Contacts of the helix formed by residues 381 - 398 (chain C) in PDB entry 7A62
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 GLY 381 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C ILE* 6.3 0.2 - - - -
355C LEU* 3.5 24.7 - - - +
377C LYS* 3.2 29.1 + - - -
378C GLY 4.6 0.9 - - - -
379C THR 3.1 0.6 - - - -
380C GLY* 1.3 77.2 - - - +
382C THR* 1.3 61.7 + - - +
383C ASP 3.4 0.4 - - - -
384C LEU* 3.2 12.1 - - - +
385C MET* 3.0 21.7 + - - +
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Residues in contact with THR 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LEU* 5.3 0.7 - - - -
378C GLY 4.3 6.3 + - - -
379C THR* 3.0 45.3 - - + +
381C GLY* 1.3 78.4 - - - +
383C ASP* 1.3 53.5 + - + +
385C MET* 3.1 25.0 + - - +
386C ASN* 2.4 35.2 + - - +
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Residues in contact with ASP 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C THR 3.4 12.4 - - - +
380C GLY* 2.6 35.1 - - - +
382C THR* 1.3 78.0 - - + +
384C LEU* 1.3 62.1 + - - +
385C MET 3.1 0.7 - - - -
386C ASN* 3.1 16.4 + - + +
387C PHE* 2.8 27.4 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C VAL* 4.2 22.9 - - + -
354C ILE* 4.5 13.5 - - + -
355C LEU* 4.6 3.6 - - + -
377C LYS* 4.3 20.4 - - - +
380C GLY 3.3 12.8 + - - +
381C GLY* 3.2 16.8 + - - +
382C THR 3.2 0.2 - - - -
383C ASP* 1.3 83.4 + - - +
385C MET* 1.3 62.2 + - - +
387C PHE* 3.4 8.6 + - + +
388C LEU* 3.2 31.0 + - + +
504C HEM 3.9 42.4 - - + +
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Residues in contact with MET 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 4.4 10.1 - - + -
350C VAL* 6.2 0.7 - - - -
351C THR* 5.8 4.5 - - + -
355C LEU* 4.3 25.4 - - + -
381C GLY 3.0 9.4 + - - +
382C THR* 3.2 26.5 - - - +
384C LEU* 1.3 78.6 - - - +
386C ASN* 1.3 53.0 + - - +
388C LEU* 3.2 7.8 + - - +
389C LYS* 2.6 76.7 + - + +
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Residues in contact with ASN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C THR* 2.4 30.0 + - - +
383C ASP* 3.1 18.4 + - + +
385C MET* 1.3 75.5 - - - +
387C PHE* 1.3 56.4 + - - +
389C LYS* 3.5 11.6 - - - +
390C THR* 2.6 43.2 + - - +
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Residues in contact with PHE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C HIS 3.9 8.1 - - - +
288C ALA* 3.4 48.7 - - + -
291C PHE* 3.5 27.8 - + + -
292C LEU* 3.5 26.0 - - + -
383C ASP 2.8 13.2 + - - +
384C LEU* 3.6 12.3 - - + +
385C MET 3.3 0.2 - - - -
386C ASN* 1.3 76.7 - - - +
388C LEU* 1.3 86.2 + - + +
390C THR* 3.1 5.5 + - - -
391C VAL* 3.0 40.1 + - + +
504C HEM 3.9 18.8 - - + -
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ARG* 5.3 1.9 - - - +
346C HIS* 3.9 15.0 - - + +
347C LEU* 3.5 28.9 - - + -
350C VAL* 3.7 35.9 - - + -
384C LEU* 3.2 19.2 + - + +
385C MET* 3.2 4.5 + - - +
387C PHE* 1.3 101.4 - - + +
389C LYS* 1.3 62.9 + - - +
391C VAL* 3.4 5.0 + - - +
392C ARG* 3.1 22.7 + - - +
504C HEM 4.1 30.1 - - + +
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Residues in contact with LYS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 4.0 24.2 - - + +
385C MET* 2.6 57.8 + - + +
386C ASN* 3.6 11.2 - - - +
388C LEU* 1.3 72.7 - - - +
390C THR* 1.3 56.3 + - - +
392C ARG* 3.5 20.7 + - - +
393C SER* 2.7 40.5 + - - +
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Residues in contact with THR 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C GLN* 6.0 0.2 - - - +
