Contacts of the helix formed by residues 320 - 326 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264S LYS* 6.2 0.4 - - - +
276S GLU* 3.8 34.1 - - + +
279S GLN* 2.4 72.6 - - - +
280S ARG* 3.5 33.9 - - - +
283S LEU* 4.9 1.1 - - + -
319S LEU* 1.3 69.0 - - - +
321S PRO* 1.3 74.2 - - + +
322S GLU* 3.0 10.6 + - + +
323S LEU* 3.1 33.0 + - + +
324S GLN 3.2 7.8 + - - -
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Residues in contact with PRO 321 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S LYS* 6.1 2.7 - - - +
319S LEU 3.3 2.9 - - - +
320S ILE* 1.3 86.0 - - + +
322S GLU* 1.3 79.2 + - - +
324S GLN* 3.1 25.9 + - - +
325S GLY 3.2 1.7 + - - -
59T THR* 4.6 9.0 - - + -
389T GLU* 4.4 12.8 - - + -
390T ASN 6.0 0.7 - - - -
391T ILE* 3.1 35.0 - - + +
394T ARG* 4.9 0.3 + - - -
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Residues in contact with GLU 322 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280S ARG* 3.7 14.8 + - - +
283S LEU* 3.3 41.0 - - + +
287S GLU* 5.4 0.2 - - - +
320S ILE* 3.0 7.3 + - + +
321S PRO* 1.3 95.7 - - - +
323S LEU* 1.3 61.2 + - - +
325S GLY* 3.1 8.8 + - - -
326S ARG* 3.2 16.5 + - - +
59T THR* 3.6 11.2 - - - +
257T ASP* 5.5 1.8 - - - +
258T GLU* 2.6 30.7 - - - +
394T ARG* 3.4 25.0 + - - +
457T ATP 4.2 12.6 - - - +
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Residues in contact with LEU 323 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256S ILE* 6.5 0.9 - - + -
259S ILE* 4.5 15.0 - - + -
262S ILE* 5.7 0.4 - - + -
279S GLN* 3.5 30.1 - - + +
282S LEU* 4.9 9.4 - - + +
283S LEU* 3.2 34.3 - - + +
286S VAL* 4.4 13.7 - - + -
319S LEU* 4.9 6.1 - - + -
320S ILE* 3.1 29.9 + - + +
322S GLU* 1.3 76.1 - - - +
324S GLN* 1.3 65.2 + - - +
326S ARG* 3.0 15.5 + - - +
327S LEU* 3.2 42.1 + - + +
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Residues in contact with GLN 324 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S LEU* 6.0 0.9 - - - -
316S PRO 4.4 3.5 - - - +
317S SER* 3.4 28.1 + - - -
319S LEU* 2.6 37.8 + - + +
320S ILE 3.4 7.9 - - - +
321S PRO* 3.1 18.3 + - + +
323S LEU* 1.3 78.0 - - - +
325S GLY* 1.3 58.6 + - - +
327S LEU* 4.1 9.5 + - - -
330S ARG* 3.1 32.1 + - - +
389T GLU* 3.5 35.8 - - - +
391T ILE* 4.6 12.3 - - + +
395T ARG* 5.6 2.6 + - - +
398T THR* 4.2 6.4 - - - +
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Residues in contact with GLY 325 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321S PRO 3.2 5.6 + - - -
322S GLU 3.1 7.1 + - - -
323S LEU 3.0 0.6 - - - -
324S GLN* 1.3 76.5 - - - +
326S ARG* 1.3 68.1 + - - +
327S LEU 3.3 4.7 - - - -
328S PRO* 3.4 15.9 - - - +
391T ILE* 4.2 12.3 - - - +
394T ARG* 4.1 26.2 - - - +
397T HIS* 4.7 4.5 + - - -
398T THR* 4.4 5.2 - - - -
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Residues in contact with ARG 326 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S THR* 3.8 25.7 + - - +
50S PRO 5.4 1.6 + - - -
52S ASN* 3.5 22.9 + - - +
283S LEU* 5.1 0.9 - - + -
286S VAL* 3.3 31.6 + - + +
287S GLU* 3.4 37.2 + - + +
322S GLU 3.2 19.0 + - - +
323S LEU* 3.0 7.7 + - - +
325S GLY* 1.3 84.5 - - - +
327S LEU* 1.3 72.9 + - - +
328S PRO* 3.3 6.0 - - - +
394T ARG* 3.6 33.5 - - - +
397T HIS* 5.6 6.7 + - - -
457T ATP 5.5 4.4 + - - -
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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