Contacts of the helix formed by residues 404 - 413 (chain B) in PDB entry 5TQW
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 SER 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B SER* 3.2 2.1 - - - +
403B LEU* 1.3 76.0 - - - +
405B ASP* 1.3 55.4 + - - +
406B CYS* 3.6 8.7 + - - +
407B VAL* 3.3 31.0 + - - +
408B ASN* 2.7 27.4 + - - -
425B LYS* 5.2 1.0 + - - -
426B VAL* 4.9 0.2 - - - +
429B GLU* 2.8 36.9 + - - -
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ARG* 5.2 5.0 + - - -
402B SER 4.1 1.2 - - - +
403B LEU 3.4 12.0 + - - +
404B SER* 1.3 71.2 + - - +
406B CYS* 1.3 62.3 + - - +
407B VAL 3.3 0.4 - - - -
408B ASN* 2.8 24.8 + - + +
409B TYR* 2.9 47.7 + - + +
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Residues in contact with CYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B SER* 3.3 8.9 + - - +
405B ASP* 1.3 77.8 - - - +
407B VAL* 1.3 60.1 + - - +
409B TYR* 3.1 22.1 + - + +
410B ILE* 2.9 30.1 + - - +
416B ILE* 5.2 3.3 - - + +
418B LEU* 5.5 8.5 - - + +
422B GLN* 5.3 5.6 - - - -
425B LYS* 6.2 1.6 - - - -
426B VAL* 4.3 19.5 - - + -
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B SER* 3.8 18.8 - - - -
404B SER* 3.3 32.2 + - - +
406B CYS* 1.3 75.0 - - - +
408B ASN* 1.3 61.1 + - - +
410B ILE* 3.2 11.1 + - + +
411B VAL* 2.9 29.5 + - + +
426B VAL* 3.8 24.4 - - + +
429B GLU* 4.9 3.8 - - + +
430B ALA* 4.3 24.0 - - + -
433B TYR* 6.5 0.7 - - + -
586B MET* 5.7 2.0 - - + -
590B ILE* 4.5 15.5 - - + -
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Residues in contact with ASN 408 (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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401B ARG* 5.6 1.2 - - - +
402B SER* 2.0 38.2 + - - -
404B SER 2.7 18.5 + - - -
405B ASP* 2.8 29.5 + - + +
407B VAL* 1.3 79.8 - - - +
409B TYR* 1.3 61.0 + - + +
411B VAL* 3.4 10.3 + - - +
412B GLN* 2.9 33.3 + - - +
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Residues in contact with TYR 409 (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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405B ASP* 2.9 33.0 + - + +
406B CYS* 3.1 23.3 + - + +
408B ASN* 1.3 79.3 - - + +
410B ILE* 1.3 51.1 + - - +
412B GLN* 3.2 19.3 + - - +
413B ASP* 2.4 40.9 + - - +
416B ILE* 4.1 21.8 - - + -
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Residues in contact with ILE 410 (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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406B CYS 2.9 14.3 + - - +
407B VAL* 3.2 13.9 + - + +
409B TYR* 1.3 73.7 - - - +
411B VAL* 1.3 64.1 + - - +
413B ASP 3.3 9.4 - - - +
414B SER* 2.9 34.5 + - - +
416B ILE* 4.6 11.9 - - + +
418B LEU* 4.6 13.5 - - + -
423B LEU* 6.1 1.3 - - + -
426B VAL* 3.7 31.4 - - + -
427B TRP* 5.1 4.7 - - + +
583B SER* 3.6 34.3 - - - +
586B MET* 5.4 2.5 - - + -
587B VAL* 3.3 19.9 - - + +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 2.9 21.9 + - + +
408B ASN* 3.7 10.8 - - - +
409B TYR 3.3 0.2 - - - -
410B ILE* 1.3 76.4 - - - +
412B GLN* 1.3 64.7 + - + +
587B VAL* 3.6 27.4 - - + +
590B ILE* 3.8 35.4 - - + -
591B VAL* 4.9 10.3 - - + -
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASN* 2.9 19.6 + - - +
409B TYR* 3.5 24.2 - - - +
410B ILE 3.9 0.2 - - - -
411B VAL* 1.3 80.7 - - + +
413B ASP* 1.3 61.6 + - + +
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Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR 2.4 30.1 + - - +
410B ILE* 3.2 1.4 - - - -
412B GLN* 1.3 71.7 - - + +
414B SER* 1.3 64.3 + - - +
415B LYS* 3.2 34.5 + - - +
416B ILE* 3.2 24.9 - - + +
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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