Contacts of the helix formed by residues 413 - 430 (chain A) in PDB entry 3OEH
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 ASP 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A LEU* 1.3 79.1 - - - +
414A ALA* 1.3 62.8 + - - +
415A SER* 3.5 19.0 - - - +
416A THR* 3.2 22.5 + - + +
417A LYS* 3.3 24.1 + - - +
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Residues in contact with ALA 414 (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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413A ASP* 1.3 73.0 - - - +
415A SER* 1.3 60.8 + - - +
417A LYS* 4.3 4.3 - - - +
418A GLN* 3.3 22.0 + - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASP* 3.5 16.1 + - - +
414A ALA* 1.3 79.9 - - - +
416A THR* 1.3 65.0 + - - +
418A GLN* 3.5 4.7 + - - +
419A THR* 3.3 28.8 + - - -
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 3.8 27.5 - - + +
405A PHE* 5.4 8.3 - - + -
412A LEU* 3.6 9.9 - - - +
413A ASP* 3.2 34.1 + - + +
415A SER* 1.3 80.0 - - - +
417A LYS* 1.3 58.7 + - - +
419A THR* 3.8 9.9 - - - -
420A LEU* 3.3 30.3 + - - +
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Residues in contact with LYS 417 (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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410A SER 4.4 9.6 + - - -
412A LEU* 4.0 43.0 + - + +
413A ASP 3.3 14.1 + - - +
414A ALA* 4.8 3.6 - - - +
416A THR* 1.3 76.0 + - - +
418A GLN* 1.3 56.4 + - - +
419A THR 3.3 0.4 - - - -
420A LEU* 3.1 10.6 + - + +
421A VAL* 2.7 48.7 + - + +
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Residues in contact with GLN 418 (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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395A PHE* 5.3 4.2 - - + -
414A ALA 3.3 20.3 + - - +
415A SER* 3.5 4.6 + - - +
417A LYS* 1.3 76.0 - - - +
419A THR* 1.3 65.8 + - - +
421A VAL* 3.3 8.1 + - - +
422A ARG* 2.9 65.2 + - - +
456A ASP* 3.9 9.9 + - - +
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Residues in contact with THR 419 (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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395A PHE* 2.8 46.1 - - + -
398A GLN* 4.0 16.0 + - + +
399A TYR* 3.9 26.0 - - + +
402A VAL* 4.2 18.1 - - + +
415A SER* 3.3 16.9 + - - -
416A THR* 3.8 8.6 - - - -
418A GLN* 1.3 79.5 - - - +
420A LEU* 1.3 63.1 + - - +
423A GLY* 3.1 6.4 + - - -
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Residues in contact with LEU 420 (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 TYR* 3.9 25.2 - - + +
402A VAL* 4.7 7.9 - - + +
403A ALA 4.4 5.6 - - - +
405A PHE* 4.2 9.6 - - + +
406A ALA* 3.9 39.5 - - + +
412A LEU* 3.8 26.5 - - + -
416A THR 3.3 17.7 + - - +
417A LYS* 3.1 12.6 + - + +
419A THR* 1.3 80.0 - - + +
421A VAL* 1.3 62.2 + - + +
424A GLU* 3.1 42.6 + - - +
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Residues in contact with VAL 421 (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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417A LYS* 2.7 33.1 + - + +
418A GLN* 3.3 11.0 + - - +
420A LEU* 1.3 72.9 - - + +
422A ARG* 1.3 63.8 + - - +
424A GLU* 4.1 5.2 - - - +
425A ARG* 2.9 52.6 + - - +
456A ASP* 3.8 33.0 - - + +
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Residues in contact with ARG 422 (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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395A PHE* 3.5 26.2 - - + -
418A GLN* 2.9 38.1 + - - +
421A VAL* 1.3 75.7 - - - +
423A GLY* 1.3 65.7 + - - +
425A ARG* 3.0 7.6 + - - +
426A LEU* 3.0 34.0 + - + +
450A GLY 3.4 22.9 - - - -
451A VAL* 3.1 19.6 + - - +
452A ASN* 4.9 0.8 - - - +
453A GLY* 3.4 16.8 - - - +
455A LEU* 6.3 0.2 - - - -
456A ASP* 2.8 38.6 + - - -
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Residues in contact with GLY 423 (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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395A PHE* 3.2 18.4 - - - -
