Contacts of the helix formed by residues 320 - 326 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264T LYS* 6.2 0.4 - - - +
276T GLU* 3.8 34.1 - - + +
279T GLN* 2.4 73.3 - - - +
280T ARG* 3.5 34.5 - - - +
283T LEU* 4.9 1.1 - - + -
319T LEU 1.3 68.2 - - - +
321T PRO* 1.3 75.5 - - + +
322T GLU* 3.1 10.6 + - + +
323T LEU* 3.1 33.2 + - + +
324T GLN* 3.2 7.6 + - - +
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Residues in contact with PRO 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264T LYS* 6.1 2.5 - - - +
319T LEU 3.3 2.9 - - - +
320T ILE* 1.3 86.9 - - + +
322T GLU* 1.3 77.1 + - - +
324T GLN* 3.1 25.4 + - - +
325T GLY* 3.2 1.6 + - - -
59U THR* 4.5 10.8 - - + -
389U GLU* 4.5 12.8 - - + -
390U ASN 5.9 0.9 - - - +
391U ILE* 3.0 35.4 - - + +
394U ARG* 4.8 0.6 + - - -
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Residues in contact with GLU 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280T ARG* 3.7 14.7 + - - -
283T LEU* 3.3 41.2 - - + +
287T GLU* 5.5 0.2 - - - +
320T ILE* 3.1 6.9 + - + -
321T PRO* 1.3 96.6 - - - +
323T LEU* 1.3 62.9 + - - +
325T GLY* 3.1 8.7 + - - -
326T ARG* 3.3 16.5 + - - +
59U THR* 3.5 11.5 + - - +
82U GLU* 5.3 0.6 - - - +
257U ASP* 5.4 0.9 - - - +
258U GLU* 2.7 30.0 - - - +
394U ARG* 3.3 24.4 + - - +
458U ATP 4.0 14.1 - - - +
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Residues in contact with LEU 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256T ILE* 6.5 1.1 - - + -
259T ILE* 4.5 15.3 - - + -
262T ILE* 5.7 0.2 - - + -
279T GLN* 3.5 31.2 - - + +
282T LEU* 4.9 8.3 - - + +
283T LEU* 3.2 34.3 - - + +
286T VAL* 4.4 13.7 - - + -
319T LEU* 4.9 6.5 - - + -
320T ILE* 3.1 28.8 + - + +
322T GLU* 1.3 77.4 - - - +
324T GLN* 1.3 66.1 + - - +
326T ARG* 3.0 14.8 + - - +
327T LEU* 3.2 40.3 + - + +
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Residues in contact with GLN 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T LEU* 6.0 0.7 - - - -
316T PRO 4.4 3.8 - - - +
317T SER* 3.4 28.2 + - - -
319T LEU* 2.6 37.3 + - + +
320T ILE 3.4 8.1 - - - +
321T PRO* 3.1 18.1 + - + +
323T LEU* 1.3 78.8 - - - +
325T GLY* 1.3 59.8 + - - +
327T LEU* 4.1 6.9 + - - +
330T ARG* 3.1 32.2 + - - +
389U GLU* 3.4 35.3 - - - +
391U ILE* 4.4 11.5 - - + +
395U ARG* 5.3 3.6 + - - -
398U THR* 4.0 9.2 - - - +
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Residues in contact with GLY 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321T PRO 3.2 6.3 + - - -
322T GLU 3.1 6.7 + - - -
323T LEU 3.0 0.4 - - - -
324T GLN* 1.3 76.3 - - - +
326T ARG* 1.3 69.3 + - - +
327T LEU 3.3 3.6 - - - -
328T PRO* 3.4 17.0 - - - +
391U ILE* 4.2 10.3 - - - +
394U ARG* 4.0 28.0 - - - +
397U HIS* 4.5 4.7 + - - -
398U THR* 4.4 5.6 - - - -
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Residues in contact with ARG 326 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T THR* 3.9 25.0 + - - +
50T PRO 5.4 1.2 + - - -
52T ASN* 3.4 23.7 + - - +
283T LEU* 5.1 0.7 - - + -
286T VAL* 3.3 29.8 + - + +
287T GLU* 3.4 37.6 + - + +
322T GLU 3.3 17.0 - - - +
323T LEU* 3.0 8.9 + - - +
325T GLY* 1.3 82.9 - - - +
327T LEU* 1.3 71.9 + - - +
328T PRO* 3.3 6.7 - - - +
394U ARG* 3.6 36.1 - - - +
397U HIS* 5.5 7.6 + - - -
458U ATP 5.1 6.7 + - - -
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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