Contacts of the helix formed by residues 2467 - 2484 (chain C) in PDB entry 5Y3R
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 THR2467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2463C SER 4.7 1.6 - - - +
2465C PRO 3.9 7.9 - - - +
2466C SER* 1.3 67.2 - - - +
2468C THR* 1.3 57.2 + - - +
2469C CYS* 2.9 12.8 - - - -
2470C ARG* 2.4 59.0 + - + +
2471C GLU* 3.1 9.3 + - - +
2514C ASN* 6.1 0.7 - - + +
2515C PRO* 4.0 22.3 - - + +
2518C GLN* 4.2 16.6 - - - +
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Residues in contact with THR2468 (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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2434C VAL* 6.6 0.2 - - + -
2437C ASP* 5.0 0.6 - - - +
2466C SER* 2.8 17.7 + - - -
2467C THR* 1.3 77.1 + - - +
2469C CYS* 1.3 63.5 + - - +
2471C GLU* 2.9 51.0 + - - +
2472C GLN* 4.1 2.3 + - - +
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Residues in contact with CYS2469 (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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2433C LYS* 5.4 7.4 - - + -
2437C ASP* 3.5 34.0 + - - +
2462C VAL* 3.4 40.8 - - + -
2465C PRO* 3.9 10.3 - - + -
2466C SER 3.0 26.1 + - - +
2467C THR* 3.4 7.6 - - - -
2468C THR* 1.3 76.3 - - - +
2470C ARG* 1.3 77.3 + - - -
2471C GLU 2.8 1.7 + - - -
2472C GLN* 3.3 2.8 + - - +
2473C MET* 3.1 18.3 + - - +
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Residues in contact with ARG2470 (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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2459C VAL* 4.7 3.4 - - - +
2462C VAL* 2.3 41.6 + - - -
2463C SER* 2.4 40.4 + - - +
2467C THR* 2.4 49.0 + - + +
2469C CYS* 1.3 73.3 - - - +
2471C GLU* 1.3 68.1 + - - +
2473C MET* 2.8 11.7 + - - -
2474C TYR* 2.8 56.9 + - + -
2518C GLN* 5.6 4.0 - - + +
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Residues in contact with GLU2471 (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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2467C THR* 3.5 6.0 + - - +
2468C THR* 2.9 50.7 + - - +
2469C CYS 2.8 0.8 + - - -
2470C ARG* 1.3 81.8 - - - +
2472C GLN* 1.3 65.5 + - + +
2474C TYR* 4.0 1.9 - - - +
2475C ASN* 3.0 19.3 + - - +
2515C PRO* 6.6 0.2 - - + -
2517C LEU* 5.6 11.1 - - + +
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Residues in contact with GLN2472 (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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2437C ASP* 5.5 8.3 - - + -
2438C ILE* 5.7 7.9 - - - -
2468C THR 4.1 1.3 + - - +
2469C CYS 3.3 3.9 + - - +
2471C GLU* 1.3 82.8 - - + +
2473C MET* 1.3 68.0 + - - +
2475C ASN* 2.3 37.3 + - - +
2476C ILE* 2.9 42.5 + - + +
2479C TRP* 4.3 4.9 - - - -
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Residues in contact with MET2473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2437C ASP* 5.5 14.0 - - - +
2440C TYR* 6.3 4.5 - - + -
2458C VAL* 2.9 47.3 - - + +
2461C PHE* 6.5 0.4 - - - -
2462C VAL* 3.3 17.3 - - + -
2469C CYS 3.1 14.4 + - - +
2470C ARG* 2.8 9.7 + - - +
2472C GLN* 1.3 80.5 - - - +
2474C TYR* 1.3 108.1 + - + +
2476C ILE* 3.0 14.1 - - + +
2477C LEU* 2.9 27.5 + - + +
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Residues in contact with TYR2474 (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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2459C VAL* 3.1 23.5 - - + +
2462C VAL* 3.0 24.1 - - - +
2470C ARG* 2.8 67.0 + - + +
2471C GLU* 4.2 1.3 - - - +
2473C MET* 1.3 90.2 - - + +
2475C ASN* 1.3 56.5 + - - +
2477C LEU* 2.6 40.8 + - + +
2478C MET* 2.9 14.9 + - - +
2505C VAL* 3.8 14.1 - - + -
2506C LEU* 5.4 2.8 - - + +
2508C GLN 6.5 0.2 - - - -
2509C GLY* 5.4 17.5 - - - -
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Residues in contact with ASN2475 (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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2471C GLU 3.0 21.3 + - - +
2472C GLN* 2.3 43.8 + - - +
2474C TYR* 1.3 75.4 - - - +
2476C ILE* 1.3 56.0 + - - +
2478C MET* 3.0 43.8 - - + +
2479C TRP* 3.0 18.8 + - - +
2521C ILE* 5.9 0.5 - - - +
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Residues in contact with ILE2476 (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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2437C ASP 4.4 10.3 - - - +
