Contacts of the helix formed by residues 2314 - 2332 (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 GLU2314 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2268C LYS* 6.4 1.3 - - + -
2270C ASN* 5.1 11.7 - - - +
2271C SER* 4.2 17.5 - - - +
2274C ILE* 4.0 25.1 - - + +
2312C TYR* 3.1 18.9 + - + +
2313C LYS* 1.3 124.2 + - - +
2315C VAL* 1.3 55.1 + - + +
2316C TYR* 2.7 32.3 + - - -
2317C ALA* 5.2 0.2 - - - +
2318C ALA* 3.8 10.4 + - - +
-9D C 4.5 1.4 - - - +
-8D T 4.7 1.6 + - - -
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Residues in contact with VAL2315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2270C ASN* 5.5 5.8 - - - +
2274C ILE* 5.4 6.7 - - + +
2306C ASN* 3.1 34.8 - - - +
2307C MET* 3.0 40.8 - - + +
2309C PHE* 4.7 3.6 - - + +
2310C VAL* 5.7 1.6 - - + +
2312C TYR 4.7 5.6 - - - +
2313C LYS 2.4 20.7 + - - +
2314C GLU* 1.3 73.7 - - + +
2316C TYR* 1.3 59.7 + - - +
2318C ALA* 3.0 7.8 - - - +
2319C ALA* 2.3 39.7 + - + +
2363C CYS* 4.5 9.4 - - - -
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Residues in contact with TYR2316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2313C LYS* 2.8 58.8 + - + +
2314C GLU* 2.7 32.2 + - - -
2315C VAL* 1.3 82.2 - - - +
2317C ALA* 1.3 77.3 + - + -
2319C ALA* 3.3 2.0 - - - +
2320C ALA* 2.4 36.6 + - - +
2363C CYS* 3.7 12.8 - - - +
2366C LYS* 5.4 12.6 - - + -
2367C VAL* 3.4 31.1 - - + +
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Residues in contact with ALA2317 (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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2316C TYR* 1.3 101.4 - - + +
2318C ALA* 1.3 54.8 + - - +
2320C ALA* 3.4 10.1 - - - -
2321C GLU* 2.0 47.1 + - + +
2366C LYS* 5.1 12.1 - - - +
2367C VAL 5.6 0.2 - - - +
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Residues in contact with ALA2318 (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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2274C ILE* 4.0 36.3 - - + +
2275C GLN* 5.7 0.9 - - - +
2278C GLY* 5.4 2.9 - - - +
2314C GLU 3.8 7.7 + - - +
2315C VAL* 3.0 15.9 - - - +
2317C ALA* 1.3 77.4 - - - +
2319C ALA* 1.3 53.8 + - - +
2321C GLU* 3.4 9.8 - - - +
2322C VAL* 2.5 44.4 + - + +
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Residues in contact with ALA2319 (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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2303C LEU 5.8 0.7 - - - +
2307C MET* 3.6 33.0 - - + -
2315C VAL* 2.3 30.9 + - + +
2316C TYR* 3.3 2.9 - - - +
2318C ALA* 1.3 66.1 - - - +
2320C ALA* 1.3 52.3 + - - +
2322C VAL* 2.7 10.4 - - - +
2323C LEU* 2.2 60.9 + - + +
2367C VAL* 4.6 1.3 - - + -
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Residues in contact with ALA2320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2316C TYR 2.4 28.1 + - - +
2317C ALA* 3.0 13.9 - - - +
2319C ALA* 1.3 67.0 - - - +
2321C GLU* 1.3 61.4 + - - +
2323C LEU* 2.8 1.7 + - - +
2324C GLY* 2.6 34.2 + - - +
2366C LYS* 4.4 4.0 - - - +
2367C VAL* 3.2 44.7 - - - +
2369C LYS* 5.7 0.4 - - + -
2370C SER* 4.0 7.6 - - - +
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Residues in contact with GLU2321 (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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2275C GLN 4.6 1.2 - - - +
2278C GLY* 3.1 42.9 - - - +
2279C ILE* 3.6 16.7 + - - +
2282C ALA* 3.1 16.7 - - + +
2317C ALA* 2.0 34.8 + - + +
2318C ALA* 3.4 7.2 - - - +
2320C ALA* 1.3 67.7 - - - +
