Contacts of the helix formed by residues 441 - 453 (chain C) in PDB entry 4R0C
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 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C VAL* 4.1 13.4 + - - +
134C ASP* 2.4 37.4 + - - -
137C TYR* 3.4 71.1 - + + -
138C VAL* 4.6 1.3 - - + -
439C MET* 3.3 10.1 - - + -
440C PRO* 1.3 90.8 - - + +
442C PHE* 1.3 65.2 + - - +
443C VAL 3.4 2.2 - - - -
444C LEU* 3.2 26.1 + - + +
445C VAL* 3.1 23.5 + - + +
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Residues in contact with PHE 442 (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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163C PHE* 4.6 12.8 - + - -
434C ILE 4.5 8.7 - - - -
436C THR 3.5 21.1 - - - +
437C PRO* 3.7 19.5 - - + +
439C MET* 3.1 25.1 + - + +
440C PRO 3.5 0.4 - - - -
441C TYR* 1.3 77.6 - - - +
443C VAL* 1.3 65.4 + - + +
445C VAL* 3.3 5.7 + - - +
446C LEU* 2.8 34.2 + - + +
458C ILE* 3.6 52.5 - - + -
461C LEU* 3.8 28.0 - - + -
462C ILE* 3.9 18.6 - - + -
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Residues in contact with VAL 443 (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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437C PRO 5.3 3.8 + - - +
439C MET 4.7 1.0 + - - -
440C PRO 5.2 2.8 + - - +
441C TYR 3.4 0.8 - - - -
442C PHE* 1.3 82.7 - - + +
444C LEU* 1.3 59.9 + - + +
446C LEU* 3.2 14.7 + - + +
447C GLY* 2.8 24.8 + - - -
458C ILE* 6.5 0.9 - - + -
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Residues in contact with LEU 444 (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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137C TYR* 4.5 2.2 - - + -
138C VAL* 3.7 30.5 - - + -
440C PRO 5.7 0.2 - - - +
441C TYR* 3.2 32.1 + - + +
443C VAL* 1.3 78.5 - - + +
445C VAL* 1.3 63.1 + - + +
447C GLY* 3.1 4.1 + - - -
448C PHE* 2.8 59.8 + - + -
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Residues in contact with VAL 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TYR* 4.4 6.7 - - + -
141C ILE* 3.5 29.2 - - + -
159C ILE* 4.5 15.0 - - + -
163C PHE* 3.8 46.7 - - + -
441C TYR 3.1 15.5 + - - +
442C PHE 3.8 3.1 - - - +
444C LEU* 1.3 76.8 - - + +
446C LEU* 1.3 67.3 + - - +
448C PHE* 3.1 12.8 + - + +
449C ALA* 2.9 21.8 + - - +
461C LEU* 4.1 9.9 - - + -
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C PHE* 2.8 21.7 + - + +
443C VAL* 3.2 18.2 - - + +
444C LEU 3.2 0.2 - - - -
445C VAL* 1.3 75.6 - - - +
447C GLY* 1.3 60.2 + - - +
449C ALA* 3.1 13.2 + - + +
450C ARG* 2.9 47.3 + - - +
456C THR* 3.9 17.9 - - + +
457C GLY 3.7 23.6 - - - +
458C ILE* 3.8 31.4 - - + +
461C LEU* 3.5 20.3 - - + +
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Residues in contact with GLY 447 (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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443C VAL 2.8 14.4 + - - -
444C LEU* 3.4 5.2 - - - -
446C LEU* 1.3 73.3 - - - +
448C PHE* 1.3 66.3 + - - +
450C ARG* 3.0 25.6 + - - +
451C ARG* 3.4 11.2 + - - +
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Residues in contact with PHE 448 (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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137C TYR 3.2 28.9 - - - -
138C VAL* 4.1 10.3 - - + -
141C ILE* 3.9 19.5 - - + -
142C PRO* 3.8 26.5 - - + -
159C ILE* 3.4 23.0 - - + +
244C ASP* 4.4 1.6 - - - -
444C LEU* 2.8 50.4 + - + -
445C VAL* 3.1 18.6 + - + +
447C GLY* 1.3 72.9 - - - +
449C ALA* 1.3 61.5 + - - +
451C ARG* 3.1 51.7 + - - +
452C TYR* 3.8 0.9 - - - -
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Residues in contact with ALA 449 (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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156C ILE* 3.7 18.5 - - + +
159C ILE* 3.8 20.1 - - + +
445C VAL 2.9 11.7 + - - +
446C LEU* 3.1 11.4 + - + +
448C PHE* 1.3 71.8 - - - +
450C ARG* 1.3 56.9 + - - +
451C ARG 3.1 5.8 - - - -
452C TYR 3.5 2.2 + - - -
453C GLN* 3.0 30.1 + - - +
456C THR* 4.2 13.0 - - + +
461C LEU* 4.8 14.4 - - + -
464C LEU* 6.2 0.7 - - + -
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Residues in contact with ARG 450 (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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446C LEU* 2.9 50.0 - - + +
447C GLY* 3.0 13.3 + - - +
449C ALA* 1.3 76.1 - - - +
451C ARG* 1.3 62.1 + - - +
452C TYR 3.3 0.2 - - - -
453C GLN 3.4 11.9 - - - +
454C PRO* 3.5 39.1 + - + +
455C GLU 4.8 0.6 + - - -
456C THR* 2.3 43.8 + - - -
457C GLY* 3.5 10.7 - - - -
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Residues in contact with ARG 451 (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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142C PRO* 3.9 6.6 + - - +
238C VAL* 4.3 8.8 - - - +
240C ASP* 3.2 38.3 + - - +
242C SER* 3.3 26.1 + - - -
244C ASP* 2.7 44.2 + - - -
447C GLY 3.6 9.5 + - - +
448C PHE* 3.2 45.1 - - - +
449C ALA 3.1 0.8 - - - -
450C ARG* 1.3 82.3 - - - +
452C TYR* 1.3 77.7 + - + +
454C PRO* 5.4 2.4 - - - +
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Residues in contact with TYR 452 (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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142C PRO* 4.0 6.1 + - + -
145C GLY* 3.2 31.0 - - - -
146C LEU* 3.3 9.2 + - - +
149C GLN* 3.7 16.6 - - + -
155C PRO* 3.4 37.5 - - + -
156C ILE* 4.5 8.7 - - + -
159C ILE* 3.8 30.5 - - + -
237C THR* 3.5 14.1 - - + +
238C VAL 4.2 12.0 + - - -
240C ASP* 3.9 31.3 + - + +
448C PHE 3.8 0.9 - - - -
449C ALA 3.5 1.4 + - - -
451C ARG* 1.3 102.0 + - + +
453C GLN* 1.3 73.0 + - - +
454C PRO* 4.2 5.7 - - - +
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Residues in contact with GLN 453 (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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156C ILE* 3.6 20.0 - - + +
236C ASN 6.0 0.2 + - - -
237C THR* 3.9 12.0 - - - +
449C ALA 3.0 12.8 + - - +
450C ARG* 3.4 6.2 - - - -
451C ARG 3.5 0.8 - - - -
452C TYR* 1.3 92.1 + - - +
454C PRO* 1.3 71.8 - - - +
455C GLU* 2.8 35.8 + - - +
456C THR* 2.9 29.5 - - + +
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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