Contacts of the helix formed by residues 331 - 338 (chain D) in PDB entry 3G1Q
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 331 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B GLU* 5.6 6.5 + - - -
143D VAL* 3.7 10.1 - - - -
144D PRO* 5.7 1.8 - - - -
327D PRO* 5.4 3.4 - - - +
329D GLN 5.0 2.6 + - - -
330D LEU* 1.3 75.9 - - - +
332D TYR* 1.3 67.0 + - + +
333D ASN* 3.0 25.4 + - - +
334D ASN* 2.8 46.0 + - - +
335D VAL* 3.2 13.3 + - - +
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Residues in contact with TYR 332 (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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406B GLU* 3.9 30.4 + - + +
409B GLU* 4.3 8.5 - - - +
136D ILE* 3.8 25.6 - - - +
137D ALA* 5.7 0.2 - - - -
139D PHE* 3.4 38.6 - + + -
140D GLN* 4.0 38.4 - - + +
143D VAL* 3.8 18.6 - - + +
144D PRO* 5.7 0.6 - - - +
331D ASN* 1.3 74.2 - - - +
333D ASN* 1.3 74.6 + - - +
335D VAL* 3.5 0.3 + - - -
336D MET* 2.9 63.0 + - + +
337D ASP* 4.7 3.5 + - - -
430D LEU* 4.8 0.2 - - + -
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Residues in contact with ASN 333 (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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347B ARG* 3.4 45.1 + - - +
406B GLU* 5.1 4.5 - - - +
331D ASN* 3.0 14.4 + - - +
332D TYR* 1.3 91.6 - - - +
334D ASN* 1.3 66.6 + - - +
337D ASP* 2.9 41.7 + - + +
338D GLU* 3.3 15.8 + - - +
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Residues in contact with ASN 334 (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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426B LYS* 4.6 2.6 + - - -
326D PHE* 3.4 29.1 - - + -
327D PRO* 4.4 10.3 - - - +
329D GLN 4.0 3.6 + - - -
330D LEU* 3.4 25.9 - - + +
331D ASN* 2.8 50.0 + - - +
333D ASN* 1.3 77.7 - - - +
335D VAL* 1.3 59.8 + - + +
338D GLU* 3.0 49.6 + - - +
339D MET* 3.5 5.7 + - - +
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Residues in contact with VAL 335 (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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143D VAL* 4.1 12.8 - - + -
330D LEU* 4.4 15.7 - - + -
331D ASN 3.2 13.4 + - - +
332D TYR 4.3 0.7 - - - +
334D ASN* 1.3 80.4 - - + +
336D MET* 1.3 64.0 + - + +
339D MET* 3.8 21.4 + - - +
430D LEU* 3.8 28.3 - - + +
433D LYS* 2.9 52.1 + - + -
434D THR* 3.7 20.9 - - - +
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Residues in contact with MET 336 (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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409B GLU* 5.2 18.0 - - + +
139D PHE* 3.9 18.2 - - - -
332D TYR* 2.9 53.8 + - + +
335D VAL* 1.3 87.7 - - + +
337D ASP* 1.3 74.9 + - - +
339D MET 5.2 0.4 - - - -
343D GLU* 5.1 3.7 - - - +
426D LYS* 5.0 6.3 - - + +
429D LEU* 5.9 0.4 - - + -
430D LEU* 3.5 32.1 - - + +
433D LYS* 3.9 20.6 + - - +
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Residues in contact with ASP 337 (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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347B ARG* 5.3 2.8 + - - -
406B GLU* 4.8 8.7 - - - +
409B GLU* 5.4 3.3 - - - +
410B GLY* 4.6 17.6 + - - -
412B PHE 5.7 2.1 - - - +
421B LYS* 4.9 10.0 - - - +
332D TYR* 4.7 5.6 + - - -
333D ASN* 2.9 32.3 + - + +
336D MET* 1.3 97.0 - - - +
338D GLU* 1.3 67.4 + - + +
339D MET 3.7 1.6 - - - -
340D PRO* 4.8 4.4 - - - +
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Residues in contact with GLU 338 (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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347B ARG* 5.4 1.2 + - - -
421B LYS* 5.6 8.7 - - + +
425B GLN* 4.5 21.0 + - - +
426B LYS* 2.6 35.6 + - - -
322D GLU* 3.7 8.7 - - - +
326D PHE* 3.3 22.1 - - + -
333D ASN* 3.3 29.5 - - - +
334D ASN* 3.0 23.6 + - - +
337D ASP* 1.3 86.9 - - + +
339D MET* 1.3 58.8 + - - +
340D PRO* 3.3 11.5 - - - +
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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