Contacts of the helix formed by residues 404 - 413 (chain B) in PDB entry 3THY
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 GLU 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B PHE* 3.8 16.1 - - + +
397B GLN 4.2 11.0 - - - +
398B ASP* 3.0 24.4 + - + +
403B SER* 1.3 80.9 + - - +
405B LEU* 1.3 61.8 + - - +
407B THR* 3.6 14.5 + - - +
408B ARG* 2.7 63.4 + - - +
529B ASN* 4.8 3.9 + - - -
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Residues in contact with LEU 405 (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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360B LEU* 5.3 0.9 - - + -
362B ILE* 4.1 25.1 - - + -
379B ILE* 4.3 15.5 - - + -
381B ILE* 4.6 15.9 - - + -
396B PHE* 3.9 13.9 - - + -
398B ASP* 2.7 13.4 + - - +
402B ARG* 3.1 10.3 + - + +
404B GLU* 1.3 71.9 - - - +
406B GLU* 1.3 59.1 + - - +
407B THR 2.9 10.5 + - - -
408B ARG* 3.0 15.9 + - + -
409B MET* 3.0 30.1 + - + +
427B THR* 3.9 24.7 - - + -
430B LEU* 3.6 21.1 - - + -
431B ILE* 5.2 1.1 - - + -
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Residues in contact with GLU 406 (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 SER 5.5 0.4 - - - +
402B ARG 2.9 16.2 + - - +
403B SER* 4.1 13.9 - - - +
404B GLU 3.5 0.2 - - - -
405B LEU* 1.3 75.9 - - - +
407B THR* 1.3 57.7 + - - +
409B MET* 4.0 8.6 - - + +
410B SER* 3.0 43.2 + - - +
430B LEU* 3.9 28.5 - - + +
433B ARG* 5.8 0.2 - - - +
529B ASN* 5.2 0.7 - - - +
530B GLY* 3.9 10.7 - - - +
531B THR* 4.3 5.4 + - - -
534B ARG* 3.2 40.3 + - - -
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Residues in contact with THR 407 (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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403B SER 2.9 17.3 + - - -
404B GLU* 3.6 17.8 + - - +
405B LEU 2.9 0.6 - - - -
406B GLU* 1.3 78.1 - - - +
408B ARG* 1.3 77.8 + - - +
410B SER* 3.1 2.9 + - - -
411B SER* 3.0 26.3 + - - +
527B THR* 6.5 0.2 - - + -
528B ILE 3.5 23.6 - - - +
529B ASN* 3.2 8.7 + - - -
530B GLY* 2.8 24.8 + - - +
533B LEU* 4.5 3.0 - - + +
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Residues in contact with ARG 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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360B LEU* 5.2 1.3 - - + -
381B ILE* 3.7 19.7 - - + -
394B ASP* 2.7 25.7 + - - -
396B PHE* 3.1 56.6 - - + +
404B GLU* 2.7 65.3 + - - +
405B LEU* 3.0 7.4 + - + +
407B THR* 1.3 86.2 - - - +
409B MET* 1.3 58.3 + - + +
411B SER* 3.3 7.9 + - - -
412B LEU* 2.9 35.1 + - + +
519B LEU* 4.4 13.6 - - + +
520B SER* 4.1 14.2 + - - -
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Residues in contact with MET 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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360B LEU* 4.0 12.1 - - + -
362B ILE* 4.6 8.5 - - - -
405B LEU* 3.0 44.5 + - + +
406B GLU* 4.3 6.5 - - + +
408B ARG* 1.3 75.9 - - - +
410B SER* 1.3 59.7 + - - +
412B LEU* 4.5 0.7 - - - -
413B GLN* 2.8 29.1 + - - +
414B PRO* 3.4 15.2 - - + +
417B LEU* 4.0 32.1 - - + -
430B LEU* 4.7 11.9 - - - -
431B ILE* 4.8 6.7 - - + -
434B ALA* 4.3 22.2 - - + -
444B ILE* 4.7 9.4 - - + -
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Residues in contact with SER 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 GLU* 3.0 37.8 + - - +
407B THR 3.1 5.8 + - - -
409B MET* 1.3 76.7 - - - +
411B SER* 1.3 58.0 + - - +
413B GLN* 3.4 19.5 + - - +
530B GLY* 4.3 7.9 - - - -
533B LEU* 4.1 15.8 - - - +
534B ARG* 3.9 11.6 + - - -
539B LEU* 3.8 10.4 - - - +
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Residues in contact with SER 411 (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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407B THR* 3.0 14.8 + - - +
408B ARG* 3.3 12.6 + - - -
410B SER* 1.3 76.5 - - - +
412B LEU* 1.3 70.0 + - - +
413B GLN* 4.2 0.9 - - - -
519B LEU* 5.4 6.6 - - - +
533B LEU* 3.9 13.9 - - - -
539B LEU* 4.0 8.1 - - - -
568B LYS* 4.2 16.5 - - - -
572B THR* 4.3 24.2 + - - +
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Residues in contact with LEU 412 (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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356B THR* 3.8 12.1 + - - +
358B TYR* 4.1 45.4 - - + -
360B LEU* 4.0 34.3 - - + -
383B GLY* 4.9 1.6 - - - -
392B VAL* 4.7 9.0 - - + -
408B ARG 2.9 16.1 + - - +
411B SER* 1.3 83.0 + - - +
413B GLN* 1.3 73.4 + - - +
414B PRO* 4.0 9.2 - - + -
519B LEU* 4.1 38.4 - - + -
568B LYS* 4.1 3.5 + - - -
569B LYS* 6.5 0.4 - - - -
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Residues in contact with GLN 413 (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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354B THR* 3.4 38.5 + - + +
356B THR* 4.2 4.0 + - - -
358B TYR* 4.8 2.1 + - - +
409B MET 2.8 17.5 + - - +
410B SER 3.4 21.6 + - - +
411B SER 4.2 1.8 - - - -
412B LEU* 1.3 79.0 - - - +
414B PRO* 1.3 71.0 - - - +
415B VAL* 3.6 5.5 + - - +
444B ILE* 6.1 0.7 - - - -
539B LEU* 4.4 10.9 - - - +
540B GLN* 3.1 33.1 + - - +
568B LYS* 2.7 28.8 + - - +
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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