Contacts of the helix formed by residues 331 - 343 (chain B) in PDB entry 1D8D
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 HIS 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A THR 3.5 24.5 - - - -
351A ILE* 3.3 26.6 + - + +
353A LYS* 3.7 31.6 + - - +
354A GLU* 5.5 0.9 - - - -
24B TYR* 3.2 37.6 - + - -
281B GLN* 3.0 33.9 + - - +
330B PHE* 1.3 71.4 - - - +
332B GLN* 1.3 63.1 + - - +
333B GLN* 3.3 29.8 - - + +
334B ALA* 3.1 24.6 + - + +
335B LEU 3.1 9.5 + - - -
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Residues in contact with GLN 332 (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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326B SER 4.9 0.2 + - - -
327B HIS* 3.2 30.7 - - + +
328B TRP* 2.9 40.9 + - + +
330B PHE* 2.9 37.8 + - + +
331B HIS* 1.3 71.0 + - - +
333B GLN* 1.3 64.2 + - - +
335B LEU* 3.4 2.8 + - - +
336B GLN* 3.1 32.1 + - - +
372B ILE 4.6 0.2 + - - -
373B ALA* 2.8 32.1 + - - +
374B GLN 4.6 4.9 - - - -
376B PHE* 4.7 8.9 - - - +
383B HIS 5.0 1.0 + - - -
385B VAL* 4.3 14.3 - - + +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LYS* 4.9 4.9 + - - +
22B PRO 3.0 25.1 + - - -
24B TYR* 3.3 17.1 - - - +
27B ARG* 3.7 9.8 + - - +
331B HIS* 3.3 19.4 + - + +
332B GLN* 1.3 78.9 - - - +
334B ALA* 1.3 57.7 + - - +
336B GLN* 3.2 5.1 + - - +
337B GLU* 2.9 55.8 + - - +
385B VAL* 4.9 7.5 - - + +
387B MET* 3.5 32.0 - - + +
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Residues in contact with ALA 334 (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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351A ILE* 3.7 25.8 - - + -
24B TYR* 3.9 14.8 - - + -
25B SER* 5.0 2.4 + - - +
281B GLN* 4.2 0.2 - - - +
285B GLU 4.5 0.3 - - - +
286B GLY* 3.9 14.0 - - - +
331B HIS* 3.1 25.3 + - + +
333B GLN* 1.3 72.9 - - - +
335B LEU* 1.3 61.1 + - - +
337B GLU* 3.3 11.7 + - - +
338B TYR* 2.9 28.9 + - - +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 4.0 4.3 - - - +
286B GLY 3.5 7.1 + - - +
287B GLY* 3.9 22.7 - - - -
288B PHE* 4.1 9.9 - - + -
301B SER* 3.6 28.5 - - - +
305B ALA* 3.9 16.6 - - + -
330B PHE* 3.6 24.9 - - + -
331B HIS 3.1 16.4 + - - +
332B GLN 3.8 4.5 - - - +
334B ALA* 1.3 74.7 - - - +
336B GLN* 1.3 63.3 + - - +
338B TYR* 3.0 4.8 + - + +
339B ILE* 2.9 34.8 + - + +
369B GLY 3.9 21.5 - - - +
373B ALA* 4.0 3.4 - - + -
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Residues in contact with GLN 336 (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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332B GLN 3.1 14.4 + - - +
333B GLN 3.6 7.0 - - - +
335B LEU* 1.3 74.6 - - - +
337B GLU* 1.3 58.6 + - - +
339B ILE* 3.4 1.4 + - - +
340B LEU* 2.9 37.6 + - + +
370B LEU* 3.6 24.4 - - + +
373B ALA* 3.0 31.8 + - + -
374B GLN* 3.6 16.5 + - - +
385B VAL* 2.8 34.1 + - - +
387B MET* 3.0 39.7 + - + +
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Residues in contact with GLU 337 (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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23B LEU* 3.6 10.0 - - + -
24B TYR* 3.0 10.7 + - - +
25B SER* 2.5 45.3 + - - +
59B PHE* 5.3 0.2 - - - -
71B LEU* 4.2 17.5 - - + -
333B GLN* 2.9 54.8 + - - +
334B ALA* 3.6 5.8 - - - +
335B LEU 3.2 0.2 - - - -
