Contacts of the helix formed by residues 375 - 385 (chain C) in PDB entry 2DB3
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 375 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C VAL* 4.9 0.9 - - - -
325C SER 3.5 8.5 - - - +
327C THR* 3.3 37.5 - - - +
328C ARG* 3.6 11.9 - - + +
331C ALA* 4.3 5.4 - - + -
352C VAL 3.2 3.1 + - - +
353C TYR* 3.3 17.2 - - + +
354C GLY 3.9 0.3 + - - -
374C ALA* 1.3 78.0 - - - +
376C PRO* 1.3 70.3 - - - +
377C GLY 3.4 0.2 + - - -
379C LEU* 3.3 19.7 + - - +
5G U 3.6 17.9 + - - -
6G U 2.7 19.9 + - - -
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Residues in contact with PRO 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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324C VAL* 3.9 4.7 - - + -
325C SER 3.3 14.4 - - - +
375C THR* 1.3 84.4 - - - +
377C GLY* 1.3 62.3 + - - +
379C LEU* 3.2 6.6 + - + +
380C LEU* 2.9 26.9 + - - +
404C MET* 3.4 25.1 - - + -
409C PHE* 3.7 20.4 - - + -
412C ASP* 4.2 20.0 - - + +
413C MET* 3.6 17.7 - - + -
416C ILE* 4.6 7.1 - - + +
5G U 3.8 8.5 - - - +
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Residues in contact with GLY 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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375C THR 3.4 1.4 + - - -
376C PRO* 1.3 74.6 - - - +
378C ARG* 1.3 64.0 + - - +
380C LEU* 3.2 4.9 + - - +
381C ASP 3.0 16.5 + - - -
412C ASP* 4.6 6.3 + - - -
5G U 3.0 18.9 + - - -
6G U 2.9 38.1 - - - +
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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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352C VAL* 3.5 17.0 - - + -
353C TYR* 3.4 20.2 - - - +
354C GLY* 3.6 2.4 - - - -
356C THR* 2.7 40.8 + - - +
358C PHE* 3.6 40.1 - - - +
361C GLN* 2.7 37.0 + - - +
375C THR* 3.8 0.6 + - - +
377C GLY* 1.3 72.1 - - - +
379C LEU* 1.3 63.4 + - - +
381C ASP* 3.1 3.4 + - - +
382C PHE* 3.0 30.2 + - + -
6G U 2.8 49.3 + - - +
7G U 2.9 26.6 + - - -
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Residues in contact with LEU 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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322C VAL* 4.1 26.0 - - + -
324C VAL* 4.2 9.0 - - + -
352C VAL* 3.7 7.9 - - + +
372C VAL* 5.3 4.0 - - + -
374C ALA* 4.0 16.4 - - + -
375C THR 3.3 18.2 + - - +
376C PRO* 3.2 5.3 + - + +
377C GLY 3.2 0.6 - - - -
378C ARG* 1.3 78.4 - - - +
380C LEU* 1.3 58.1 + - - +
382C PHE* 3.1 6.0 + - - +
383C VAL* 2.9 34.7 + - + +
388C ILE* 4.2 32.1 - - + -
390C PHE* 4.5 7.4 - - + -
416C ILE* 3.5 33.0 - - + -
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Residues in contact with LEU 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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376C PRO 2.9 16.7 + - - +
377C GLY* 3.7 4.7 - - - +
379C LEU* 1.3 74.2 - - - +
381C ASP* 1.3 56.3 + - - +
383C VAL* 4.1 18.4 - - + -
384C ASP* 2.8 41.3 + - - +
412C ASP* 3.4 52.0 - - + +
415C ARG* 3.5 42.0 - - + +
416C ILE* 3.6 27.4 - - + +
419C HIS* 5.9 0.4 - - - +
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Residues in contact with ASP 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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358C PHE* 3.5 19.9 - - - -
377C GLY 3.0 7.2 + - - +
378C ARG* 3.2 12.3 - - - +
380C LEU* 1.3 77.3 - - - +
382C PHE* 1.3 62.6 + - - +
384C ASP* 3.5 5.4 + - - +
385C ARG* 2.6 63.1 + - - +
6G U 2.7 50.7 + - - +
7G U 4.6 5.9 - - - +
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Residues in contact with PHE 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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352C VAL* 3.3 32.1 - - + -
358C PHE* 3.6 28.0 - + - -
361C GLN* 4.0 7.0 - - + -
362C ASN* 3.5 45.1 - - - -
365C ILE* 4.1 8.1 - - + -
378C ARG* 3.0 37.7 + - + -
379C LEU 3.4 7.4 - - - +
381C ASP* 1.3 76.5 - - - +
383C VAL* 1.3 60.4 + - - +
385C ARG* 3.3 6.6 + - - +
386C THR 3.2 2.9 + - - -
387C PHE* 2.9 45.5 + - + +
388C ILE* 3.7 28.5 - - + -
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Residues in contact with VAL 383 (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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379C LEU* 2.9 21.4 + - + +
380C LEU* 3.7 20.2 - - + +
382C PHE* 1.3 76.4 - - - +
384C ASP* 1.3 64.0 + - - +
386C THR* 2.9 21.7 + - - +
388C ILE* 3.6 23.1 - - + +
390C PHE* 3.7 30.7 - - + -
415C ARG* 5.6 0.7 - - - +
419C HIS* 3.3 41.9 + - + +
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Residues in contact with ASP 384 (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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380C LEU* 2.8 26.7 + - - +
381C ASP* 4.0 6.1 - - - +
383C VAL* 1.3 78.7 - - - +
385C ARG* 1.3 60.3 + - + +
386C THR* 3.1 8.3 + - - +
415C ARG* 2.7 38.6 + - - -
419C HIS* 5.6 1.0 - - - -
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Residues in contact with ARG 385 (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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358C PHE* 3.0 48.9 - - - +
381C ASP* 2.6 46.8 + - - +
382C PHE 3.8 4.3 - - - +
383C VAL 3.2 0.8 - - - -
384C ASP* 1.3 75.9 - - + +
386C THR* 1.3 77.1 + - - +
387C PHE* 3.3 30.6 + - + -
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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