Contacts of the helix formed by residues 379 - 387 (chain C) in PDB entry 4K9N
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 379 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C PRO* 3.4 33.7 - - + -
359C PHE* 3.5 21.2 - - - -
374C ASN* 4.9 0.6 + - - -
376C SER* 2.8 33.6 + - - +
378C SER* 1.3 95.3 - - - +
380C THR* 1.3 64.5 + - - +
381C ALA 3.3 2.5 - - - -
382C GLN* 3.2 16.6 + - - +
383C MET* 3.1 20.9 + - - +
453C MET* 4.7 2.6 - - + +
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Residues in contact with THR 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 4.1 12.8 - - + -
374C ASN* 2.8 32.3 + - - +
376C SER 3.6 7.4 + - - -
377C THR* 3.9 13.3 + - - -
378C SER 3.7 1.6 - - - -
379C THR* 1.3 76.7 - - - +
381C ALA* 1.3 62.9 + - - +
383C MET* 3.2 5.1 + - - +
384C TRP* 3.0 40.7 + - + +
395C TYR* 4.0 3.1 - - - +
397C PHE* 4.4 11.3 - - + -
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Residues in contact with ALA 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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252C LEU* 5.1 7.6 - - + -
379C THR 3.3 0.4 - - - -
380C THR* 1.3 80.7 - - - +
382C GLN* 1.3 72.2 + - + +
384C TRP* 3.4 5.1 + - - +
385C GLN* 3.2 37.7 + - - +
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Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C PRO* 4.3 7.9 - - - +
356C GLU* 3.8 37.4 + - + +
359C PHE* 4.1 14.1 - - + -
378C SER 3.7 9.5 + - - +
379C THR* 3.2 39.4 + - - +
380C THR 4.0 0.2 + - - -
381C ALA* 1.3 84.0 - - + +
383C MET* 1.3 67.1 + - - +
385C GLN* 3.2 9.1 + - - +
386C ARG* 3.0 33.5 + - - +
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Residues in contact with MET 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C PHE* 3.6 29.3 - - + -
372C TYR* 3.8 20.4 - - + -
373C LEU 3.9 17.0 - - - +
374C ASN* 3.6 34.5 - - + +
379C THR 3.1 11.9 + - - +
380C THR 3.5 10.1 - - - +
382C GLN* 1.3 77.4 - - - +
384C TRP* 1.3 62.9 + - - +
387C LEU* 3.2 54.2 + - + +
389C MET* 5.4 1.2 - - + +
395C TYR* 4.2 13.9 - - + -
425C VAL* 4.1 14.8 - - + -
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Residues in contact with TRP 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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233C VAL* 3.9 13.7 - - + -
237C ALA* 3.8 14.5 + - + +
239C ARG 3.8 9.6 - - - -
240C CYS* 3.6 44.2 - - + -
244C THR* 4.1 11.0 - - + +
245C ARG* 4.8 4.0 + - - -
249C PHE* 3.9 31.6 - + - -
251C GLY* 6.1 0.7 - - - -
252C LEU* 3.6 42.7 - - + +
380C THR* 3.0 30.7 + - + +
381C ALA* 3.8 5.8 - - - +
382C GLN 3.3 0.2 - - - -
383C MET* 1.3 77.5 - - - +
385C GLN* 1.3 62.2 + - + +
387C LEU 4.2 9.2 - - - +
389C MET* 4.3 8.9 - - + +
395C TYR* 3.3 43.2 + + - -
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Residues in contact with GLN 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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245C ARG* 3.0 23.8 + - - +
343C PRO* 3.6 21.3 - - + +
381C ALA* 3.2 27.9 + - - +
382C GLN* 3.2 8.7 + - - +
383C MET 3.1 0.6 - - - -
384C TRP* 1.3 81.7 - - + +
386C ARG* 1.3 68.3 + - + +
387C LEU 3.7 0.4 - - - -
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Residues in contact with ARG 386 (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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245C ARG* 4.0 6.0 + - - +
343C PRO* 3.9 26.0 + - + +
344C ALA* 3.0 31.7 + - - +
345C LYS* 4.7 0.6 - - - +
346C VAL* 3.9 7.9 - - - +
356C GLU* 3.4 49.9 - - - +
359C PHE* 3.8 14.5 - - + +
360C ASP* 3.0 40.8 + - - +
363C ASN* 3.3 28.2 + - - +
382C GLN* 3.0 23.0 + - - +
385C GLN* 1.3 89.2 + - + +
387C LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 387 (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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244C THR* 3.0 17.2 + - - -
245C ARG* 4.2 5.2 + - - -
359C PHE* 3.5 35.4 - - + +
362C LEU* 4.2 6.7 - - + -
363C ASN* 3.7 12.8 - - + +
372C TYR* 3.6 46.2 - - + +
383C MET* 3.2 43.5 + - + +
384C TRP 4.2 5.5 - - - +
385C GLN 3.7 0.2 - - - -
386C ARG* 1.3 79.0 - - - +
388C ASN* 1.3 60.0 + - - +
389C MET* 3.4 22.9 + - + +
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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