Contacts of the helix formed by residues 414 - 422 (chain A) in PDB entry 1OFD
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 PRO 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A TYR* 1.3 85.7 - - + +
415A TYR* 1.3 64.2 + - - +
416A GLY 3.2 3.2 + - - -
417A GLU* 3.2 32.2 + - + +
418A TRP* 3.1 46.9 + - + +
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Residues in contact with TYR 415 (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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290A GLU* 4.1 5.7 + - - -
311A GLU 5.2 0.4 - - - -
314A ASP* 3.7 21.8 - - + +
315A PHE* 3.6 34.1 - + + -
318A TYR* 3.5 41.1 - + + -
319A TYR* 3.0 28.3 + + - -
409A ALA 4.4 2.7 + - - -
410A ALA 3.5 18.2 - - - -
413A TYR* 2.9 54.0 + + + -
414A PRO* 1.3 73.8 - - - +
416A GLY* 1.3 56.6 + - - +
418A TRP* 3.2 22.6 + + - +
419A ILE* 3.1 31.6 + - - +
531A PRO* 4.3 2.2 - - + -
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Residues in contact with GLY 416 (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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314A ASP* 3.7 33.0 + - - +
414A PRO 3.3 1.0 - - - -
415A TYR* 1.3 74.9 - - - +
417A GLU* 1.3 64.7 + - - +
419A ILE* 3.2 9.9 + - - +
420A LYS* 2.9 35.0 + - - +
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Residues in contact with GLU 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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414A PRO* 3.2 30.3 + - + +
416A GLY* 1.3 74.4 - - - +
418A TRP* 1.3 66.6 + - + +
420A LYS* 3.2 17.9 + - + +
421A ILE* 3.1 26.5 + - - +
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Residues in contact with TRP 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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318A TYR* 3.5 30.1 - + + -
413A TYR* 3.6 28.0 - + + -
414A PRO* 3.1 39.0 + - + +
415A TYR* 3.2 26.5 - + - +
417A GLU* 1.3 82.2 - - + +
419A ILE* 1.3 56.2 + - - +
421A ILE* 3.3 11.0 - - + +
422A GLN* 2.9 33.8 + - - +
531A PRO* 3.7 18.2 - - + -
532A LYS* 3.7 19.1 - - - -
533A ALA* 3.6 35.0 - - + +
536A ALA* 4.1 8.7 - - + -
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Residues in contact with ILE 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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314A ASP* 3.7 7.0 - - - +
317A ASP* 3.6 25.6 - - + +
318A TYR* 3.5 35.4 - - + +
415A TYR 3.1 18.8 + - - +
416A GLY* 3.6 10.1 - - - +
418A TRP* 1.3 73.9 - - - +
420A LYS* 1.3 66.3 + - + +
423A ARG* 3.0 63.1 + - + +
536A ALA* 4.3 14.8 - - + -
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Residues in contact with LYS 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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416A GLY 2.9 24.8 + - - +
417A GLU* 3.2 17.8 + - + +
419A ILE* 1.3 79.4 - - + +
421A ILE* 1.3 59.5 + - - +
423A ARG 4.5 5.7 - - - +
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Residues in contact with ILE 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 GLU 3.1 18.2 - - - +
418A TRP* 3.3 19.3 - - + +
420A LYS* 1.3 81.6 - - - +
422A GLN* 1.3 79.6 + - + +
423A ARG 5.0 1.1 - - - +
533A ALA* 5.7 1.6 - - + -
558A GLN* 5.4 1.4 - - - +
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Residues in contact with GLN 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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418A TRP 2.9 18.8 + - - +
421A ILE* 1.3 98.3 - - + +
423A ARG* 1.3 59.7 + - - +
533A ALA* 3.4 34.3 - - + +
534A GLU* 4.6 4.7 - - - +
536A ALA* 3.6 19.7 - - + -
537A ARG* 3.5 33.2 - - - +
558A GLN* 3.0 27.5 + - - +
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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