288C ALA* 4.4 18.6 - - + -
386C ASN* 2.6 30.4 + - - +
387C PHE* 3.1 7.7 + - - -
389C LYS* 1.3 75.1 - - - +
391C VAL* 1.3 58.0 + - + +
393C SER* 3.2 4.7 + - - -
394C THR* 2.8 43.8 + - - +
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Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C GLN* 3.1 29.5 + - + +
288C ALA* 5.2 2.0 - - + -
292C LEU* 3.9 14.8 - - + -
343C ARG* 3.3 31.9 - - - +
387C PHE* 3.0 44.0 + - + +
388C LEU* 3.9 4.3 - - - +
390C THR* 1.3 77.7 - - + +
392C ARG* 1.3 54.0 + - - +
394C THR 3.5 0.2 + - - -
395C THR* 2.5 37.1 + - - -
504C HEM 3.5 12.1 - - - +
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Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C VAL* 4.3 16.8 - - + -
343C ARG* 4.3 19.7 - - + +
344C SER* 3.2 41.5 + - - +
347C LEU* 3.9 28.0 - - + +
388C LEU 3.1 17.1 + - - +
389C LYS* 3.9 22.3 + - - +
391C VAL* 1.3 77.0 - - - +
393C SER* 1.3 54.8 + - - +
395C THR* 2.8 9.4 + - - -
396C GLU* 2.6 44.1 + - - +
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Residues in contact with SER 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LYS* 2.7 25.3 + - - +
390C THR* 3.7 4.9 - - - -
392C ARG* 1.3 79.4 + - - +
394C THR* 1.3 57.9 + - - +
396C GLU* 3.0 14.7 + - - +
397C LYS* 2.8 47.7 + - - +
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Residues in contact with THR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.8 5.6 - - + +
280C GLN 4.0 16.8 - - - +
281C GLN* 3.3 30.0 + - - +
390C THR* 2.8 32.1 + - - +
391C VAL 3.6 0.4 - - - -
393C SER* 1.3 74.0 - - - +
395C THR* 1.3 63.4 + - - +
397C LYS* 3.5 26.6 + - + +
398C SER* 3.5 13.0 + - - -
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Residues in contact with THR 395 (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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279C ILE* 3.7 26.2 - - + -
281C GLN* 2.9 13.9 + - - -
336C VAL* 3.5 13.5 - - - +
339C LEU* 4.0 22.2 - - + -
340C VAL* 3.5 21.3 - - + +
343C ARG* 3.2 12.9 + - - +
391C VAL 2.5 21.1 + - - -
392C ARG* 2.8 10.5 + - - -
394C THR* 1.3 76.6 - - - +
396C GLU* 1.3 61.9 + - - +
398C SER* 3.1 14.2 + - - -
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C VAL* 4.9 0.2 - - - -
340C VAL* 3.8 29.1 - - + +
392C ARG* 2.6 27.6 + - - +
393C SER* 3.5 13.8 + - - +
395C THR* 1.3 73.6 - - - +
397C LYS* 1.3 62.8 + - - +
398C SER 3.1 1.2 + - - -
399C LEU* 3.3 37.1 + - + +
401C LYS* 5.4 2.3 + - - +
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Residues in contact with LYS 397 (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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317C ARG* 4.6 3.5 + - - -
393C SER* 2.8 32.5 + - - +
394C THR* 3.7 20.5 + - + +
395C THR 3.2 0.4 - - - -
396C GLU* 1.3 76.2 - - + +
398C SER* 1.3 61.1 + - - +
399C LEU* 3.2 7.7 + - - +
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Residues in contact with SER 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C GLY 5.0 0.3 + - - -
279C ILE* 3.3 43.4 - - - +
317C ARG* 2.5 42.6 + - - +
332C TYR* 3.7 6.9 - - - -
336C VAL* 4.4 4.9 - - - -
394C THR 3.5 4.4 + - - -
395C THR 3.1 12.2 + - - -
397C LYS* 1.3 74.4 - - - +
399C LEU* 1.3 69.3 + - - +
400C LEU 3.4 0.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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