Contacts of the helix formed by residues 320 - 326 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264V LYS* 6.2 0.2 - - - +
276V GLU* 3.8 32.8 - - + +
279V GLN* 2.4 72.4 - - + +
280V ARG* 3.5 35.4 - - - +
283V LEU* 4.9 1.3 - - + -
319V LEU 1.3 68.5 - - - +
321V PRO* 1.3 74.8 - - + +
322V GLU* 3.1 9.8 + - + +
323V LEU* 3.1 32.5 + - + +
324V GLN* 3.3 7.6 + - - +
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Residues in contact with PRO 321 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264V LYS* 6.1 2.2 - - - +
319V LEU 3.3 3.1 - - - +
320V ILE* 1.3 86.6 - - + +
322V GLU* 1.3 78.4 + - - +
324V GLN* 3.1 24.8 + - - +
325V GLY* 3.2 2.4 + - - -
59W THR* 4.6 8.7 - - + -
389W GLU* 4.4 14.1 - - + -
390W ASN 6.0 0.7 - - - -
391W ILE* 3.1 36.6 - - + +
394W ARG* 4.9 0.7 + - - -
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Residues in contact with GLU 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280V ARG* 3.7 16.0 + - - +
283V LEU* 3.4 40.5 - - + +
287V GLU* 5.4 0.2 - - - +
320V ILE* 4.6 6.7 - - + +
321V PRO* 1.3 94.8 - - - +
323V LEU* 1.3 62.6 + - - +
325V GLY* 3.1 8.7 + - - -
326V ARG* 3.2 17.3 + - - +
59W THR* 3.6 11.9 - - - +
82W GLU* 5.1 0.3 - - - +
257W ASP* 5.3 0.9 - - - +
258W GLU* 2.7 29.6 - - - +
394W ARG* 3.4 26.0 + - - +
460W ATP 4.2 12.3 - - - +
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Residues in contact with LEU 323 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256V ILE* 6.5 0.9 - - + -
259V ILE* 4.5 15.3 - - + -
262V ILE* 5.7 0.4 - - + -
279V GLN* 3.5 43.1 - - + +
282V LEU* 4.9 8.5 - - + +
283V LEU* 3.2 34.3 - - + +
286V VAL* 4.4 14.4 - - + -
319V LEU* 4.9 6.1 - - + -
320V ILE* 3.1 16.3 + - + +
322V GLU* 1.3 76.1 - - - +
324V GLN* 1.3 66.5 + - - +
326V ARG* 3.0 15.8 + - - +
327V LEU* 3.1 41.5 + - + +
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Residues in contact with GLN 324 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V LEU* 6.0 0.9 - - - -
316V PRO 4.4 2.9 - - - +
317V SER* 3.4 31.7 + - - -
319V LEU* 2.5 37.5 + - + +
320V ILE 3.4 7.6 - - - +
321V PRO* 3.1 18.7 + - + +
323V LEU* 1.3 77.2 - - - +
325V GLY* 1.3 58.0 + - - +
326V ARG 3.8 0.2 + - - -
327V LEU* 4.1 7.0 + - - -
330V ARG* 3.1 32.1 + - - +
389W GLU* 3.6 31.7 - - - +
391W ILE* 4.6 11.8 - - + +
395W ARG* 5.5 3.7 + - - +
398W THR* 4.1 9.5 - - - +
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Residues in contact with GLY 325 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321V PRO 3.2 6.5 + - - -
322V GLU 3.1 7.3 + - - -
323V LEU 3.0 0.6 - - - -
324V GLN* 1.3 76.3 - - - +
326V ARG* 1.3 70.2 + - - +
327V LEU 3.4 3.1 - - - -
328V PRO* 3.5 16.3 - - - +
391W ILE* 4.2 10.5 - - - +
394W ARG* 4.1 26.7 - - - +
397W HIS* 4.6 5.4 + - - -
398W THR* 4.2 5.4 - - - -
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Residues in contact with ARG 326 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49V THR* 3.9 25.3 + - - +
50V PRO 5.4 1.2 + - - -
52V ASN* 3.4 24.2 + - - +
283V LEU* 5.1 0.7 - - + -
286V VAL* 3.3 30.7 + - + +
287V GLU* 3.4 37.6 + - + +
322V GLU 3.2 18.1 + - - +
323V LEU* 3.0 7.8 + - - +
325V GLY* 1.3 84.5 - - - +
327V LEU* 1.3 72.8 + - - +
328V PRO* 3.3 7.0 - - - -
394W ARG* 3.7 33.2 - - - +
397W HIS* 5.4 7.1 + - - -
460W ATP 5.2 4.9 + - - -
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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