Contacts of the helix formed by residues 398 - 411 (chain B) in PDB entry 1O94
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 GLY 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B GLY 3.7 2.6 - - - -
397B ALA* 1.3 75.5 - - - +
399B PRO* 1.3 78.4 - - - -
400B SER 3.0 3.6 + - - -
401B GLY 3.3 0.8 + - - +
402B SER* 2.7 25.2 + - - -
425B GLY* 3.6 2.2 - - - -
426B GLY* 3.6 13.1 - - - +
1731B ADP 3.2 24.4 + - - -
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Residues in contact with PRO 399 (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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398B GLY* 1.3 82.4 - - - +
400B SER* 1.3 59.5 + - - +
402B SER* 3.6 5.9 + - - +
403B GLU* 3.2 25.6 + - - +
425B GLY* 3.7 13.2 - - - +
427B HIS* 4.0 9.9 - - + +
428B LEU* 4.7 7.0 - - + -
443B HIS* 3.5 27.5 - - + +
681B ILE* 3.9 24.2 - - + +
684B ALA* 4.6 2.0 - - + -
685B THR* 3.6 16.1 + - - +
1731B ADP 3.3 28.3 - - - +
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PRO* 1.3 75.8 - - - +
401B GLY* 1.3 58.4 + - - +
404B ALA 3.0 23.9 + - - -
486B ALA* 3.8 6.6 - - - +
672B ILE* 3.5 19.1 + - - +
673B GLY* 3.6 21.2 - - - -
684B ALA* 3.1 27.1 + - - -
687B THR* 3.8 0.2 - - - -
688B GLY* 3.4 10.4 - - - -
1731B ADP 2.9 33.4 + - - -
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Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ILE* 3.7 12.5 - - - +
396B GLY 3.3 24.0 + - - -
398B GLY 3.3 4.0 + - - +
400B SER* 1.3 81.4 + - - +
402B SER* 1.3 57.6 + - - +
404B ALA* 3.5 2.4 + - - +
405B ALA* 2.9 29.5 + - - +
417B LEU* 4.4 1.6 - - - -
486B ALA* 3.6 14.8 - - - +
672B ILE* 4.2 2.2 - - - -
1731B ADP 4.2 0.8 + - - -
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Residues in contact with SER 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ALA* 3.8 16.4 + - - +
398B GLY 2.7 27.5 + - - -
399B PRO* 3.6 1.7 + - - +
401B GLY* 1.3 73.7 - - - +
403B GLU* 1.3 59.8 + - - +
405B ALA* 3.4 4.3 + - - +
406B ARG* 2.9 28.9 + - - +
417B LEU* 4.4 3.8 - - - -
424B ILE* 4.2 7.6 - - - +
425B GLY* 5.3 0.5 + - - -
444B ARG* 5.9 0.5 - - - +
447B ARG* 3.4 27.5 - - - +
451B ILE* 3.6 22.5 - - - +
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA* 4.3 5.5 + - - +
399B PRO 3.2 21.4 + - - +
400B SER 3.9 1.3 - - - +
402B SER* 1.3 73.2 + - - +
404B ALA* 1.3 67.4 + - - +
406B ARG* 2.9 32.1 + - - +
407B VAL* 2.9 24.7 + - - +
447B ARG* 2.9 37.8 + - - +
685B THR* 3.4 30.5 - - + +
688B GLY 4.4 0.4 - - - -
689B HIS* 2.7 35.9 + - + +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ILE* 3.9 12.6 - - + -
400B SER 3.0 17.9 + - - +
401B GLY* 3.6 5.6 - - - +
403B GLU* 1.3 74.3 - - - +
405B ALA* 1.3 57.6 + - - +
407B VAL 3.4 0.2 + - - -
408B LEU* 2.9 36.6 + - + +
484B ILE* 4.3 13.9 - - + -
672B ILE* 4.1 11.4 - - + -
688B GLY* 3.4 26.8 - - - +
691B VAL* 4.4 1.1 - - + -
692B ALA* 3.8 2.9 - - + +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ILE* 3.5 17.1 - - + +
401B GLY 2.9 18.4 + - - +
402B SER 3.5 4.9 - - - +
404B ALA* 1.3 72.5 - - - +
406B ARG* 1.3 67.1 + - - +
408B LEU* 4.7 0.2 - - - -