336B GLN* 1.3 74.6 - - - +
338B TYR* 1.3 64.7 + - - +
341B MET* 2.9 49.4 + - + +
387B MET* 3.4 9.3 - - + +
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Residues in contact with TYR 338 (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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25B SER* 5.2 0.6 + - - -
55B ILE* 4.0 14.8 - - + -
59B PHE* 5.2 2.2 - - - -
285B GLU* 3.3 31.6 + - + +
287B GLY* 3.6 21.8 - - - +
296B VAL* 3.6 27.9 - - + +
297B ASP 4.5 0.2 - - - -
298B GLY* 4.1 14.1 - - - -
301B SER* 5.0 0.4 - - - -
334B ALA 2.9 11.5 + - - +
335B LEU* 3.0 8.9 + - + +
337B GLU* 1.3 77.4 - - - +
339B ILE* 1.3 64.9 + - + +
342B CYS* 2.8 58.7 + - + +
343B CYS* 3.3 22.8 + - - -
352B ASP 3.0 19.1 + - - -
353B LYS* 3.4 19.2 - - - +
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Residues in contact with ILE 339 (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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73B LEU* 6.1 0.2 - - + -
301B SER* 3.6 27.8 - - - +
335B LEU* 2.9 28.0 + - + +
336B GLN* 3.8 4.5 - - - +
338B TYR* 1.3 79.3 - - + +
340B LEU* 1.3 62.9 + - + +
343B CYS* 3.0 39.0 + - + +
344B GLN* 3.9 1.7 + - - +
350B LEU* 3.9 23.8 - - + -
366B CYS* 3.4 31.2 - - + +
370B LEU* 3.6 35.7 - - + +
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Residues in contact with LEU 340 (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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71B LEU* 4.0 29.6 - - + -
72B VAL 4.4 0.7 - - - -
73B LEU* 3.9 44.6 - - + +
336B GLN* 2.9 30.7 + - + +
337B GLU 4.2 1.1 - - - +
339B ILE* 1.3 74.7 - - + +
341B MET* 1.3 61.7 + - - +
344B GLN* 2.9 30.7 + - - +
370B LEU* 4.2 20.0 - - + -
374B GLN* 6.0 0.4 - - - +
387B MET* 3.9 26.7 - - + +
392B ASN* 3.9 9.2 - - + +
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Residues in contact with MET 341 (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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23B LEU* 4.3 15.5 - - + -
25B SER* 4.2 3.4 - - - +
26B LEU* 4.4 7.4 - - + -
58B VAL* 3.4 22.8 - - + +
59B PHE* 3.9 28.0 - - + -
62B TYR* 3.8 31.4 + - - +
71B LEU* 3.3 24.9 - - + -
337B GLU* 2.9 51.2 + - + +
340B LEU* 1.3 77.6 - - - +
342B CYS* 1.3 64.5 + - - +
344B GLN 5.2 1.2 + - - -
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Residues in contact with CYS 342 (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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55B ILE* 4.0 28.9 - - - -
58B VAL* 3.8 19.3 - - - -
59B PHE* 4.2 11.0 - - - -
338B TYR* 2.8 42.9 + - + +
341B MET* 1.3 78.6 - - - +
343B CYS* 1.3 58.7 + - - +
344B GLN 3.6 3.9 + - - +
351B LEU* 3.7 10.2 - - - +
354B PRO* 3.6 31.2 - - + +
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Residues in contact with CYS 343 (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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298B GLY* 4.2 6.3 - - - -
338B TYR* 3.3 45.8 - - - -
339B ILE* 3.0 21.7 + - + +
342B CYS* 1.3 79.3 - - - +
344B GLN* 1.3 61.4 + - - +
350B LEU* 3.1 7.5 - - + +
351B LEU* 2.8 54.4 + - - +
352B ASP 3.8 6.3 - - - -
366B CYS* 4.0 11.0 - - - -
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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