Contacts of the helix formed by residues 398 - 411 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A GLY 3.6 3.8 + - - -
397A ALA* 1.3 76.3 - - - +
399A PRO* 1.3 72.3 - - - +
400A SER 3.1 4.2 + - - -
401A GLY 3.3 1.0 + - - +
402A SER* 2.7 29.7 + - - -
425A GLY* 4.4 1.3 - - - -
426A GLY* 3.6 16.1 - - - +
486A ALA 5.1 0.2 + - - -
1731A ADP 3.2 20.0 + - - -
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Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLY* 1.3 82.2 - - - +
400A SER* 1.3 55.9 + - - +
402A SER* 3.7 5.5 + - - +
403A GLU* 3.1 29.8 + - - +
425A GLY* 3.5 15.0 - - - +
427A HIS* 4.1 10.1 - - + +
428A LEU* 4.6 7.0 - - + -
443A HIS* 3.6 19.2 - - + +
681A ILE* 3.9 21.5 - - + +
684A ALA* 4.6 1.3 - - + -
685A THR* 3.6 27.3 + - - +
1731A ADP 3.4 27.4 - - - +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A PRO* 1.3 71.5 - - - +
401A GLY* 1.3 61.7 + - - +
403A GLU 3.4 0.3 + - - -
404A ALA* 3.0 24.8 + - - +
486A ALA* 3.6 13.9 - - - +
672A ILE* 3.8 10.7 - - - +
673A GLY* 3.6 18.5 - - - -
684A ALA 3.0 26.4 + - - -
685A THR* 4.4 0.2 - - - +
687A THR* 3.9 1.1 - - - -
688A GLY* 3.3 12.3 - - - -
1731A ADP 2.9 33.5 + - - -
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 3.7 12.5 - - - +
396A GLY 3.3 24.5 - - - -
398A GLY 3.3 3.8 + - - +
400A SER* 1.3 81.2 + - - +
402A SER* 1.3 63.7 + - - +
404A ALA* 3.3 3.0 + - - +
405A ALA* 3.0 23.7 + - - +
417A LEU* 4.3 1.7 - - - +
486A ALA* 3.7 13.9 - - - +
672A ILE* 4.3 2.5 - - - -
1731A ADP 4.1 0.4 + - - -
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA* 3.7 17.0 + - - -
398A GLY 2.7 26.5 + - - -
399A PRO* 3.7 1.7 + - - +
401A GLY* 1.3 76.9 - - - +
403A GLU* 1.3 58.2 + - - +
405A ALA* 3.5 3.5 + - - +
406A ARG* 3.0 28.9 + - - +
417A LEU* 4.5 3.6 - - - -
424A ILE* 4.2 8.2 - - - +
425A GLY* 5.4 0.3 + - - -
444A ARG* 6.0 0.2 - - - -
447A ARG* 3.4 26.7 - - - +
451A ILE* 3.7 23.4 - - - +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A GLN 5.0 1.0 - - - +
368A ALA* 4.4 4.3 + - - +
399A PRO 3.1 19.1 + - - +
400A SER 3.9 1.6 - - - +
401A GLY 3.3 0.2 - - - -
402A SER* 1.3 83.0 + - - +
404A ALA* 1.3 55.4 + - - +
406A ARG* 2.8 36.2 + - - +
407A VAL* 3.0 35.9 + - - +
447A ARG* 2.6 42.6 + - - +
685A THR* 3.4 33.4 - - + +
689A HIS* 2.8 28.4 + - + +
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 4.0 12.3 - - + -
400A SER 3.0 17.2 + - - +
401A GLY* 3.3 6.5 + - - +
403A GLU* 1.3 75.1 - - - +
405A ALA* 1.3 57.9 + - - +
407A VAL 3.4 0.2 + - - -
408A LEU* 2.9 35.9 + - - +
484A ILE* 4.2 6.5 - - + -
672A ILE* 4.2 10.3 - - + -
688A GLY* 3.4 25.9 - - - +
691A VAL* 4.2 9.2 - - + -
