Contacts of the helix formed by residues 354 - 365 (chain D) in PDB entry 6AH0
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 354 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D MET 2.7 7.0 - - - +
351D GLU 3.1 14.3 - - - +
352D ALA 4.5 0.4 - - - +
353D ASP* 1.3 72.0 - - - +
355D GLU* 1.3 62.6 + - - +
356D LEU 3.2 2.7 - - - -
357D SER* 3.3 13.2 + - - +
358D LYS 3.7 6.6 + - - -
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Residues in contact with GLU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D MET* 3.2 3.2 + - - +
353D ASP* 3.3 4.8 + - - +
354D PRO* 1.3 78.7 - - - +
356D LEU* 1.3 51.7 + - - +
358D LYS 3.3 0.7 + - - -
359D PHE* 2.4 39.6 + - - -
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Residues in contact with LEU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D MET 5.2 2.2 - - - -
350D MET* 3.2 26.0 + - - +
351D GLU* 4.1 4.0 - - - +
355D GLU* 1.3 74.3 - - - +
357D SER* 1.3 62.9 + - - +
360D LEU* 2.7 34.9 + - - +
361D TYR 3.6 0.9 + - - -
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Residues in contact with SER 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLU* 4.5 7.4 - - - +
354D PRO* 3.3 11.8 + - - -
355D GLU 3.2 1.0 - - - -
356D LEU* 1.3 77.1 - - - +
358D LYS* 1.3 58.5 + - - +
361D TYR* 4.0 9.2 + - - -
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Residues in contact with LYS 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D PRO 3.7 6.1 + - - -
355D GLU 3.3 2.8 + - - -
357D SER* 1.3 76.4 - - - +
359D PHE* 1.3 61.4 + - - +
360D LEU 3.4 0.4 - - - -
361D TYR* 3.5 1.9 + - - +
362D GLN* 3.1 21.8 + - - -
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Residues in contact with PHE 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D GLU 2.4 27.9 + - - -
356D LEU* 4.6 0.2 - - - -
358D LYS* 1.3 66.1 - - - +
360D LEU* 1.3 57.6 + - - +
362D GLN* 3.2 3.2 + - - +
363D LEU* 2.9 25.6 + - - -
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Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D LEU* 2.7 29.6 + - - +
359D PHE* 1.3 72.1 - - - +
361D TYR* 1.3 54.3 + - - +
363D LEU* 4.4 1.3 - - - +
364D HIS* 2.9 28.9 + - - -
365D GLU 4.8 0.5 - - - +
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Residues in contact with TYR 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D LEU 3.6 5.1 + - - -
357D SER 4.0 8.2 + - - -
358D LYS 3.5 6.7 + - - -
359D PHE 3.3 0.6 - - - -
360D LEU* 1.3 75.7 - - - +
362D GLN* 1.3 57.0 + - - +
365D GLU* 2.8 40.8 + - - -
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Residues in contact with GLN 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D LYS 3.1 14.5 + - - -
359D PHE* 3.2 4.4 + - - +
361D TYR* 1.3 80.4 - - - +
363D LEU* 1.3 62.4 + - - +
365D GLU* 4.0 3.1 + - - -
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Residues in contact with LEU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D PHE 2.9 14.1 + - - -
360D LEU* 3.2 3.3 + - - +
362D GLN* 1.3 79.1 - - - +
364D HIS* 1.3 58.2 + - - +
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Residues in contact with HIS 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D LEU 2.9 13.4 + - - -
363D LEU* 1.3 76.4 - - - +
365D GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D LEU 4.8 0.2 - - - +
361D TYR* 2.8 29.1 + - - +
362D GLN 4.0 2.5 + - - -
363D LEU 3.6 1.6 - - - -
364D HIS* 1.3 82.4 - - - +
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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