2438C ILE 4.8 1.8 - - - +
2440C TYR* 3.2 37.7 - - + +
2441C LYS* 5.8 0.4 - - + -
2472C GLN* 2.9 39.9 + - + +
2473C MET* 3.0 18.8 - - + +
2475C ASN* 1.3 70.7 - - - +
2477C LEU* 1.3 69.7 + - + +
2478C MET 2.9 2.0 - - - -
2479C TRP* 2.8 55.1 + - + -
2480C ILE* 2.9 16.6 + - + +
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Residues in contact with LEU2477 (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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2455C LEU* 5.0 10.8 - - + -
2458C VAL* 3.5 36.6 - - + -
2473C MET* 2.9 14.9 + - + +
2474C TYR* 2.6 51.1 + - + +
2476C ILE* 1.3 73.1 - - + +
2478C MET* 1.3 54.3 + - - -
2480C ILE* 3.0 16.4 - - + +
2481C HIS* 3.0 29.6 + - - +
2502C ALA* 5.6 1.5 - - + +
2505C VAL* 4.2 7.4 - - + -
2506C LEU* 3.8 22.2 - - + +
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Residues in contact with MET2478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2474C TYR 2.9 10.5 + - - +
2475C ASN* 3.0 35.2 - - + +
2477C LEU* 1.3 72.6 - - - +
2479C TRP* 1.3 62.5 + - + +
2481C HIS* 2.5 29.6 + - - +
2482C ASP* 2.9 15.3 + - - +
2485C ARG* 4.4 0.3 + - - -
2506C LEU* 4.6 3.5 - - + +
2521C ILE* 3.8 40.6 - - + +
2522C ARG* 4.7 5.6 - - - +
2525C TRP* 4.1 45.3 - - + +
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Residues in contact with TRP2479 (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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2441C LYS* 4.4 33.4 - - + -
2443C MET* 3.9 40.4 - - + -
2472C GLN* 4.3 7.6 - - - -
2475C ASN* 3.0 41.7 + - - +
2476C ILE* 2.8 36.2 + - + +
2478C MET* 1.3 81.5 - - + +
2480C ILE* 1.3 55.0 + - - +
2482C ASP* 3.2 10.8 + - - +
2483C ASN* 2.7 38.5 + - - +
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Residues in contact with ILE2480 (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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2442C MET 4.4 9.6 - - - +
2443C MET 4.0 10.3 - - - +
2447C LYS* 6.2 3.8 - - + -
2451C LEU* 4.6 17.5 - - + -
2455C LEU* 6.1 2.5 - - + -
2476C ILE 2.9 13.2 + - - +
2477C LEU* 3.0 38.6 - - + +
2479C TRP* 1.3 79.8 - - - +
2481C HIS* 1.3 56.7 + - - +
2483C ASN* 2.8 24.1 + - + +
2484C TYR* 2.8 68.5 + - + +
2502C ALA* 6.0 1.8 - - + -
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Residues in contact with HIS2481 (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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2477C LEU 3.0 21.0 + - - +
2478C MET* 2.5 14.5 + - - +
2480C ILE* 1.3 68.3 - - + +
2482C ASP* 1.3 59.9 + - - +
2484C TYR* 2.8 24.3 + - - +
2485C ARG* 2.9 41.8 + - - +
2499C PHE* 2.7 63.5 - + - -
2502C ALA* 3.3 15.5 - - + +
2503C LYS* 3.2 23.6 + - + +
2506C LEU* 3.3 19.3 - - + +
2525C TRP* 5.4 3.4 - - + -
2530C ARG* 4.9 3.1 - - + -
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Residues in contact with ASP2482 (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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2443C MET* 5.6 2.3 - - + +
2478C MET 2.9 6.3 + - - +
2479C TRP* 3.3 13.0 - - - +
2481C HIS* 1.3 73.2 - - - +
2483C ASN* 1.3 60.7 + - - +
2485C ARG* 2.3 72.7 + - + +
2525C TRP* 2.8 33.3 - - - -
2529C THR* 5.2 0.5 - - - -
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Residues in contact with ASN2483 (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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2443C MET* 3.2 59.8 - - - +
2447C LYS* 3.9 24.7 + - + +
2479C TRP 2.7 22.1 + - - +
2480C ILE* 2.8 24.8 + - + +
2482C ASP* 1.3 78.9 - - - +
2484C TYR* 1.3 58.5 + - - +
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Residues in contact with TYR2484 (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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2447C LYS* 4.9 23.6 - - + +
2451C LEU* 3.3 32.4 - - - +
2452C ARG 5.0 0.3 + - - -
2455C LEU* 3.7 6.4 - - + +
2480C ILE* 2.8 51.7 + - + +
2481C HIS* 2.8 13.4 + - - +
2483C ASN* 1.3 78.5 - - - +
2485C ARG* 1.3 67.8 + - - +
2486C ASP* 2.7 22.4 - - - +
2491C THR* 6.0 0.9 - - - -
2495C SER* 4.3 10.3 - - - -
2498C ILE* 3.2 49.3 - - + +
2499C PHE* 2.9 20.8 - - + -
2502C ALA* 4.8 4.3 - - + -
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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