Contacts of the helix formed by residues 373 - 377 (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 ILE 373 (chain D).
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Specific contacts
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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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Residues in contact with PRO 374 (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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393C CYS 4.6 1.1 - - - +
394C MET* 3.8 33.7 - - + +
395C GLN* 4.6 9.6 - - - +
137D TYR* 5.1 1.0 + - - -
372D HIS 3.2 7.4 - - - +
373D ILE* 1.3 86.9 - - + -
375D VAL* 1.3 63.1 + - - +
376D ASN 3.1 1.6 + - - -
377D CYS* 3.1 23.5 + - + +
379D TYR* 5.2 4.5 - - - +
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Residues in contact with VAL 375 (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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82D PHE* 3.9 14.6 - - + -
135D LYS* 3.8 4.7 - - - +
137D TYR* 2.6 36.3 + - - +
327D ALA 3.5 25.1 + - - +
328D GLU* 3.7 17.9 - - + +
332D ILE* 3.7 38.8 - - + +
373D ILE* 4.1 8.0 - - + +
374D PRO* 1.3 77.5 - - - +
376D ASN* 1.3 71.1 + - - +
377D CYS 3.5 0.2 - - - -
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Residues in contact with ASN 376 (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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135D LYS* 4.1 6.3 + - - +
142D ASN* 3.3 14.2 + - - -
331D GLN 3.0 24.2 + - - -
332D ILE* 3.3 12.0 - - - +
333D ALA* 2.7 42.3 + - - +
366D LEU* 4.1 4.0 - - - +
370D TYR 3.4 23.2 + - - +
371D LEU* 3.9 22.9 - - + +
373D ILE* 2.8 19.6 + - - +
375D VAL* 1.3 75.5 - - - +
377D CYS* 1.3 64.4 + - - +
378D PRO* 3.5 4.9 - - - +
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Residues in contact with CYS 377 (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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137D TYR* 3.5 17.7 - - - -
142D ASN* 3.8 0.2 - - - -
371D LEU 3.5 10.3 + - - +
372D HIS 4.7 3.4 - - - -
373D ILE 3.1 8.9 + - - +
374D PRO* 3.1 18.6 + - + +
376D ASN* 1.3 78.3 - - - +
378D PRO* 1.4 68.9 - - - +
379D TYR* 2.8 25.7 + - + +
383D VAL* 6.0 2.5 - - - -
395D GLN* 4.0 23.1 - - - -
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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