Contacts of the helix formed by residues 441 - 452 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B PRO 5.6 1.6 + - - -
354B GLY* 3.4 25.5 + - - +
355B GLU 2.9 12.2 + - - +
357B ILE* 4.0 28.1 - - + +
439B GLN 3.8 1.8 + - - -
440B ALA* 1.3 67.4 - - - +
442B THR* 1.3 56.8 + - - +
443B GLU* 3.7 7.4 + - - +
444B ARG* 3.2 29.4 + - - +
445B ILE* 2.9 31.2 + - - +
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Residues in contact with THR 442 (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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228B ILE* 4.0 32.8 - - + -
440B ALA* 3.0 15.1 + - + +
441B ASN* 1.3 71.8 + - - +
443B GLU* 1.3 60.5 + - - +
445B ILE* 4.2 7.9 - - - -
446B ASN* 2.9 46.6 + - - -
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ASN* 3.2 6.8 + - - +
442B THR* 1.3 82.5 + - - +
444B ARG* 1.3 62.3 + - - +
446B ASN* 3.6 8.3 + - - +
447B LYS* 3.2 21.7 + - - +
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Residues in contact with ARG 444 (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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349B PRO 4.0 19.1 + - - -
350B ARG* 3.7 22.6 + - - +
352B GLY 3.2 25.7 + - - -
353B LEU 3.1 17.2 + - - -
354B GLY* 3.3 23.4 - - - +
441B ASN* 3.1 27.3 + - - +
443B GLU* 1.3 75.6 - - - +
445B ILE* 1.3 61.0 + - - +
447B LYS* 3.2 6.8 + - + +
448B LEU* 2.9 50.8 + - + +
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Residues in contact with ILE 445 (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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228B ILE* 3.8 24.2 - - + -
229B ILE 3.1 31.2 - - - +
230B LYS* 4.1 11.0 - - + -
244B LEU* 3.8 15.7 - - + -
355B GLU* 3.6 40.8 - - + +
440B ALA* 4.4 0.9 - - + -
441B ASN 2.9 27.2 + - - +
442B THR* 3.8 5.4 - - - +
444B ARG* 1.3 76.6 - - + +
446B ASN* 1.3 59.8 + - - +
448B LEU* 3.2 9.1 + - + +
449B MET* 2.8 28.3 + - + +
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Residues in contact with ASN 446 (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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228B ILE* 5.8 1.7 - - - +
229B ILE 5.1 2.3 - - - +
442B THR* 2.9 33.2 + - - +
443B GLU* 3.9 6.6 - - - +
445B ILE* 1.3 80.8 - - - +
447B LYS* 1.3 64.5 + - - +
449B MET* 3.2 7.9 + - - +
450B ASN* 3.0 35.0 + - - +
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Residues in contact with LYS 447 (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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443B GLU 3.2 14.3 + - - +
444B ARG* 3.2 11.2 + - + +
446B ASN* 1.3 77.7 - - - +
448B LEU* 1.3 59.4 + - + +
450B ASN* 3.3 8.3 + - - +
451B GLU* 3.0 56.9 + - + +
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Residues in contact with LEU 448 (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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231B ILE* 4.4 7.2 - - + +
233B ARG* 5.6 4.7 - - - +
353B LEU 4.0 11.7 - - - +
355B GLU* 5.5 5.6 - - + -
444B ARG* 2.9 55.8 + - + +
445B ILE* 3.8 6.3 - - - +
447B LYS* 1.3 76.6 - - + +
449B MET* 1.3 65.5 + - - +
451B GLU* 3.7 17.7 - - + +
452B SER* 3.0 24.6 + - - -
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Residues in contact with MET 449 (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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229B ILE* 3.6 26.0 - - + +
230B LYS* 3.7 19.5 - - - +
231B ILE* 3.5 26.0 - - + -
241B PRO* 4.6 1.3 - - + -
445B ILE 2.8 20.0 + - - +
446B ASN* 3.5 9.6 - - - +
448B LEU* 1.3 77.9 - - - +
450B ASN* 1.3 65.8 + - - +
452B SER* 3.3 17.8 + - - +
455B LEU* 3.8 36.1 - - + +
503B PRO* 3.6 38.4 - - + -
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Residues in contact with ASN 450 (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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446B ASN* 3.0 27.1 + - - +
447B LYS* 3.8 7.5 - - - +
449B MET* 1.3 79.3 - - - +
451B GLU* 1.3 62.2 + - + +
452B SER 3.3 4.2 + - - +
455B LEU* 5.9 0.9 - - - -
481B THR* 3.8 19.2 - - + -
482B LEU* 4.6 3.3 + - - +
483B LYS* 5.5 1.0 + - - +
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Residues in contact with GLU 451 (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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447B LYS* 3.0 36.9 + - + +
448B LEU* 3.7 21.1 - - + +
449B MET 3.2 0.2 - - - -
450B ASN* 1.3 78.1 - - + +
452B SER* 1.3 64.2 + - - +
453B LEU* 3.6 10.6 + - - +
480B SER 5.1 4.0 - - - +
481B THR* 4.1 22.2 - - + -
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Residues in contact with SER 452 (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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231B ILE* 3.4 24.1 - - - +
238B ASP* 4.9 5.9 + - - -
448B LEU 3.0 16.0 + - - -
449B MET 3.3 11.7 + - - +
450B ASN 4.3 3.5 - - - +
451B GLU* 1.3 80.8 - - - +
453B LEU* 1.3 57.8 + - - +
454B MET* 3.0 31.9 + - - +
455B LEU* 4.6 5.6 + - - +
482B LEU* 3.4 21.3 - - - +
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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