + - - +
445A ILE* 1.3 77.0 - - - +
447A LYS* 1.3 62.3 + - - +
449A MET* 3.2 9.5 + - - +
450A ASN* 3.1 43.5 + - - +
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Residues in contact with LYS 447 (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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443A GLU 3.0 18.8 + - - +
444A ARG* 3.7 11.0 - - + +
446A ASN* 1.3 79.4 - - - +
448A LEU* 1.3 62.9 + - + +
450A ASN* 3.3 10.5 + - - +
451A GLU* 3.0 51.5 + - + +
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Residues in contact with LEU 448 (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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231A ILE* 4.3 8.6 - - + +
233A ARG* 5.4 8.1 - - - +
353A LEU* 4.3 8.1 - - - +
355A GLU* 5.9 3.6 - - + -
444A ARG* 3.0 52.5 + - + +
445A ILE* 3.9 4.9 - - - +
447A LYS* 1.3 79.0 - - + +
449A MET* 1.3 60.0 + - - +
451A GLU* 3.7 23.0 - - + +
452A SER* 3.0 30.0 + - - -
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Residues in contact with MET 449 (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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229A ILE* 3.7 25.6 - - + +
230A LYS* 3.9 18.4 - - - +
231A ILE* 3.4 33.9 - - + -
241A PRO* 4.6 1.3 - - + -
445A ILE 3.0 17.9 + - - +
446A ASN* 3.4 14.4 - - - +
447A LYS 3.2 0.4 - - - -
448A LEU* 1.3 77.4 - - - +
450A ASN* 1.3 66.1 + - - +
451A GLU 3.4 0.3 + - - -
452A SER* 3.4 11.6 + - - +
455A LEU* 3.7 34.3 - - + +
503A PRO* 3.4 42.2 - - + -
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Residues in contact with ASN 450 (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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446A ASN* 3.1 39.2 + - - +
447A LYS* 3.3 8.3 + - - +
449A MET* 1.3 78.2 - - - +
451A GLU* 1.3 62.7 + - + +
452A SER 3.4 3.3 + - - +
481A THR* 3.6 21.7 - - + -
482A LEU* 4.5 4.0 + - - +
483A LYS 5.6 0.3 + - - -
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Residues in contact with GLU 451 (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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447A LYS* 3.0 42.8 + - + +
448A LEU* 3.5 22.3 + - + +
449A MET 3.2 0.2 - - - -
450A ASN* 1.3 78.5 - - + +
452A SER* 1.3 62.7 + - - +
453A LEU* 3.8 7.8 + - - +
480A SER 5.1 4.9 - - - +
481A THR* 4.2 22.0 - - + -
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Residues in contact with SER 452 (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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231A ILE* 3.5 24.3 - - - +
238A ASP* 4.9 6.9 + - - -
448A LEU 3.0 17.0 + - - -
449A MET 3.8 8.8 - - - +
450A ASN 3.4 4.0 - - - +
451A GLU* 1.3 81.0 - - - +
453A LEU* 1.3 61.8 + - - +
454A MET* 3.0 27.0 + - - +
455A LEU* 4.6 4.0 + - - +
482A LEU* 3.2 23.0 - - - +
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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