Contacts of the helix formed by residues 319 - 322 (chain A) in PDB entry 1ZMD
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 GLY 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 1.3 73.2 - - - +
320A ASP* 1.3 66.7 + - - -
321A VAL 3.1 3.1 - - - -
322A VAL* 3.0 10.6 + - - +
330A LYS* 3.0 22.0 + - - -
331A ALA* 3.6 20.2 - - - -
334A GLU* 2.7 19.5 + - - +
480A FAD 3.5 9.6 - - - -
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Residues in contact with ASP 320 (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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149A GLY 3.6 21.5 - - - -
150A SER* 2.6 25.1 + - - +
280A ARG* 4.7 2.3 + - - -
282A PRO* 3.7 14.9 - - - +
301A ARG* 5.0 1.0 - - - +
319A GLY* 1.3 70.5 - - - -
321A VAL* 1.3 60.0 + - - +
322A VAL 3.2 4.8 + - - +
325A PRO 4.8 0.2 - - - +
326A MET* 3.2 44.1 - - + +
327A LEU 3.9 1.9 + - - +
330A LYS* 5.1 0.8 - - - +
480A FAD 2.9 54.2 + - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.9 15.5 - - + +
148A THR* 3.1 28.3 - - - +
149A GLY* 3.3 20.5 + - - +
282A PRO* 3.9 5.8 - - + -
283A PHE 3.5 9.2 - - - +
284A THR* 4.0 12.3 - - + -
301A ARG* 3.2 9.7 - - - -
302A ILE* 2.9 33.2 + - + -
317A ALA* 4.2 5.8 - - + -
318A ILE 3.1 22.0 - - - +
320A ASP* 1.3 77.5 - - - +
322A VAL* 1.3 66.9 + - + +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 4.1 9.4 - - - -
302A ILE 3.6 17.3 - - - +
304A VAL* 4.1 11.4 - - + -
308A PHE* 4.6 5.8 - - + -
317A ALA* 3.5 42.8 - - + +
318A ILE* 3.7 4.7 - - - +
319A GLY 3.0 26.1 + - - +
320A ASP* 3.9 6.2 - - - +
321A VAL* 1.3 83.9 - - - +
323A ALA* 1.3 69.2 + - - +
324A GLY 3.8 3.8 + - - +
326A MET* 5.4 2.1 - - - +
330A LYS* 3.6 5.6 + - - +
334A GLU* 3.5 22.4 - - - +
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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