Contacts of the helix formed by residues 320 - 325 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264F LYS* 4.0 5.8 - - - +
276F GLU* 4.1 22.9 - - + +
279F GLN* 2.8 48.4 + - + +
280F ARG* 3.7 26.7 - - + +
283F LEU* 3.6 30.1 - - + -
319F LEU* 1.3 72.0 - - - +
321F PRO* 1.3 60.6 - - + -
322F GLU* 4.2 7.4 - - + +
323F LEU* 2.8 23.7 + - + +
324F GLN 2.7 28.8 + - - -
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Residues in contact with PRO 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E THR* 4.8 12.3 - - + +
389E GLU* 3.7 34.5 - - + +
390E ASN 5.5 1.1 - - - +
391E ILE* 3.6 25.6 - - + +
394E ARG* 5.8 1.6 - - - +
319F LEU 3.5 6.0 - - - +
320F ILE* 1.3 82.2 - - + +
322F GLU* 1.3 79.1 + - - +
324F GLN* 2.9 21.3 + - + +
325F GLY* 3.0 10.4 + - - -
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Residues in contact with GLU 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR* 4.3 12.6 + - + +
82E GLU* 5.4 2.2 - - - +
257E ASP* 5.5 0.9 - - - +
258E GLU* 2.6 34.0 - - - +
394E ARG* 5.4 4.8 - - - +
454E ATP 3.4 28.2 + - - +
280F ARG* 5.4 2.6 + - - -
283F LEU* 3.4 33.6 - - + +
287F GLU* 4.3 8.1 - - - +
320F ILE* 4.1 8.2 - - + +
321F PRO* 1.3 94.2 - - - +
323F LEU* 1.3 57.6 + - - +
325F GLY* 3.7 3.6 + - - -
326F ARG* 3.3 22.5 + - - +
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Residues in contact with LEU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F ILE* 6.6 0.2 - - + -
259F ILE* 4.3 22.2 - - + -
279F GLN* 3.8 37.0 - - + +
282F LEU* 5.4 6.5 - - + -
283F LEU* 3.9 13.7 - - + +
286F VAL* 4.3 31.9 - - + -
319F LEU* 4.5 9.9 - - + -
320F ILE* 2.8 21.5 + - + +
322F GLU* 1.3 71.9 - - - +
324F GLN* 1.3 63.1 + - - +
325F GLY 2.9 7.7 + - - -
326F ARG* 3.0 11.3 + - - +
327F LEU* 3.3 30.1 + - + +
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Residues in contact with GLN 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E GLU* 4.0 30.6 + - - +
391E ILE* 4.8 10.5 - - + +
395E ARG* 4.7 9.7 + - - +
398E THR* 4.9 3.3 + - - -
316F PRO 4.1 3.3 + - - +
317F SER* 3.7 34.6 + - - -
319F LEU* 3.2 34.0 + - + +
320F ILE 2.7 15.8 + - - +
321F PRO* 2.9 9.4 + - + +
323F LEU* 1.3 73.6 - - - +
325F GLY* 1.3 57.9 + - - +
327F LEU* 3.8 9.3 - - - +
330F ARG* 3.2 31.2 + - - +
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Residues in contact with GLY 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E ILE* 4.2 18.4 - - - -
394E ARG* 4.0 26.6 + - - +
397E HIS* 5.1 4.7 - - - +
398E THR* 4.7 9.3 + - - -
321F PRO 3.0 11.5 + - - -
322F GLU 4.2 1.3 - - - -
323F LEU 2.9 0.8 - - - -
324F GLN* 1.3 79.7 - - - +
326F ARG* 1.3 59.9 + - - +
327F LEU* 3.1 6.5 + - - -
328F PRO* 4.4 8.8 - - - +
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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