Contacts of the helix formed by residues 406 - 415 (chain A) in PDB entry 2DDH
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 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A HIS* 2.9 14.1 + - - -
404A SER 3.1 0.6 - - - -
405A SER* 1.3 79.0 + - - +
407A ILE* 1.3 62.5 + - - +
408A PRO* 3.5 2.5 - - - -
409A ASN* 3.6 10.3 + - - +
410A ILE* 3.4 27.8 + - - +
617A LEU 4.0 4.4 - - - +
618A GLY 3.3 21.5 - - - -
619A SER* 4.0 2.9 - - - -
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Residues in contact with ILE 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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296A ALA* 4.0 19.5 - - + +
299A ILE* 3.9 28.3 - - + -
389A ILE* 3.6 25.6 - - + +
390A GLU* 5.0 1.1 - - - +
392A CYS* 3.9 8.7 - - + +
393A ARG* 3.5 45.8 - - + +
396A CYS* 4.3 9.0 - - - -
405A SER* 3.1 15.0 - - - +
406A GLY* 1.3 75.7 - - - +
408A PRO* 1.3 73.7 - - + +
410A ILE* 3.1 6.7 + - + +
411A TYR* 2.9 21.5 + - - +
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU* 5.5 1.6 - - - +
393A ARG* 4.2 10.5 - - + +
400A GLY 3.6 13.2 - - - +
401A TYR* 4.0 15.9 - - + +
402A SER 4.0 5.6 - - - +
403A HIS* 3.7 23.6 - - + +
405A SER* 3.2 14.8 - - - +
406A GLY* 3.7 2.9 - - - +
407A ILE* 1.3 91.6 - - + +
409A ASN* 1.3 56.6 + - - +
411A TYR* 3.7 6.7 - - + +
412A VAL* 3.0 33.7 + - - +
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Residues in contact with ASN 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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52A ASN* 5.0 7.5 - - - +
59A ARG* 4.3 9.2 + - - -
94A ARG 5.3 0.4 + - - -
95A GLY 5.5 1.6 - - - -
96A HIS* 3.0 47.0 + - - +
233A GLU* 5.0 2.1 - - - +
234A GLU* 5.3 0.5 - - - +
403A HIS* 4.2 15.8 + - + +
406A GLY* 3.6 10.8 + - - +
407A ILE 3.2 0.6 - - - -
408A PRO* 1.3 79.5 - - - +
410A ILE* 1.3 59.8 + - - +
412A VAL* 3.8 9.8 - - - +
413A THR* 2.6 49.7 + - - -
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Residues in contact with ILE 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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292A SER* 3.7 35.2 + - - +
295A LYS* 3.7 33.4 - - + +
296A ALA* 4.3 3.4 - - + +
299A ILE* 3.7 25.1 - - + -
389A ILE* 4.2 12.6 - - + -
406A GLY 3.4 17.0 + - - +
407A ILE* 3.1 9.5 + - - +
409A ASN* 1.3 80.7 - - + +
411A TYR* 1.3 57.0 + - - +
413A THR* 3.8 4.4 - - - -
414A PHE* 2.9 29.8 + - - +
616A THR 5.8 0.9 - - - +
617A LEU 4.3 9.0 - - - +
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Residues in contact with TYR 411 (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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230A PHE* 3.8 34.4 - + - -
386A ASN* 3.3 55.8 + - - -
387A ALA* 5.5 0.2 - - - -
389A ILE* 3.7 22.9 - - + +
390A GLU* 3.5 39.3 - - + +
407A ILE 2.9 15.0 + - - +
408A PRO* 3.7 6.5 - - + +
410A ILE* 1.3 78.6 - - - +
412A VAL* 1.3 57.2 + - + +
414A PHE* 3.1 0.5 + - - +
415A THR* 2.8 45.7 + - - -
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Residues in contact with VAL 412 (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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230A PHE* 2.9 55.0 - - + +
231A GLY* 3.1 28.0 + - - -
232A TYR* 4.3 3.0 - - - +
233A GLU* 4.7 4.5 - - - +
408A PRO 3.0 13.8 + - - +
409A ASN* 3.8 14.4 - - - +
411A TYR* 1.3 81.5 - - + +
413A THR* 1.3 67.6 + - - +
415A THR* 3.6 8.3 - - - +
416A PRO* 3.4 18.0 - - - +
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Residues in contact with THR 413 (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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95A GLY 3.7 22.4 - - - +
96A HIS* 5.1 0.2 - - - -
97A PRO* 4.0 26.1 - - + +
232A TYR* 3.5 20.2 + - + +
409A ASN* 2.6 39.9 + - - -
410A ILE* 3.8 4.9 - - - -
412A VAL* 1.3 81.4 - - - +
414A PHE* 1.3 62.8 + - - +
416A PRO* 3.3 8.3 - - - +
420A PHE* 5.8 1.0 - - - -
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Residues in contact with PHE 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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288A ASN* 3.7 14.6 - - + +
289A ALA* 3.3 32.3 - - + -
292A SER* 3.5 30.5 - - - +
382A THR* 3.4 48.7 - - + -
385A ALA* 4.0 2.2 - - + -
386A ASN* 3.8 17.7 - - + -
389A ILE* 3.8 15.9 - - + -
410A ILE 2.9 19.6 + - - +
411A TYR* 3.8 1.6 - + - +
413A THR* 1.3 76.3 - - - +
415A THR* 1.3 62.4 + - - +
416A PRO* 2.9 6.7 - - - +
417A ALA* 2.9 42.4 + - + +
418A CYS* 4.7 1.1 - - - -
420A PHE* 5.4 0.3 - - - -
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Residues in contact with THR 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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230A PHE* 4.2 21.9 - - + -
386A ASN* 2.9 31.2 + - - -
411A TYR* 2.8 32.6 + - - +
412A VAL* 3.6 12.8 - - - +
414A PHE* 1.3 74.0 - - - +
416A PRO* 1.3 74.5 - - + +
417A ALA 3.0 1.9 + - - -
418A CYS* 3.1 20.0 + - - +
419A THR* 4.2 2.9 + - - -
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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