Contacts of the helix formed by residues 383 - 388 (chain A) in PDB entry 3DGR
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 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY* 3.4 20.7 - - - -
356A VAL 5.0 0.4 + - - -
382A SER* 1.3 73.0 + - - +
384A GLY* 1.3 65.1 + - - +
385A GLY 3.3 1.2 - - - +
386A LEU* 3.0 14.7 + - - +
387A LEU* 3.0 16.8 + - - +
501A A12 3.2 27.9 + - - -
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Residues in contact with GLY 384 (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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194A GLY* 4.7 0.2 - - - -
197A GLY* 4.6 12.3 - - - -
383A GLY* 1.3 71.8 - - - +
385A GLY* 1.3 55.4 + - - +
388A GLN* 2.9 23.6 + - - -
389A LYS* 2.7 34.6 + - - -
501A A12 4.7 0.4 + - - -
391B THR* 5.4 7.0 - - - -
392B ARG 6.3 0.2 - - - -
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Residues in contact with GLY 385 (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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164A ASN* 4.1 13.9 + - - -
168A GLN* 5.8 0.9 - - - -
356A VAL 3.7 19.8 + - - -
357A ASP* 4.1 18.4 - - - +
358A ILE 5.5 0.2 + - - -
382A SER* 3.7 4.1 + - - -
383A GLY 3.3 1.8 - - - +
384A GLY* 1.3 75.1 - - - +
386A LEU* 1.3 57.9 + - - +
389A LYS* 4.3 23.2 + - - +
390A LEU* 4.7 1.9 - - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 3.9 7.8 - - + +
164A ASN* 4.8 5.1 + - - +
165A SER* 4.3 9.2 - - - -
168A GLN* 3.7 23.8 - - - +
190A LEU* 3.9 11.4 - - + -
191A HIS 4.6 2.0 - - - +
192A ASP* 3.6 44.6 - - + +
211A HIS* 3.7 32.5 - - + +
382A SER* 3.2 19.6 + - - +
383A GLY 3.0 8.5 + - - +
385A GLY* 1.3 78.4 - - - +
387A LEU* 1.3 69.0 + - + +
390A LEU* 3.4 17.5 - - - +
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Residues in contact with LEU 387 (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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157A TYR* 2.7 34.3 + - - +
161A VAL* 3.7 10.5 - - + -
192A ASP* 3.3 32.8 - - - +
194A GLY* 4.1 9.2 - - - -
195A TYR 4.8 0.7 - - - +
198A VAL* 3.4 29.0 - - + +
204A ALA* 4.3 8.7 - - - +
207A GLY* 3.4 29.6 - - - +
208A ALA 3.9 10.5 - - - +
211A HIS* 4.8 0.9 - - + -
220A THR* 5.1 1.1 - - - +
383A GLY 3.0 11.7 + - - +
386A LEU* 1.3 95.9 - - + +
388A GLN* 1.3 61.8 + - - +
390A LEU* 4.4 4.3 - - - -
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Residues in contact with GLN 388 (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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197A GLY 3.3 23.6 - - - +
198A VAL* 3.4 5.1 - - - +
199A SER* 3.2 33.7 + - - -
203A THR* 4.7 2.1 - - - +
384A GLY* 2.9 13.8 + - - +
386A LEU 3.8 0.4 - - - -
387A LEU* 1.3 80.8 - - - +
389A LYS* 1.3 59.8 + - - +
390A LEU* 2.8 20.4 + - - +
156B TRP* 3.8 17.7 - - + -
157B TYR* 4.8 3.8 - - - -
199B SER* 4.8 0.5 + - - -
388B GLN* 3.4 35.9 + - - +
390B LEU 3.1 26.5 + - - +
391B THR* 4.3 7.0 - - + -
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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