Contacts of the helix formed by residues 2492 - 2509 (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 ASP2492 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2490C GLU* 2.9 21.5 - - - +
2491C THR* 1.3 80.1 - - - +
2493C ASN* 1.3 78.5 + - - +
2494C ASP* 2.5 35.7 + - - +
2495C SER* 2.2 34.6 + - - +
2496C GLN* 3.4 7.8 + - - +
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Residues in contact with ASN2493 (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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2490C GLU* 4.1 10.7 + - - +
2492C ASP* 1.3 87.9 + - - +
2494C ASP* 1.3 92.2 + - - +
2496C GLN* 2.9 11.6 + - - +
2497C GLU* 2.9 34.6 + - + +
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Residues in contact with ASP2494 (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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2449C VAL* 3.1 28.6 - - + +
2452C ARG* 2.2 61.4 + - - -
2492C ASP* 2.5 16.2 + - - +
2493C ASN* 1.3 88.7 + - - +
2495C SER* 1.3 60.4 + - - +
2497C GLU* 2.6 32.0 + - - +
2498C ILE* 2.9 5.0 + - - +
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Residues in contact with SER2495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2447C LYS* 5.8 5.2 - - - -
2484C TYR* 4.3 9.9 - - - -
2486C ASP* 3.7 7.0 + - - -
2491C THR* 2.9 23.2 + - - -
2492C ASP* 2.2 48.5 + - - +
2494C ASP* 1.3 78.7 + - - +
2496C GLN* 1.3 57.9 + - - +
2498C ILE* 3.2 16.5 - - - +
2499C PHE* 2.8 23.7 + - - +
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Residues in contact with GLN2496 (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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2486C ASP* 3.0 39.1 + - + +
2490C GLU* 5.2 8.1 + - - +
2492C ASP 4.0 7.8 - - - +
2493C ASN* 2.9 9.8 + - - +
2495C SER* 1.3 79.0 + - - +
2497C GLU* 1.3 60.3 + - - +
2499C PHE* 3.6 3.1 - - + -
2500C LYS* 2.8 65.2 + - + +
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Residues in contact with GLU2497 (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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2452C ARG* 3.0 20.0 + - - +
2493C ASN* 2.9 29.6 + - + +
2494C ASP* 2.6 39.2 + - - +
2496C GLN* 1.3 73.3 - - - +
2498C ILE* 1.3 67.0 + - - +
2500C LYS* 4.1 3.6 - - - +
2501C LEU* 2.9 21.1 + - - +
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Residues in contact with ILE2498 (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 5.2 6.7 - - - +
2449C VAL* 5.4 4.0 - - + -
2452C ARG* 2.8 48.6 - - + +
2455C LEU* 4.6 9.9 - - + -
2484C TYR* 3.2 49.1 - - + +
2494C ASP* 2.9 25.9 + - - +
2495C SER* 3.2 14.8 - - - +
2497C GLU* 1.3 72.4 - - - +
2499C PHE* 1.3 56.5 + - - +
2500C LYS 2.6 2.4 + - - -
2501C LEU* 2.2 42.1 + - + -
2502C ALA* 2.7 13.7 + - + +
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Residues in contact with PHE2499 (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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2481C HIS* 2.7 64.1 - + - -
2484C TYR* 2.9 28.3 - - + -
2485C ARG* 3.3 42.0 - - - -
2486C ASP* 3.1 39.9 - - + +
2495C SER 2.8 8.2 + - - +
2496C GLN* 3.0 4.0 + - + +
2498C ILE* 1.3 78.4 - - - +
2500C LYS* 1.3 75.0 + - + +
2502C ALA* 3.1 2.9 - - - +
2503C LYS* 2.9 28.5 + - + +
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Residues in contact with LYS2500 (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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2496C GLN* 2.8 49.4 + - + +
2497C GLU* 4.1 3.8 - - - +
2498C ILE 2.6 5.2 + - - -
2499C PHE* 1.3 78.8 - - + +
2501C LEU* 1.3 55.1 + - - +
2503C LYS* 2.2 57.4 + - + +
2504C ASP* 2.7 16.6 + - - +
2545C LEU* 6.0 1.6 - - - +
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Residues in contact with LEU2501 (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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2452C ARG* 5.1 19.5 - - + +
2455C LEU* 6.2 5.2 - - + -
2497C GLU 2.9 20.9 + - - +
2498C ILE* 2.2 21.2 + - + +
2500C LYS* 1.3 68.1 - - - +
2502C ALA* 1.3 66.3 + - - +
