Contacts of the helix formed by residues 369 - 373 (chain D) in PDB entry 1DGH
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 ASN 369 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C HIS* 2.8 35.0 - - - -
392C MET* 3.1 22.1 - - + +
367D GLY 3.2 0.8 - - - -
368D PRO* 1.3 78.4 + - - +
370D TYR* 1.3 56.8 - - - +
371D LEU* 3.1 4.3 - - - +
372D HIS* 2.9 55.1 + - - +
389D ASP 3.1 17.6 + - - +
390D GLY* 3.4 6.8 - - - +
391D PRO 2.8 26.2 + - - +
392D MET 4.2 0.9 - - - +
393D CYS* 3.8 3.5 - - - -
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Residues in contact with TYR 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C MET* 4.3 2.9 - - - -
333D ALA* 3.8 21.5 - - + -
335D ASP* 2.8 25.0 + - - -
359D PRO* 3.3 19.5 - - - +
362D HIS* 3.6 33.4 - - + -
363D ARG* 3.8 22.0 + - + -
366D LEU* 3.5 24.5 - - + -
367D GLY 3.0 24.8 + - - +
368D PRO 3.4 7.9 - - - -
369D ASN* 1.3 75.6 - - - +
371D LEU* 1.3 90.8 + - + +
372D HIS 3.0 4.6 + - - -
373D ILE* 3.2 25.0 + - - +
376D ASN* 3.4 13.3 + - - +
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY* 3.5 40.2 - - - +
31C ALA* 3.8 14.4 - - + +
59C ASP* 4.7 8.5 - - - +
135D LYS* 6.1 1.3 - - - +
142D ASN* 5.9 0.2 - - - +
333D ALA 5.8 1.8 - - - +
335D ASP* 4.5 6.5 - - - +
338D ASN* 5.0 2.9 - - - +
368D PRO 5.1 0.2 + - - -
369D ASN* 3.1 2.5 - - - -
370D TYR* 1.3 113.1 - - + +
372D HIS* 1.3 66.1 + - + +
373D ILE 3.4 1.3 - - - -
376D ASN* 3.9 20.9 - - + +
377D CYS* 3.5 26.9 - - - +
378D PRO* 4.4 2.8 - - + +
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Residues in contact with HIS 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C HIS* 5.5 0.2 - - - -
392C MET* 4.5 0.7 - - + -
394C MET* 4.0 9.9 - - - +
369D ASN* 2.9 48.4 + - + +
371D LEU* 1.3 84.3 - - + +
373D ILE* 1.3 64.5 + - - +
374D PRO* 3.2 8.1 - - - +
377D CYS* 4.6 3.8 - - - +
389D ASP 5.3 0.2 - - - -
393D CYS* 4.1 13.5 - - - -
394D MET* 3.1 45.4 + - + +
395D GLN* 3.4 37.3 + - - +
397D ASN* 6.1 0.7 - - - -
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Residues in contact with ILE 373 (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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392C MET* 4.0 23.1 - - + -
393C CYS 4.2 2.0 - - - +
394C MET* 3.7 15.3 - - - -
327D ALA* 4.4 2.5 - - + +
331D GLN* 3.6 42.4 - - + +
366D LEU* 4.2 20.0 - - + -
370D TYR 3.2 15.7 + - - +
372D HIS* 1.3 75.9 - - - +
374D PRO* 1.3 78.0 - - + -
375D VAL* 4.1 19.5 - - + +
376D ASN* 2.8 27.7 + - - +
377D CYS 3.1 8.7 + - - -
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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
------------------------------------------------------------
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