Contacts of the helix formed by residues 373 - 382 (chain C) in PDB entry 1G88
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 THR 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371C HIS 3.5 11.2 - - - +
372C ARG* 1.3 80.4 - - - +
374C GLU* 1.3 60.9 + - - +
375C ALA* 3.1 13.0 + - - +
376C ILE* 2.8 31.5 + - + +
377C GLU* 2.9 34.2 + - - +
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Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C THR* 1.3 74.6 - - - +
375C ALA* 1.3 57.4 + - - +
377C GLU* 3.2 17.8 + - + +
378C ARG* 2.9 60.8 + - + +
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Residues in contact with ALA 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C THR* 3.1 9.2 + - - +
374C GLU* 1.3 78.3 - - - +
376C ILE* 1.3 67.7 + - + +
378C ARG* 3.1 26.6 + - - +
379C ALA* 3.0 22.1 + - - +
522C PRO* 4.7 2.9 - - + +
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Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C GLU* 3.4 44.4 - - + +
331C MET* 4.4 18.6 - - + -
369C ASN* 6.0 0.2 - - - +
372C ARG* 3.9 7.9 - - + -
373C THR* 2.8 44.8 + - + +
375C ALA* 1.3 78.3 - - + +
377C GLU* 1.3 57.5 + - - +
379C ALA* 3.3 1.7 + - - +
380C ARG* 2.8 40.4 + - + +
522C PRO* 3.7 31.4 - - + +
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Residues in contact with GLU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A ASP* 4.3 24.0 - - + +
372C ARG* 3.8 21.9 - - + +
373C THR 2.9 18.8 + - - +
374C GLU* 3.5 20.3 - - + +
376C ILE* 1.3 74.9 - - - +
378C ARG* 1.3 66.4 + - + +
380C ARG* 3.5 8.6 + - - +
381C LEU* 3.3 24.8 + - - +
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Residues in contact with ARG 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLU* 2.9 51.7 + - + +
375C ALA* 3.4 31.9 - - - +
377C GLU* 1.3 76.3 - - - +
379C ALA* 1.3 58.8 + - - +
381C LEU* 3.0 33.0 - - + +
382C HIS* 3.4 15.6 + - + +
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ALA 3.0 8.8 + - - +
376C ILE 3.5 3.6 - - - +
378C ARG* 1.3 75.9 - - - +
380C ARG* 1.3 65.6 + - - +
382C HIS* 3.1 14.9 + - - -
383C ILE* 3.8 1.6 + - - +
506C VAL* 3.4 23.2 - - + +
507C LYS* 4.6 13.2 - - - +
522C PRO* 3.4 41.5 - - + -
523C CYS* 4.0 6.7 - - - -
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Residues in contact with ARG 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A VAL* 5.4 11.8 - - + +
493A ASP* 3.0 27.1 + - + +
328C TYR* 3.2 29.0 + - - +
330C GLU* 3.7 4.6 + - - -
352C GLY* 5.2 4.2 - - - +
364C LEU* 3.0 23.0 + - - +
365C GLY* 2.7 31.7 + - - -
367C LEU 3.7 2.4 + - - -
372C ARG* 3.5 26.0 - - - +
376C ILE* 2.8 41.9 + - + +
377C GLU* 4.0 6.7 - - - +
378C ARG 3.4 0.2 - - - -
379C ALA* 1.3 72.7 - - - +
381C LEU* 1.3 64.0 + - - +
382C HIS 3.1 1.4 + - - -
383C ILE* 3.1 31.0 + - + +
384C GLY 4.6 1.0 + - - -
523C CYS* 4.6 3.8 - - - -
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A GLY* 3.9 28.3 - - - -
492A VAL* 4.5 14.4 - - + +
493A ASP* 6.3 1.3 - - + -
545A ILE* 5.1 6.7 - - + -
377C GLU 3.3 14.3 + - - +
378C ARG* 3.0 23.1 + - + +
380C ARG* 1.3 79.7 - - - +
382C HIS* 1.3 64.6 + - + +
383C ILE 3.8 0.3 + - - -
384C GLY* 4.5 5.0 + - - -
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Residues in contact with HIS 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C ARG* 3.4 26.1 + - + +
379C ALA* 3.1 2.5 + - - -
380C ARG 3.1 1.2 - - - -
381C LEU* 1.3 83.7 + - + +
383C ILE* 1.3 62.6 + - - +
384C GLY* 3.4 2.4 - - - -
403C SER* 3.3 13.9 + - - -
405C HIS* 3.2 41.2 + + + +
506C VAL* 3.6 32.1 - - + +
507C LYS* 5.7 3.4 - - - -
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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