2504C ASP* 2.9 48.5 - - + +
2505C VAL* 3.1 14.6 + - + +
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Residues in contact with ALA2502 (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* 6.4 1.1 - - + -
2477C LEU* 5.6 2.0 - - + +
2480C ILE* 6.0 1.3 - - + -
2481C HIS* 3.3 20.0 - - + +
2484C TYR* 4.8 5.2 - - + -
2498C ILE* 2.7 20.9 + - + +
2499C PHE* 3.1 17.3 - - - +
2501C LEU* 1.3 68.7 - - - +
2503C LYS* 1.3 55.6 + - - +
2505C VAL* 2.5 36.3 + - - +
2506C LEU* 2.7 20.6 + - + -
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Residues in contact with LYS2503 (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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2481C HIS* 3.2 18.8 + - + +
2485C ARG* 5.2 1.6 - - - +
2499C PHE* 2.9 37.1 + - + +
2500C LYS* 2.2 50.8 + - + +
2502C ALA* 1.3 68.5 - - - +
2504C ASP* 1.3 63.4 + - - +
2506C LEU* 3.4 10.0 - - + +
2507C ILE* 2.9 26.9 + - + +
2530C ARG* 4.0 23.3 + - - +
2545C LEU* 3.9 37.0 - - + +
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Residues in contact with ASP2504 (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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2500C LYS* 2.7 17.1 + - - +
2501C LEU* 2.9 39.4 - - + +
2502C ALA 2.7 3.2 + - - -
2503C LYS* 1.3 72.4 - - - +
2505C VAL* 1.3 68.7 + - + +
2507C ILE* 3.5 6.7 - - - +
2508C GLN* 3.0 31.6 + - - +
2548C PRO* 5.9 7.6 - - + +
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Residues in contact with VAL2505 (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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2458C VAL* 4.5 5.4 - - + -
2459C VAL* 3.6 31.4 - - + -
2474C TYR* 3.8 18.2 - - + -
2477C LEU* 4.2 11.7 - - + -
2501C LEU* 3.3 22.0 - - + +
2502C ALA* 2.5 15.7 + - - +
2504C ASP* 1.3 77.4 - - + +
2506C LEU* 1.3 56.0 + - + +
2508C GLN* 2.7 39.3 + - + +
2509C GLY* 2.8 9.9 + - - -
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Residues in contact with LEU2506 (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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2474C TYR* 5.4 3.4 - - + +
2477C LEU* 3.8 40.2 - - + +
2478C MET* 4.6 2.5 - - + +
2481C HIS* 3.3 45.3 - - + +
2502C ALA* 2.7 26.7 + - + +
2503C LYS* 3.0 16.8 + - - +
2505C VAL* 1.3 74.4 - - + +
2507C ILE* 1.3 58.7 + - - +
2509C GLY* 2.9 17.3 + - - -
2510C LEU 2.9 8.0 + - - -
2522C ARG* 3.0 11.9 + - - +
2525C TRP* 6.2 0.2 - - - +
2530C ARG* 3.2 22.2 - - - +
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Residues in contact with ILE2507 (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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2503C LYS 2.9 17.5 + - - +
2504C ASP* 3.5 6.5 - - - +
2506C LEU* 1.3 73.9 - - - +
2508C GLN* 1.3 65.5 + - + +
2509C GLY 2.9 0.9 - - - -
2510C LEU* 2.5 45.7 + - + +
2511C ILE* 3.3 7.8 + - - +
2522C ARG* 3.2 23.8 - - - +
2530C ARG* 3.2 14.6 - - - +
2545C LEU* 3.8 43.1 - - + +
2546C TYR* 5.1 6.3 - - + -
2548C PRO* 4.7 10.8 - - + -
2549C LYS* 6.1 4.7 - - - +
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Residues in contact with GLN2508 (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* 5.3 8.3 - - + +
2504C ASP* 3.0 29.3 + - - +
2505C VAL* 2.7 35.7 + - + +
2507C ILE* 1.3 75.5 - - + +
2509C GLY* 1.3 54.3 + - - +
2511C ILE* 3.0 41.3 - - + +
2551C GLU* 5.3 4.5 - - - +
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Residues in contact with GLY2509 (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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2474C TYR* 5.4 20.5 - - - -
2505C VAL 2.8 10.4 + - - -
2506C LEU* 3.0 9.9 - - - -
2507C ILE 2.9 0.4 - - - -
2508C GLN* 1.3 72.8 - - - +
2510C LEU* 1.3 60.8 + - - +
2511C ILE 2.8 15.6 + - - +
2512C ASP 4.3 0.3 + - - -
2518C GLN* 4.8 6.2 - - - +
2522C ARG* 3.5 16.2 - - - +
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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
------------------------------------------------------------
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