Contacts of the helix formed by residues 436 - 443 (chain B) in PDB entry 4LEY
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 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A GLU* 5.7 3.2 + - - +
488A PHE* 5.5 7.4 - - + -
491A LYS* 4.3 27.5 - - + +
380B ILE* 3.1 27.9 - - - +
434B ASP 3.3 0.8 - - - -
435B PRO* 1.3 80.0 - - + +
437B ASP* 1.3 60.1 + - - +
438B SER* 3.4 21.2 + - - +
439B GLN* 3.0 37.8 + - + +
440B TRP* 3.1 17.5 - - - -
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Residues in contact with ASP 437 (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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379B GLY* 3.4 0.5 - - - -
380B ILE* 3.2 23.2 + - + +
381B GLU* 3.1 39.6 + - + +
384B CYS* 3.8 19.0 - - - +
392B CYS* 4.7 3.3 - - + +
394B ARG* 2.9 33.9 + - - +
435B PRO 3.4 0.2 + - - -
436B GLN* 1.3 70.0 - - - +
438B SER* 1.3 59.9 + - - +
440B TRP* 2.9 28.3 + - - +
441B ASP* 3.5 1.6 + - - -
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Residues in contact with SER 438 (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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436B GLN* 3.4 21.6 + - - +
437B ASP* 1.3 79.2 - - - +
439B GLN* 1.3 59.8 + - - +
440B TRP 3.1 3.7 + - - -
441B ASP* 3.6 20.5 + - - +
444B ASN* 4.5 8.3 + - - -
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Residues in contact with GLN 439 (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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414A GLU* 5.0 2.8 + - - -
488A PHE* 3.6 31.7 - - + -
492A LYS* 4.5 1.8 - - - +
434B ASP* 3.6 42.0 + - + +
435B PRO* 3.8 4.0 - - - +
436B GLN* 3.0 44.0 + - + +
438B SER* 1.3 78.7 + - - +
440B TRP* 1.3 65.5 + - - +
441B ASP 3.7 0.9 - - - -
444B ASN* 5.8 1.8 - - - +
448B CYS* 3.2 20.3 - - - -
451B LYS* 4.7 8.5 - - - +
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Residues in contact with TRP 440 (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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392B CYS* 3.1 14.4 - - + +
393B CYS* 2.9 25.0 + - - +
394B ARG* 3.6 46.8 - - + +
397B CYS* 4.1 17.9 - - + -
427B ILE* 5.1 3.6 - - + -
430B MET* 4.0 31.6 - - + -
431B TRP* 3.5 28.9 - + - -
434B ASP* 2.6 37.9 + - + +
436B GLN 3.1 24.2 - - - -
437B ASP 2.9 10.6 + - - +
439B GLN* 1.3 83.1 - - - +
441B ASP* 1.3 59.5 + - - +
448B CYS* 4.0 34.8 - - + -
451B LYS* 5.9 1.3 - - + -
452B LEU* 5.3 3.8 - - + -
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Residues in contact with ASP 441 (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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391B LYS 4.9 1.2 - - - +
393B CYS* 3.4 8.5 - - - -
437B ASP 3.5 3.0 + - - +
438B SER* 3.6 18.2 + - - +
439B GLN 3.7 1.2 - - - -
440B TRP* 1.3 75.7 - - - +
442B PRO* 1.3 67.7 - - - +
443B ARG* 3.1 45.2 + - - +
444B ASN* 2.8 41.9 + - - +
448B CYS* 4.8 1.0 - - - -
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Residues in contact with PRO 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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151B LYS* 5.1 7.4 - - - -
391B LYS* 3.3 39.5 - - + +
392B CYS 4.3 7.4 - - - +
393B CYS* 3.9 14.1 - - + -
440B TRP 3.7 2.7 - - - +
441B ASP* 1.3 94.4 - - - +
443B ARG* 1.3 58.9 + - + +
445B LEU* 2.9 28.9 + - - +
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Residues in contact with ARG 443 (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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151B LYS* 5.8 4.7 - - - +
441B ASP* 3.1 19.8 + - - +
442B PRO* 1.3 78.4 - - + +
444B ASN* 1.3 64.9 + - - +
445B LEU* 3.3 2.5 + - - +
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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