Contacts of the helix formed by residues 320 - 326 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264W LYS* 6.2 0.2 - - - +
276W GLU* 3.8 33.9 - - + +
279W GLN* 2.4 72.0 - - - +
280W ARG* 3.5 33.4 - - - +
283W LEU* 4.9 1.3 - - + -
319W LEU* 1.3 69.5 - - - +
321W PRO* 1.3 76.6 - - + +
322W GLU* 3.0 10.7 + - + +
323W LEU* 3.1 33.2 + - + +
324W GLN 3.2 7.6 + - - -
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Residues in contact with PRO 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264W LYS* 6.1 2.2 - - - +
319W LEU 3.3 2.9 - - - +
320W ILE* 1.3 86.3 - - + +
322W GLU* 1.3 78.6 + - - +
324W GLN* 3.1 25.8 + - - +
325W GLY 3.2 1.0 + - - -
59X THR* 4.5 10.5 - - + -
389X GLU* 4.4 13.5 - - + -
390X ASN 5.7 1.3 - - - +
391X ILE* 2.9 35.8 - - + +
394X ARG* 4.9 0.4 - - - -
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Residues in contact with GLU 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280W ARG* 3.7 14.7 + - - -
283W LEU* 3.3 40.6 - - + +
320W ILE* 3.0 8.3 + - + +
321W PRO* 1.3 95.6 - - - +
323W LEU* 1.3 61.7 + - - +
325W GLY* 3.1 7.8 + - - -
326W ARG* 3.2 17.3 + - - +
59X THR* 3.4 17.0 - - - +
82X GLU* 5.5 0.3 - - - +
257X ASP* 5.6 2.0 - - - +
258X GLU* 2.7 29.2 - - - +
394X ARG* 3.1 25.8 + - - +
461X ATP 4.1 7.6 - - - +
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Residues in contact with LEU 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256W ILE* 6.5 1.1 - - + -
259W ILE* 4.5 15.3 - - + -
262W ILE* 5.7 0.4 - - + -
279W GLN* 3.5 31.9 - - + +
282W LEU* 4.9 9.0 - - + +
283W LEU* 3.2 34.3 - - + +
286W VAL* 4.4 13.2 - - + -
319W LEU* 4.9 6.1 - - + -
320W ILE* 3.1 27.9 + - + +
322W GLU* 1.3 75.9 - - - +
324W GLN* 1.3 64.9 + - - +
326W ARG* 3.0 15.4 + - - +
327W LEU* 3.2 42.3 + - + +
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Residues in contact with GLN 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54W LEU* 6.0 1.1 - - - -
316W PRO 4.4 3.5 - - - +
317W SER* 3.4 27.6 + - - -
319W LEU* 2.5 36.7 + - + +
320W ILE 3.4 7.9 - - - +
321W PRO* 3.1 17.4 + - + +
323W LEU* 1.3 77.4 - - - +
325W GLY* 1.3 59.8 + - - +
327W LEU* 4.1 7.2 + - - -
330W ARG* 3.1 32.3 + - - +
389X GLU* 3.4 37.1 - - - +
391X ILE* 4.4 12.0 - - + +
395X ARG* 5.3 3.1 + - - -
398X THR* 4.0 9.4 - - - +
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Residues in contact with GLY 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321W PRO 3.2 5.6 + - - -
322W GLU 3.1 7.3 + - - -
323W LEU 3.0 0.4 - - - -
324W GLN* 1.3 78.7 - - - +
326W ARG* 1.3 67.1 + - - +
327W LEU 3.3 3.8 - - - -
328W PRO* 3.4 16.5 - - - +
391X ILE* 4.0 11.6 - - - +
394X ARG* 3.9 27.8 - - - +
397X HIS* 4.5 4.9 + - - -
398X THR* 4.2 4.9 - - - -
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Residues in contact with ARG 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49W THR* 3.9 24.9 + - - +
50W PRO 5.4 1.4 + - - -
52W ASN* 3.5 23.0 + - - +
283W LEU* 5.0 0.9 - - + -
286W VAL* 3.3 29.8 + - + +
287W GLU* 3.4 37.1 + - + +
322W GLU 3.3 16.8 - - - +
323W LEU* 3.0 8.2 + - - +
325W GLY* 1.3 82.7 - - - +
327W LEU* 1.3 72.7 + - - +
328W PRO* 3.3 6.3 - - - +
394X ARG* 3.5 37.3 - - - +
397X HIS* 5.3 8.7 + - - -
461X ATP 5.1 5.1 + - - -
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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