Contacts of the helix formed by residues 390 - 401 (chain C) in PDB entry 4RPP
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 TYR 390 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C ASP* 3.1 36.3 + - - -
25C THR* 3.6 6.9 - - - -
26C PHE* 3.8 34.8 - + + -
29C HIS* 3.5 39.9 - + + +
388C ALA 3.5 2.0 + - - -
389C ILE* 1.3 73.1 - - - +
391C HIS* 1.3 66.7 + - - +
392C LEU* 3.2 31.2 + - + +
393C GLN* 3.3 53.4 + - + +
394C LEU* 3.9 6.1 + - - +
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Residues in contact with HIS 391 (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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44C ASN* 5.4 6.5 - - - -
386C GLU* 4.0 12.8 + - + +
389C ILE* 3.3 41.1 + - + +
390C TYR* 1.3 73.4 - - - +
392C LEU* 1.3 64.2 + - - +
394C LEU* 3.6 4.5 + - - +
395C PHE* 3.2 25.9 + - - +
421C PHE* 4.2 15.4 - - + -
445C ARG* 5.0 5.1 + - - +
446C PRO 4.7 4.2 + - - -
447C ARG* 3.7 62.2 + - + +
467C ARG* 4.9 8.4 + - - -
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 4.8 13.2 - - - +
390C TYR* 3.2 35.1 + - + +
391C HIS* 1.3 78.0 - - - +
393C GLN* 1.3 63.1 + - - +
395C PHE* 4.1 6.5 - - + +
396C GLU* 3.1 48.9 + - + +
421C PHE* 5.3 3.8 - - + -
447C ARG* 5.3 4.1 - - - +
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Residues in contact with GLN 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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26C PHE* 3.9 21.4 - - - +
390C TYR* 3.3 39.2 + - + +
391C HIS 3.3 0.8 - - - -
392C LEU* 1.3 80.8 - - - +
394C LEU* 1.3 59.2 + - - +
396C GLU* 3.1 4.1 + - - +
397C GLU* 2.8 61.8 + - + +
26D PHE* 3.6 22.9 - - + +
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Residues in contact with LEU 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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318C ASN* 4.0 22.9 - - + +
355C GLY* 5.6 2.7 - - - -
389C ILE* 6.1 3.8 - - + -
390C TYR 3.9 5.4 + - - +
391C HIS* 3.6 7.2 + - - +
392C LEU 3.6 0.2 - - - -
393C GLN* 1.3 81.9 - - - +
395C PHE* 1.3 61.3 + - - +
397C GLU* 3.5 10.3 + - + +
398C LEU* 3.2 43.2 + - + +
445C ARG* 3.7 38.4 - - + -
467C ARG* 4.9 8.7 - - - +
27D LEU* 4.9 17.5 - - + -
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Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 4.7 3.4 - - - -
391C HIS 3.2 17.3 + - - +
392C LEU* 4.5 5.8 - - + -
394C LEU* 1.3 78.5 - - - +
396C GLU* 1.3 78.6 + - - +
398C LEU* 3.4 3.7 + - - +
399C ARG* 3.2 44.5 + - + +
414C VAL* 5.6 2.5 - - + -
417C VAL* 3.5 19.5 - - + -
418C GLU* 3.4 31.2 - - + -
421C PHE* 3.5 43.3 - + + -
444C TYR* 3.4 34.0 - + + +
445C ARG 4.2 2.6 + - - +
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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
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396A GLU* 3.4 5.6 - - - +
399A ARG* 2.3 34.4 + - - -
392C LEU* 3.1 40.0 + - + +
393C GLN* 3.7 3.8 - - - +
395C PHE* 1.3 88.4 - - - +
397C GLU* 1.3 65.3 + - + +
399C ARG* 2.9 24.5 + - - +
400C ARG* 3.2 31.8 + - - +
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Residues in contact with GLU 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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393C GLN* 2.8 45.5 + - + +
394C LEU* 3.9 10.8 - - + +
396C GLU* 1.3 79.0 - - + +
398C LEU* 1.3 61.5 + - - +
400C ARG* 3.4 30.7 + - - +
401C LEU* 3.5 16.7 + - - +
25D THR* 2.7 30.1 + - + +
26D PHE* 3.0 25.3 + - - +
27D LEU* 3.3 28.6 + - + +
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Residues in contact with LEU 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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422A ARG* 4.6 3.8 + - - -
318C ASN* 4.2 18.4 - - + +
319C ARG* 4.4 9.9 - - + +
394C LEU* 3.2 32.2 + - + +
395C PHE 3.7 4.0 - - - +
397C GLU* 1.3 74.4 - - - +
399C ARG* 1.3 62.0 + - - +
401C LEU* 2.9 31.6 + - + +
443C ARG* 3.2 33.0 - - - +
444C TYR* 4.0 31.0 - - + -
445C ARG* 4.3 7.0 - - + -
27D LEU* 4.1 22.2 - - + -
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Residues in contact with ARG 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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392A LEU* 6.1 1.8 - - - +
395A PHE* 3.9 12.5 - - - -
396A GLU* 3.6 20.6 + - - -
399A ARG* 3.4 11.7 - - - +
418A GLU* 2.8 37.7 + - - +
422A ARG* 3.3 29.4 + - - +
395C PHE* 3.2 50.3 + - + +
396C GLU* 2.9 37.8 + - - +
397C GLU 3.3 0.2 - - - -
398C LEU* 1.3 76.9 - - - +
400C ARG* 1.3 60.9 + - - +
401C LEU 3.4 2.9 + - - -
414C VAL* 5.9 2.2 - - + -
418C GLU* 3.9 2.8 + - - -
444C TYR* 5.6 4.0 - - + -
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Residues in contact with ARG 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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396C GLU* 3.2 20.0 + - - +
397C GLU* 3.4 22.3 + - - +
398C LEU 3.2 0.2 - - - -
399C ARG* 1.3 80.7 - - - +
401C LEU* 1.3 64.9 + - + +
24D ASP* 3.6 34.4 + - - -
25D THR* 4.0 19.0 + - - +
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Residues in contact with LEU 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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422A ARG* 5.0 5.9 + - - -
319C ARG* 4.5 16.8 - - + +
397C GLU 3.5 12.5 + - - +
398C LEU* 2.9 25.4 + - + +
399C ARG 4.2 3.8 - - - +
400C ARG* 1.3 88.0 - - + +
404C ILE 5.9 5.2 - - - -
443C ARG* 5.7 2.8 + - - -
444C TYR* 6.1 0.2 - - - -
25D THR* 5.0 15.0 - - + -
27D LEU* 4.2 23.6 - - + -
28D GLU* 6.1 1.8 - - + +
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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