Contacts of the helix formed by residues 436 - 445 (chain B) in PDB entry 4QYJ
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 ASP 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 4.8 0.7 - - + +
279B ASP* 3.9 13.8 + - - +
434B THR* 3.3 17.2 - - - +
435B ASN* 1.3 74.6 - - - +
437B LEU* 1.3 66.8 + - - +
438B SER* 3.0 25.5 + - - -
439B ALA* 3.5 15.5 + - + +
440B ALA* 2.9 22.2 + - - +
435C ASN* 3.6 16.1 + - - +
437C LEU* 4.8 0.4 - - - -
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ASN 3.3 5.9 + - - -
436B ASP* 1.3 70.7 - - - +
438B SER* 1.3 67.3 + - - +
440B ALA* 4.0 2.8 - - - +
441B LEU* 3.0 64.7 + - + +
434C THR 5.0 3.8 - - - +
435C ASN* 3.3 19.1 + - - +
437C LEU* 3.8 36.1 - - + +
440C ALA* 5.0 10.1 - - + -
441C LEU* 5.6 4.9 - - + -
454C VAL* 4.2 25.4 - - + -
455C ASN* 4.5 11.9 - - - +
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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
----------------------------------------------------------
436B ASP* 3.0 13.0 + - - -
437B LEU* 1.3 80.4 - - - +
439B ALA* 1.3 68.5 + - - +
441B LEU* 3.4 3.8 + - - +
442B ARG* 2.9 26.9 + - - +
435C ASN* 3.7 15.1 + - - -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 4.0 15.7 - - + -
414B ILE* 4.3 17.5 - - + -
436B ASP* 3.3 25.0 + - + +
438B SER* 1.3 80.0 + - - +
440B ALA* 1.3 64.2 + - - +
442B ARG* 2.9 5.2 + - - +
443B ILE* 2.8 32.0 + - + +
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Residues in contact with ALA 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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277B LEU* 4.8 0.4 - - - +
432B ILE* 3.4 21.0 - - + +
434B THR* 3.5 24.5 - - + +
436B ASP 2.9 19.0 + - - +
437B LEU* 4.0 3.8 - - - +
439B ALA* 1.3 76.7 - - - +
441B LEU* 1.3 62.4 + - + +
444B ASN* 3.3 18.0 + - - +
454B VAL* 4.3 19.9 - - + +
437C LEU* 5.4 6.5 - - + -
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Residues in contact with LEU 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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492A LEU* 4.8 13.0 - - + -
494A ILE* 4.8 18.6 - - + -
437B LEU* 3.0 50.9 + - + +
438B SER* 3.8 3.4 - - - +
440B ALA* 1.3 80.7 - - + +
442B ARG* 1.3 58.6 + - - +
443B ILE 3.5 0.2 - - - -
444B ASN* 3.7 8.5 - - - +
445B ASP* 3.2 29.1 + - - +
437C LEU* 5.7 0.9 - - + -
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Residues in contact with ARG 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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438B SER 2.9 19.1 + - - +
439B ALA* 3.9 3.8 - - - +
441B LEU* 1.3 74.9 - - - +
443B ILE* 1.3 64.5 + - - +
444B ASN 3.3 0.2 - - - -
445B ASP* 3.5 23.0 - - + +
446B GLU* 3.6 15.8 - - - +
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Residues in contact with ILE 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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275B ILE* 4.8 11.7 - - + -
277B LEU* 4.2 21.8 - - + -
414B ILE* 4.2 29.8 - - + -
417B VAL* 5.3 2.2 - - + -
418B VAL* 3.9 20.8 - - + +
432B ILE* 3.9 40.4 - - + -
439B ALA* 2.8 20.3 + - - +
442B ARG* 1.3 76.5 - - - +
444B ASN* 1.3 58.8 + - - +
446B GLU* 2.9 18.0 + - - +
447B LEU* 3.0 23.4 + - + +
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Residues in contact with ASN 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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155A GLN* 4.9 6.1 - - - +
490A ARG* 2.4 46.4 + - - +
491A SER 4.8 1.6 + - - -
492A LEU* 3.6 34.8 - - + +
432B ILE* 4.2 8.2 - - + +
440B ALA 3.3 16.7 + - - +
441B LEU* 3.7 9.8 - - - +
443B ILE* 1.3 79.5 - - - +
445B ASP* 1.3 58.7 + - - +
446B GLU 3.4 0.2 + - - -
447B LEU* 3.9 7.2 + - - +
452B VAL* 3.5 29.5 - - - +
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLN* 4.8 10.5 + - - +
490A ARG* 4.4 6.1 + - - +
441B LEU* 3.2 14.6 + - - +
442B ARG* 3.5 20.6 - - + +
444B ASN* 1.3 81.1 - - - +
446B GLU* 1.3 72.0 + - + +
447B LEU 4.5 1.6 - - - +
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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