396A LEU* 4.6 2.0 - - - -
399A TYR* 3.9 18.4 - - - -
419A THR 3.1 10.0 + - - -
422A ARG* 1.3 75.3 - - - +
424A GLU* 1.3 66.5 + - - +
425A ARG 2.9 0.7 + - - -
426A LEU* 3.1 5.9 + - - +
427A THR* 2.8 30.8 + - - -
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Residues in contact with GLU 424 (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 TYR* 3.3 25.6 + - + +
406A ALA* 5.2 6.2 - - - +
420A LEU* 3.1 36.3 + - + +
421A VAL* 3.8 7.2 - - - +
423A GLY* 1.3 74.0 - - - +
425A ARG* 1.3 68.0 + - - +
427A THR* 3.7 6.2 - - - +
428A GLN* 3.2 25.5 + - - +
460A LEU* 3.7 30.2 - - + +
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Residues in contact with ARG 425 (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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421A VAL* 2.9 41.0 + - - +
422A ARG* 3.0 9.5 + - - +
423A GLY 2.9 1.8 + - - -
424A GLU* 1.3 89.2 + - - +
426A LEU* 1.3 53.6 + - + +
428A GLN* 3.0 3.9 + - - +
429A LEU* 2.7 36.3 + - - +
450A GLY* 6.2 0.4 - - - -
455A LEU* 3.2 36.5 + - + -
456A ASP* 3.7 18.7 + - - +
457A GLY 5.3 0.4 + - - -
458A ILE 3.1 26.6 + - - -
459A GLU* 4.3 3.0 - - - +
460A LEU* 3.5 36.6 - - + +
463A ILE* 3.7 16.6 - - + +
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Residues in contact with LEU 426 (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 LEU* 3.5 37.7 - - + -
395A PHE* 4.1 20.4 - - + -
396A LEU* 4.0 9.0 - - + -
422A ARG* 3.0 37.8 + - + +
423A GLY 3.8 3.1 - - - +
425A ARG* 1.3 75.4 - - + +
427A THR* 1.3 63.5 + - - +
429A LEU* 3.3 14.6 + - + +
430A LEU* 3.0 32.0 + - + +
447A ILE* 5.1 0.9 - - + +
450A GLY* 3.6 12.1 - - - -
451A VAL* 3.5 33.0 - - + +
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Residues in contact with THR 427 (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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363A ILE* 4.0 37.6 - - + +
396A LEU* 3.7 12.9 - - - +
399A TYR* 3.6 20.4 - - + -
423A GLY 2.8 18.5 + - - -
424A GLU* 3.7 8.5 - - - +
426A LEU* 1.3 77.5 - - - +
428A GLN* 1.3 62.2 + - - +
430A LEU* 3.5 13.4 + - - +
431A LYS* 3.7 14.0 + - - +
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Residues in contact with GLN 428 (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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424A GLU 3.2 14.7 + - - +
425A ARG* 3.0 9.9 + - - +
427A THR* 1.3 73.7 - - - +
429A LEU* 1.3 65.1 + - - +
430A LEU 3.1 1.3 - - - -
431A LYS* 3.1 63.7 + - - +
460A LEU* 3.9 29.2 + - + +
461A SER* 5.7 1.2 + - - +
463A ILE* 3.7 24.8 - - + -
464A GLY* 4.8 10.3 - - - +
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Residues in contact with LEU 429 (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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153A LYS* 2.8 37.9 + - + +
425A ARG 2.7 12.0 + - - +
426A LEU* 3.3 23.6 - - + +
428A GLN* 1.3 72.1 - - - +
430A LEU* 1.3 58.4 + - + +
431A LYS 3.2 1.3 - - - +
446A LEU* 3.3 54.3 - - + +
447A ILE* 4.3 12.1 - - + -
450A GLY* 3.9 19.1 - - - -
455A LEU* 3.9 19.1 - - + -
463A ILE* 4.0 11.8 - - + +
466A PHE* 5.8 3.1 - - + -
467A GLU* 3.9 9.0 - - + +
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Residues in contact with LEU 430 (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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153A LYS* 3.9 35.2 - - + +
154A ALA* 4.0 24.6 + - + +
157A ALA* 5.1 0.2 - - + -
158A LEU* 3.9 18.6 - - + -
363A ILE* 6.6 0.7 - - - -
364A ARG 4.3 3.1 - - - +
365A PRO* 4.4 3.5 - - - +
369A VAL* 5.7 1.3 - - + -
392A LEU* 4.4 19.1 - - + -
396A LEU* 3.9 27.6 - - + -
426A LEU* 3.0 19.8 + - + +
427A THR* 3.8 8.5 - - - +
428A GLN 3.1 0.6 - - - -
429A LEU* 1.3 83.5 - - + +
431A LYS* 1.3 65.0 + - - +
432A GLN* 3.8 3.8 + - - +
447A ILE* 4.5 10.1 - - + -
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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