692A ALA* 3.7 3.3 - - + +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 3.5 18.8 - - + +
401A GLY 3.0 16.1 + - - +
402A SER 3.7 4.9 - - - +
404A ALA* 1.3 72.9 - - - +
406A ARG* 1.3 68.5 + - - +
408A LEU* 4.6 0.4 - - - -
409A MET* 2.8 36.8 + - + +
415A VAL* 4.0 12.6 - - + -
417A LEU* 3.8 22.7 - - + -
451A ILE* 4.3 5.4 - - + -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 4.4 15.2 - - - +
366A GLN 5.6 0.6 + - - -
380A PRO 5.0 1.2 + - - -
383A PHE* 4.2 19.2 - - - -
402A SER 3.0 17.9 + - - +
403A GLU* 2.8 40.3 + - - +
405A ALA* 1.3 79.8 - - - +
407A VAL* 1.3 69.1 + - - +
409A MET* 3.8 5.6 - - - +
410A GLU* 3.0 47.2 + - + +
446A TYR* 3.2 40.2 + - - -
447A ARG* 4.4 7.8 - - + +
450A GLN* 4.0 23.5 + - + -
451A ILE* 4.5 12.6 - - + -
454A LEU* 4.6 4.7 - - + +
689A HIS* 4.1 9.1 - - - -
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A PHE* 3.8 22.0 - - + -
403A GLU* 3.0 24.6 + - + +
406A ARG* 1.3 82.7 - - - +
408A LEU* 1.3 55.4 + - - +
410A GLU* 3.3 8.3 + - - +
411A SER* 2.8 40.9 + - - +
689A HIS* 3.4 35.0 - - + +
692A ALA* 3.5 23.6 - - + -
693A ARG* 4.3 16.4 - - - +
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A VAL* 3.9 22.0 - - + -
394A ILE* 4.1 8.5 - - + -
404A ALA 2.9 21.1 + - - +
405A ALA 4.0 0.4 - - - +
407A VAL* 1.3 74.5 - - - +
409A MET* 1.3 61.0 + - - +
411A SER* 3.1 6.7 + - - -
412A GLY 3.3 0.3 + - - -
413A TYR* 3.0 56.7 + - + -
415A VAL* 3.7 13.0 - - + -
484A ILE* 3.9 28.7 - - + -
692A ALA* 3.8 27.6 - - + +
695A ILE* 4.0 13.9 - - + -
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ALA* 2.8 28.6 + - + +
406A ARG* 3.8 3.6 - - - +
408A LEU* 1.3 75.9 - - - +
410A GLU* 1.3 59.8 + - - +
412A GLY* 3.0 11.8 + - - -
413A TYR 4.1 0.7 - - - -
415A VAL* 3.4 23.3 - - + -
417A LEU* 6.5 0.2 - - + -
451A ILE* 3.9 37.9 - - + +
454A LEU* 3.9 33.8 - - + +
455A LEU* 4.1 13.0 - - + -
458A ASN* 3.4 19.8 + - + +
461A SER* 3.8 29.2 - - - +
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A PHE* 3.5 41.1 - - + +
385A GLN* 2.9 21.1 + - - +
406A ARG* 3.0 33.3 + - + +
407A VAL 3.3 8.7 + - - +
409A MET* 1.3 74.4 - - - +
411A SER* 1.3 56.9 + - - +
412A GLY 3.3 1.4 + - - -
450A GLN* 4.1 13.9 - - - +
454A LEU* 3.7 25.5 - - + +
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PHE* 3.6 13.9 - - - +
384A ARG 3.3 18.4 + - - -
385A GLN* 3.3 14.3 - - - +
386A THR* 2.8 31.5 + - - +
407A VAL* 2.8 26.9 + - - +
408A LEU* 3.6 6.5 - - - -
409A MET 3.1 1.0 - - - -
410A GLU* 1.3 77.4 - - - +
412A GLY* 1.3 57.4 + - - +
413A TYR* 3.4 17.3 - - - -
692A ALA 5.1 4.3 + - - -
693A ARG* 5.8 1.9 - - - -
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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