Contacts of the helix formed by residues 373 - 387 (chain C) in PDB entry 6AH0
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 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C SER 4.2 0.2 + - - -
369C PHE* 2.9 13.8 + - - +
370C VAL 3.6 0.6 + - - -
372C PHE* 1.3 80.8 - - - +
374C LEU* 1.3 64.3 + - - +
375C GLU 3.2 1.3 - - - -
376C PRO* 3.5 2.6 - - - +
377C LEU* 3.0 20.8 + - - -
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Residues in contact with LEU 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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271C PRO* 5.7 10.5 - - - +
369C PHE 3.3 11.1 + - - -
370C VAL* 3.4 5.8 + - - +
373C ILE* 1.3 75.1 - - - +
375C GLU* 1.3 64.4 + - - +
377C LEU* 3.2 1.2 + - - +
378C TYR* 2.9 22.3 + - - -
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Residues in contact with GLU 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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388A LEU 5.0 2.7 - - - +
389A LYS* 6.3 0.4 - - - -
393A LEU* 5.6 1.4 - - - -
271C PRO* 5.9 1.7 - - - +
370C VAL* 2.8 18.4 + - - +
371C GLU* 5.1 3.1 - - - +
374C LEU* 1.3 77.5 - - - +
376C PRO* 1.3 56.9 - - - +
378C TYR* 3.9 1.1 - - - +
379C LYS* 3.1 22.7 + - - -
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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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386A PRO* 6.2 0.9 - - + -
388A LEU* 3.9 30.8 - - - +
389A LYS 5.0 0.4 - - - +
371C GLU 5.1 4.2 - - - -
372C PHE 5.3 2.4 - - - +
373C ILE* 3.5 6.5 - - - +
374C LEU 3.4 0.2 - - - -
375C GLU* 1.3 71.4 - - - +
377C LEU* 1.3 59.8 + - - +
379C LYS* 3.7 0.8 - - - +
380C ILE* 2.9 26.5 + - - -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ILE 3.0 16.4 + - - -
374C LEU* 3.2 3.6 + - - +
376C PRO* 1.3 76.7 - - - +
378C TYR* 1.3 61.3 + - - +
380C ILE* 3.3 2.3 + - - +
381C LEU* 3.1 19.1 + - - -
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Residues in contact with TYR 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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393A LEU* 3.6 8.3 - - - +
374C LEU 2.9 15.8 + - - -
375C GLU 3.9 1.3 - - - -
377C LEU* 1.3 74.6 - - - +
379C LYS* 1.3 57.8 + - - +
381C LEU* 3.2 1.5 + - - +
382C ALA* 2.8 29.3 + - - -
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Residues in contact with LYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 4.7 13.5 - - - -
391A THR* 5.1 2.5 - - - -
392A PRO 4.1 8.2 - - - +
393A LEU* 4.0 19.0 - - - +
375C GLU 3.1 15.2 + - - -
376C PRO 3.3 2.7 + - - -
377C LEU 3.2 0.2 - - - -
378C TYR* 1.3 75.3 - - - +
380C ILE* 1.3 63.8 + - - +
383C GLN* 3.1 20.3 + - - -
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 5.5 1.2 - - - +
376C PRO 2.9 15.7 + - - -
377C LEU* 3.3 2.2 + - - +
378C TYR 3.2 0.2 - - - -
379C LYS* 1.3 77.8 - - - +
381C LEU* 1.3 61.0 + - - +
383C GLN* 3.5 0.9 + - - -
384C VAL* 3.2 18.0 + - - -
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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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377C LEU 3.1 13.4 + - - -
378C TYR* 3.7 2.7 - - - +
380C ILE* 1.3 77.1 - - - +
382C ALA* 1.3 58.3 + - - +
384C VAL* 3.2 1.9 + - - -
385C VAL* 2.9 28.1 + - - -
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Residues in contact with ALA 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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392A PRO 5.2 0.4 - - - -
393A LEU 3.3 25.4 - - - -
394A TYR* 5.0 4.0 - - - +
395A THR* 4.9 4.1 + - - -
398A THR* 4.5 2.0 - - - +
378C TYR 2.8 11.0 + - - -
381C LEU* 1.3 79.1 - - - +
383C GLN* 1.3 52.6 + - - +
385C VAL* 5.4 0.2 - - - +
386C GLY* 2.7 35.1 + - - +
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Residues in contact with GLN 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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392A PRO 4.8 4.1 + - - -
393A LEU 4.6 0.2 + - - -
379C LYS 3.1 16.0 + - - -
380C ILE 4.0 1.3 - - - -
382C ALA* 1.3 75.7 - - - +
384C VAL* 1.3 58.6 + - - +
387C ASP* 2.9 25.2 + - - +
388C VAL 3.1 11.6 + - - -
392C LEU* 5.1 9.7 - - - +
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Residues in contact with VAL 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 ILE 3.2 9.9 + - - -
381C LEU* 3.2 6.0 + - - +
383C GLN* 1.3 80.6 - - - +
385C VAL* 1.3 61.1 + - - +
387C ASP 4.7 0.3 - - - +
388C VAL* 4.2 15.2 - - - +
392C LEU* 6.2 0.2 - - - +
412C ILE* 5.5 7.7 - - - +
416C LEU* 6.1 5.8 - - - +
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Residues in contact with VAL 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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398A THR 4.2 2.9 - - - -
401A GLY* 3.1 32.1 - - - -
402A ILE* 5.0 1.8 - - - +
381C LEU 2.9 13.4 + - - -
382C ALA* 5.4 0.2 - - - +
384C VAL* 1.3 77.4 - - - +
386C GLY* 1.3 62.9 + - - +
387C ASP 3.6 3.3 + - - +
412C ILE* 6.1 3.6 - - - +
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Residues in contact with GLY 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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395A THR* 5.0 4.9 - - - -
397A ASN* 2.4 33.6 + - - +
398A THR* 2.5 32.5 + - - +
382C ALA* 2.7 21.7 + - - +
385C VAL* 1.3 72.9 - - - +
387C ASP* 1.3 56.7 + - - +
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Residues in contact with ASP 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR* 5.6 1.5 - - - +
397A ASN 5.5 0.7 - - - +
382C ALA 3.8 1.2 + - - -
383C GLN* 2.9 11.0 + - - +
384C VAL 4.5 2.6 - - - +
385C VAL 4.5 2.4 - - - +
386C GLY* 1.3 78.1 - - - +
388C VAL* 1.3 57.7 + - - +
389C ASP 3.1 10.6 + - - +
390C THR 4.7 5.4 - - - +
391C SER 5.7 1.6 - - - +
392C LEU 5.8 0.2 - - - +
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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