Contacts of the helix formed by residues 320 - 326 (chain U) in PDB entry 1G3I
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 320 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264U LYS* 6.2 0.4 - - - +
276U GLU* 3.8 34.1 - - + +
279U GLN* 2.4 72.4 - - + +
280U ARG* 3.5 35.2 - - - +
283U LEU* 4.9 1.1 - - + -
319U LEU 1.3 68.2 - - - +
321U PRO* 1.3 76.3 - - + +
322U GLU* 3.0 9.6 + - + +
323U LEU* 3.1 32.5 + - + +
324U GLN* 3.2 7.8 + - - +
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Residues in contact with PRO 321 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264U LYS* 6.1 2.2 - - - +
319U LEU 3.3 2.6 - - - +
320U ILE* 1.3 86.9 - - + +
322U GLU* 1.3 78.6 + - - +
324U GLN* 3.1 25.6 + - - +
325U GLY 3.2 1.4 + - - -
59V THR* 4.6 9.9 - - + -
389V GLU* 4.3 14.6 - - + -
390V ASN 5.9 0.4 - - - +
391V ILE* 3.0 37.0 - - + +
394V ARG* 4.9 0.3 + - - -
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Residues in contact with GLU 322 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U ARG* 3.7 14.7 + - - +
283U LEU* 3.3 39.2 - - + +
287U GLU* 5.4 0.2 - - - +
320U ILE* 3.1 7.5 - - + +
321U PRO* 1.3 93.5 - - - +
323U LEU* 1.3 64.4 + - - +
325U GLY* 3.1 8.7 + - - -
326U ARG* 3.2 16.8 + - - +
59V THR* 3.5 10.3 - - - +
82V GLU* 5.4 0.3 - - - +
257V ASP* 5.5 1.8 - - - +
258V GLU* 2.8 28.3 - - - +
394V ARG* 3.3 25.3 + - - +
459V ATP 3.7 14.8 - - - +
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Residues in contact with LEU 323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256U ILE* 6.5 0.7 - - + -
259U ILE* 4.5 15.5 - - + -
262U ILE* 5.7 0.4 - - + -
279U GLN* 3.5 42.2 - - + +
282U LEU* 5.0 9.0 - - + +
283U LEU* 3.2 34.5 - - + +
286U VAL* 4.4 14.6 - - + -
319U LEU* 4.9 6.1 - - + -
320U ILE* 3.1 15.6 + - + +
322U GLU* 1.3 76.1 - - - +
324U GLN* 1.3 67.4 + - - +
326U ARG* 3.0 15.7 + - - +
327U LEU* 3.2 40.8 + - + +
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Residues in contact with GLN 324 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U LEU* 5.9 0.4 - - - -
316U PRO 4.4 3.5 - - - +
317U SER* 3.4 27.4 + - - -
319U LEU* 2.6 37.8 + - + +
320U ILE 3.4 7.4 - - - +
321U PRO* 3.1 17.9 + - + +
323U LEU* 1.3 77.9 - - - +
325U GLY* 1.3 59.3 + - - +
327U LEU* 4.0 7.5 + - - -
330U ARG* 3.1 33.2 + - - +
389V GLU* 3.4 36.2 - - - +
391V ILE* 4.5 12.1 - - + +
395V ARG* 5.4 3.2 + - - +
398V THR* 4.1 9.0 - - - +
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Residues in contact with GLY 325 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321U PRO 3.2 6.0 + - - -
322U GLU 3.1 6.7 + - - -
323U LEU 3.0 0.4 - - - -
324U GLN* 1.3 77.1 - - - +
326U ARG* 1.3 69.1 + - - +
327U LEU 3.3 3.4 - - - -
328U PRO* 3.4 16.7 - - - +
391V ILE* 4.1 11.8 - - - +
394V ARG* 4.0 27.0 - - - +
397V HIS* 4.7 4.7 + - - -
398V THR* 4.3 4.5 - - - -
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Residues in contact with ARG 326 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U THR* 3.8 25.0 + - - +
50U PRO 5.4 1.4 + - - -
52U ASN* 3.4 23.3 + - - +
283U LEU* 5.1 0.9 - - + -
286U VAL* 3.3 31.2 + - + +
287U GLU* 3.4 36.5 + - + +
322U GLU 3.3 18.2 - - - +
323U LEU* 3.0 7.4 + - - +
325U GLY* 1.3 83.6 - - - +
327U LEU* 1.3 71.9 + - - +
328U PRO* 3.3 6.9 - - - +
394V ARG* 3.5 37.4 - - - +
397V HIS* 5.5 7.6 + - - -
459V ATP 5.4 4.8 + - - -
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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