409B MET* 3.0 33.1 + - - +
415B VAL* 4.1 13.5 - - + -
417B LEU* 3.7 24.0 - - + -
451B ILE* 4.1 6.5 - - + -
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Residues in contact with ARG 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 4.4 13.9 - - - +
366B GLN 5.6 0.4 + - - -
368B ALA 6.2 0.2 - - - +
380B PRO 5.2 1.2 + - - -
383B PHE* 4.1 18.8 - - - -
402B SER 2.9 16.5 + - - +
403B GLU* 2.9 42.6 + - - +
405B ALA* 1.3 78.1 - - - +
407B VAL* 1.3 65.1 + - - +
409B MET 3.5 0.2 + - - -
410B GLU* 3.0 44.9 + - + +
446B TYR* 3.2 41.8 + - - -
447B ARG* 4.5 7.3 - - + +
450B GLN* 4.0 17.2 + - + -
451B ILE* 4.5 9.8 - - + +
454B LEU* 3.6 22.8 - - + +
689B HIS* 4.0 15.0 - - - -
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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
----------------------------------------------------------
383B PHE* 3.9 21.3 - - + -
403B GLU* 2.9 23.9 + - - +
406B ARG* 1.3 84.7 - - - +
408B LEU* 1.3 56.9 + - - +
410B GLU* 3.3 7.3 + - - +
411B SER* 2.9 37.1 + - - +
689B HIS* 3.3 39.9 - - + +
692B ALA* 3.5 25.6 - - + -
693B ARG* 4.3 15.0 - - + +
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Residues in contact with LEU 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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392B VAL* 4.0 19.7 - - + -
394B ILE* 4.0 9.2 - - + -
404B ALA 2.9 21.6 + - - +
405B ALA 4.1 0.2 - - - +
407B VAL* 1.3 75.6 - - - +
409B MET* 1.3 62.6 + - - +
411B SER* 3.2 2.5 + - - -
412B GLY 3.1 5.2 + - - -
413B TYR* 3.0 49.8 + - + -
415B VAL* 3.6 16.4 - - + -
484B ILE* 3.8 29.2 - - + -
692B ALA* 3.7 29.6 - - + +
695B ILE* 3.9 17.9 - - + -
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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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405B ALA* 3.0 24.5 + - - +
406B ARG 4.1 1.6 - - - +
408B LEU* 1.3 75.0 - - - +
410B GLU* 1.3 65.0 + - - +
412B GLY* 3.0 14.6 + - - -
413B TYR 4.2 7.1 - - - +
415B VAL* 3.5 26.9 - - + +
451B ILE* 4.6 14.8 - - - +
454B LEU* 3.9 38.8 - - + +
455B LEU* 4.5 13.5 - - - -
458B ASN* 5.9 4.2 - - + +
461B SER* 4.1 23.6 - - - +
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Residues in contact with GLU 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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383B PHE* 3.7 43.4 - - + +
385B GLN* 3.2 18.9 + - - +
406B ARG* 3.0 35.5 + - - +
407B VAL 3.5 5.2 - - - +
409B MET* 1.3 75.6 - - - +
411B SER* 1.3 57.2 + - - +
412B GLY 3.2 0.9 + - - -
450B GLN* 3.9 14.6 - - - +
454B LEU* 3.6 27.2 - - + +
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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
----------------------------------------------------------
383B PHE* 3.6 12.7 - - - +
384B ARG 3.2 22.0 + - - -
385B GLN* 3.4 10.9 - - - +
386B THR* 2.9 30.0 + - - +
407B VAL* 2.9 27.5 + - - +
408B LEU* 3.7 5.8 - - - -
409B MET 3.1 0.8 - - - -
410B GLU* 1.3 75.0 - - - +
412B GLY* 1.3 57.6 + - - +
413B TYR* 3.5 18.5 + - - -
692B ALA 5.1 4.0 + - - -
693B ARG* 5.9 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