Contacts of the helix formed by residues 324 - 329 (chain A) 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 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A PRO* 4.2 2.4 - - - +
323A VAL* 1.3 79.8 - - + +
325A TYR* 1.3 66.4 + - - +
326A PHE* 3.4 5.8 + - - +
327A ALA* 3.0 30.7 + - + +
328A GLU* 3.1 29.9 + - - +
388B ARG* 4.7 2.6 - - - +
389B ASP* 5.3 0.6 + - - -
396B ASP 3.6 15.0 - - - +
397B ASN* 3.0 37.5 + - - +
399B GLY* 2.9 24.4 + - - +
172C PRO* 3.5 16.4 + - - +
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 5.4 0.5 + - - -
78A GLY* 2.6 34.2 + - - -
79A ALA* 4.5 5.8 - - - -
80A GLY 4.6 0.9 - - - -
112A ARG* 4.7 2.3 + - - -
262A ILE* 5.1 4.9 - - + -
322A PRO* 4.6 4.9 - - + -
324A ASN* 1.3 70.0 - - - +
326A PHE* 1.3 65.9 + - + +
329A VAL* 2.8 62.8 + - + +
330A GLU* 3.0 32.4 + - + -
172C PRO* 2.9 18.6 + - + +
173C GLN 3.9 16.9 + - - +
174C THR 4.9 0.9 - - - -
175C HIS* 3.1 64.5 + + + +
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Residues in contact with PHE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 4.1 6.3 - - - -
68A ARG* 5.7 0.2 - - - -
69A ILE* 3.9 36.6 - - + -
324A ASN* 3.4 6.3 + - - +
325A TYR* 1.3 80.6 - - - +
327A ALA* 1.3 59.5 + - - +
330A GLU* 3.4 22.6 - - + +
331A GLN* 3.0 53.3 + - + +
389B ASP* 3.3 47.6 - - + +
390B GLY 3.4 34.1 - - - -
393B CYS* 3.9 5.2 - - + -
397B ASN* 3.9 4.5 - - - -
172C PRO 4.6 1.0 + - - -
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Residues in contact with ALA 327 (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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324A ASN* 3.0 23.9 + - + +
326A PHE* 1.3 81.3 - - - +
328A GLU* 1.3 64.0 + - + +
331A GLN* 3.7 23.9 + - - +
373A ILE* 4.5 2.1 - - - +
375A VAL* 3.7 18.2 + - - +
393B CYS* 5.0 2.0 - - - +
395B GLN 4.3 13.0 - - - +
396B ASP* 4.4 3.1 - - - +
397B ASN* 4.0 16.8 - - + -
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Residues in contact with GLU 328 (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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82A PHE* 3.4 40.7 - - + -
320A ARG* 4.6 7.8 + - - -
321A ASN 4.6 1.4 - - - +
322A PRO* 3.8 8.2 - - + +
323A VAL* 2.9 36.5 + - - +
324A ASN* 3.1 18.8 + - - +
327A ALA* 1.3 83.5 - - + +
329A VAL* 1.3 61.2 + - - +
332A ILE* 3.5 12.0 - - - +
375A VAL* 3.5 26.8 - - + +
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Residues in contact with VAL 329 (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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72A ARG* 3.0 18.2 + - - -
79A ALA 4.2 0.4 - - - -
80A GLY* 3.8 25.4 - - - +
82A PHE* 5.0 1.8 - - + -
112A ARG* 3.9 19.7 - - + +
322A PRO* 3.7 31.9 - - + -
325A TYR* 2.8 52.5 + - + +
328A GLU* 1.3 78.3 - - + +
330A GLU* 1.3 67.9 + - - +
331A GLN 3.1 1.3 - - - -
332A ILE* 3.1 12.9 + - + +
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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