Contacts of the helix formed by residues 415 - 423 (chain A) in PDB entry 2HAS
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 THR 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.9 1.3 - - - +
231A ALA 4.2 6.5 - - - +
232A ASP* 3.5 24.0 - - - +
235A SER* 2.8 34.7 + - - -
414A LEU* 1.3 83.4 - - - +
416A PRO* 1.3 77.5 - - - +
417A LEU 3.5 1.5 + - - -
418A VAL* 3.1 18.5 + - - +
419A LEU* 2.9 29.1 + - - +
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Residues in contact with PRO 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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415A THR* 1.3 89.2 - - - +
417A LEU* 1.3 61.6 + - - +
419A LEU* 3.4 12.5 + - + +
420A GLU* 3.1 24.3 + - - +
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Residues in contact with LEU 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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235A SER* 3.6 21.5 - - - +
238A ILE* 3.6 31.4 - - + -
239A GLN* 3.6 31.0 - - + +
242A ILE* 4.7 11.7 - - + -
415A THR* 3.2 1.2 + - - -
416A PRO* 1.3 80.7 - - - +
418A VAL* 1.3 64.0 + - - +
420A GLU* 3.4 14.3 + - - +
421A VAL* 3.0 44.4 + - + +
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 3.8 12.6 - - - +
234A VAL* 4.6 5.2 - - + -
235A SER* 3.7 24.9 - - - +
238A ILE* 4.5 9.2 - - + -
401A TYR* 3.9 10.3 + - + +
414A LEU* 4.2 14.8 - - + -
415A THR* 3.1 25.6 + - + +
417A LEU* 1.3 77.4 - - - +
419A LEU* 1.3 63.1 + - - +
420A GLU 3.3 0.2 + - - -
421A VAL* 4.7 1.6 - - - -
422A PHE* 3.0 34.6 + - + +
1001A C3O 3.8 26.7 - - + -
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Residues in contact with LEU 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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401A TYR* 3.6 18.1 + - - +
405A SER* 6.5 0.4 - - - -
411A SER* 4.1 34.8 - - - +
414A LEU* 3.6 20.4 - - + -
415A THR 2.9 25.5 + - - +
416A PRO* 3.6 10.5 - - + +
418A VAL* 1.3 77.7 - - - +
420A GLU* 1.3 53.1 + - - +
423A GLY* 2.7 34.1 + - - -
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Residues in contact with GLU 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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260A ILE* 5.2 1.6 - - - +
264A LYS* 3.0 41.3 + - - +
416A PRO 3.1 16.2 + - - +
417A LEU* 3.8 17.5 - - - +
419A LEU* 1.3 77.4 - - - +
421A VAL* 1.3 68.4 + - - +
422A PHE 3.4 0.2 + - - -
423A GLY* 3.5 9.4 + - - +
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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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238A ILE* 4.3 16.2 - - + -
264A LYS* 3.9 47.6 - - + +
267A ALA* 4.0 19.1 - - + -
417A LEU* 3.0 40.8 + - + +
418A VAL 4.0 2.2 - - - +
420A GLU* 1.3 81.7 - - - +
422A PHE* 1.3 79.1 + - + +
423A GLY 4.4 2.4 - - - +
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Residues in contact with PHE 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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234A VAL* 4.3 6.1 - - + -
238A ILE* 3.9 25.6 - - + -
264A LYS 5.4 2.0 - - - -
267A ALA* 5.2 0.4 - - + -
268A ILE* 3.7 40.2 - - + -
271A ILE* 5.3 0.2 - - + -
394A ASN* 5.9 0.4 - - - -
397A HIS* 3.6 28.5 - + - -
398A SER* 5.5 6.2 + - - -
401A TYR* 3.4 38.3 - + + -
418A VAL* 3.0 26.2 + - + -
421A VAL* 1.3 90.4 - - + +
423A GLY* 1.3 67.5 + - - +
1001A C3O 4.2 17.9 - - + -
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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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401A TYR* 4.2 7.8 - - - -
419A LEU 2.7 26.6 + - - -
420A GLU* 3.5 8.7 + - - +
421A VAL 3.5 3.6 - - - +
422A PHE* 1.3 79.9 - - - +
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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