Contacts of the helix formed by residues 391 - 403 (chain C) in PDB entry 4ACR
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 ASP 391 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C ASP* 4.9 0.7 - - - -
291C ARG* 3.6 20.0 - - - +
387C ARG 5.0 1.9 - - - +
388C ASP 3.5 20.0 - - - +
389C VAL* 4.3 0.5 - - - -
390C GLN* 1.3 81.2 - - + +
392C PHE* 1.3 67.8 + - - +
393C TRP 3.1 3.1 + - - -
394C ILE* 3.2 10.6 + - + +
395C SER* 3.0 37.7 + - - -
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Residues in contact with PHE 392 (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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92C SER* 4.3 25.8 - - - -
93C SER* 4.5 10.1 - - - -
96C LEU* 3.6 42.8 - - + -
234C VAL* 5.2 1.6 - - + -
290C TRP* 4.3 8.0 - - - +
389C VAL* 3.1 24.7 + - + +
390C GLN 3.2 2.0 + - - -
391C ASP* 1.3 79.9 + - - +
393C TRP* 1.3 101.1 + + - +
395C SER* 3.0 19.6 + - - -
396C LEU* 3.3 42.8 - - + +
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Residues in contact with TRP 393 (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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93C SER* 6.1 0.7 - - - -
233C VAL* 4.4 9.9 - - + -
234C VAL* 4.3 26.0 - - + -
237C VAL* 3.6 32.5 - - + -
280C LEU* 5.2 2.1 - - - +
283C GLN* 3.3 37.6 - - + +
284C ALA* 3.7 18.5 + - - +
286C LEU* 3.6 26.0 - - + +
287C ASP* 4.2 16.1 + - + +
290C TRP* 3.2 54.0 - + + +
391C ASP 3.1 1.2 + - - -
392C PHE* 1.3 104.9 - + - +
394C ILE* 1.3 60.1 + - - +
395C SER 3.5 0.2 - - - -
396C LEU* 4.3 18.9 + - + +
397C PRO* 4.8 2.8 - - - +
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Residues in contact with ILE 394 (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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277C LYS* 5.5 2.4 - - - -
284C ALA* 4.4 7.6 - - + +
287C ASP* 3.7 29.8 + - + +
291C ARG* 3.4 24.2 - - - +
391C ASP* 3.4 15.3 - - + +
393C TRP* 1.3 77.9 - - - +
395C SER* 1.3 62.4 + - - +
396C LEU 3.3 2.7 - - - -
397C PRO* 3.7 13.1 - - - +
398C GLY 5.0 1.4 + - - -
431C ASP* 3.6 43.7 - - + +
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Residues in contact with SER 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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391C ASP* 3.0 33.5 + - - -
392C PHE* 3.0 21.5 + - - -
394C ILE* 1.3 78.1 - - - +
396C LEU* 1.3 62.0 + - - +
397C PRO 3.5 0.7 - - - -
398C GLY* 3.4 3.5 + - - +
399C THR* 2.9 40.2 + - - -
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Residues in contact with LEU 396 (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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89C LEU* 4.5 14.8 - - + -
92C SER* 4.5 15.0 - - - +
280C LEU* 3.6 25.8 - - + -
283C GLN* 5.0 9.4 - - + -
392C PHE* 3.3 53.2 - - + +
393C TRP* 4.3 19.7 - - + +
395C SER* 1.3 79.3 + - - +
397C PRO* 1.3 70.9 - - + +
399C THR* 3.9 5.1 - - + -
400C LEU* 3.1 33.4 + - + +
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Residues in contact with PRO 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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273C ARG* 4.1 11.9 - - + +
276C LEU* 3.7 29.7 - - + +
277C LYS* 3.7 42.6 - - + +
280C LEU* 4.4 5.4 - - + -
393C TRP 4.8 2.2 - - - +
394C ILE* 3.7 18.2 - - - +
396C LEU* 1.3 93.8 - - + +
398C GLY* 1.3 60.3 + - - +
401C CYS* 3.2 32.0 + - - -
431C ASP* 5.9 0.2 - - - +
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Residues in contact with GLY 398 (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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273C ARG* 4.6 22.4 + - - +
394C ILE 5.0 1.2 + - - -
395C SER* 3.4 6.5 + - - +
396C LEU 3.4 0.6 - - - -
397C PRO* 1.3 79.9 - - - +
399C THR* 1.3 60.6 + - - +
401C CYS* 4.3 0.9 - - - +
402C SER* 3.4 27.5 + - - -
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Residues in contact with THR 399 (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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92C SER* 5.6 3.6 - - - +
395C SER* 2.9 29.8 + - - -
396C LEU* 3.9 7.0 - - - -
398C GLY* 1.3 75.2 - - - +
400C LEU* 1.3 71.7 + - + +
402C SER* 3.4 2.4 + - - -
403C GLU* 3.1 57.2 + - + +
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Residues in contact with LEU 400 (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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85C LEU* 3.8 22.4 - - + -
88C ALA* 3.7 26.7 - - + +
89C LEU* 3.7 29.2 - - + -
92C SER* 4.5 15.5 - - - +
272C CYS* 5.1 1.0 - - - -
276C LEU* 3.7 15.5 - - + -
280C LEU* 4.9 2.0 - - + -
396C LEU* 3.1 22.0 + - + +
399C THR* 1.3 85.0 - - + +
401C CYS* 1.3 61.0 + - - +
402C SER 3.4 0.2 - - - -
403C GLU* 3.7 22.5 - - + +
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Residues in contact with CYS 401 (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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269C PRO* 4.8 5.8 - - + +
272C CYS* 2.0 67.9 - - + -
273C ARG* 3.6 13.9 - - + +
276C LEU* 3.6 4.9 - - - -
397C PRO 3.2 24.1 + - - +
398C GLY* 4.3 3.4 - - - +
400C LEU* 1.3 79.3 - - - +
402C SER* 1.3 60.7 + - - +
403C GLU 3.6 1.4 + - - +
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Residues in contact with SER 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ARG* 4.5 11.1 + - - -
398C GLY 3.4 17.1 + - - -
399C THR* 3.4 4.0 + - - -
401C CYS* 1.3 78.3 - - - +
403C GLU* 1.3 60.5 + - - +
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Residues in contact with GLU 403 (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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399C THR* 3.1 40.9 + - + +
400C LEU* 3.7 20.9 - - + +
401C CYS 3.3 2.4 - - - +
402C SER* 1.3 82.7 - - - +
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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