2322C VAL* 1.3 68.3 + - - +
2325C LEU* 3.0 44.9 - - + +
2329C TYR* 4.9 0.3 - - - -
2370C SER* 5.1 3.6 - - - -
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Residues in contact with VAL2322 (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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2277C LEU* 5.7 4.5 - - + -
2278C GLY* 5.1 12.8 - - - +
2281C MET* 5.8 13.0 - - + -
2303C LEU* 5.8 16.2 - - + -
2318C ALA* 2.5 27.9 + - + +
2319C ALA* 2.7 13.9 - - - +
2321C GLU* 1.3 73.7 - - - +
2323C LEU* 1.3 69.3 + - + +
2325C LEU* 3.2 1.1 - - - +
2326C ILE* 2.3 49.2 + - + +
2329C TYR* 4.5 4.4 - - - -
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Residues in contact with LEU2323 (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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2304C VAL* 6.2 1.6 - - + -
2307C MET* 4.3 3.4 - - + -
2319C ALA* 2.2 55.5 + - + +
2320C ALA* 2.8 4.3 + - - +
2322C VAL* 1.3 79.6 - - + +
2324C GLY* 1.3 68.6 - - - +
2326C ILE* 2.7 41.5 - - + +
2327C LEU* 3.1 3.3 + - - +
2341C LEU* 5.7 2.5 - - + -
2342C CYS* 5.6 7.9 - - + -
2345C VAL* 3.9 39.9 - - + -
2367C VAL* 5.2 5.6 - - + -
2371C PHE* 5.0 14.6 - - + -
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Residues in contact with GLY2324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2320C ALA* 2.6 14.5 + - - +
2323C LEU* 1.3 75.8 - - - +
2325C LEU* 1.3 62.3 + - - -
2327C LEU* 3.0 12.0 + - - +
2328C ARG* 3.1 19.4 + - - +
2370C SER* 3.2 36.5 - - - +
2371C PHE* 3.7 9.2 - - - +
2373C PRO* 6.0 0.5 - - - +
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Residues in contact with LEU2325 (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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2282C ALA* 5.3 6.7 - - + -
2321C GLU* 3.0 45.9 + - + +
2324C GLY* 1.3 75.0 - - - +
2326C ILE* 1.3 52.9 + - - +
2328C ARG* 2.7 38.7 + - + +
2329C TYR* 2.2 62.1 + - + +
2370C SER* 4.9 4.3 - - - +
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Residues in contact with ILE2326 (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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2281C MET* 6.1 4.5 - - + -
2300C PHE* 6.2 0.9 - - + -
2322C VAL* 2.3 39.3 + - + +
2323C LEU* 2.7 43.0 + - + +
2325C LEU* 1.3 68.2 - - - +
2327C LEU* 1.3 58.6 + - + +
2329C TYR* 3.1 14.3 - - + +
2330C VAL 2.9 20.1 + - - -
2338C GLU* 3.1 44.0 - - + +
2341C LEU* 4.4 21.5 - - + -
2342C CYS* 5.8 4.9 - - + +
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Residues in contact with LEU2327 (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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2323C LEU 4.4 2.7 - - - +
2324C GLY 3.0 8.2 + - - +
2326C ILE* 1.3 80.0 - - - +
2328C ARG* 1.3 66.8 + - + +
2329C TYR 3.0 1.3 - - - -
2330C VAL* 2.8 29.2 + - + -
2331C MET* 3.1 31.3 + - + +
2335C ASN* 4.5 2.9 - - - +
2338C GLU* 3.1 16.4 - - - +
2339C GLU* 5.2 5.2 - - + +
2371C PHE* 4.9 9.2 - - + +
2372C PRO 5.5 0.2 - - - -
2373C PRO* 4.2 40.2 - - + +
2374C LEU* 5.0 13.0 - - + -
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Residues in contact with ARG2328 (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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2285C LEU* 5.1 1.9 - - - +
2324C GLY 3.1 17.0 + - - +
2325C LEU* 2.7 34.6 + - + +
2327C LEU* 1.3 74.5 - - - +
2329C TYR* 1.3 64.7 + - - +
2331C MET* 3.4 32.1 + - + +
2332C GLU* 4.4 5.4 + - - +
2369C LYS 4.4 2.2 + - - -
2370C SER* 2.9 58.2 + - - +
2372C PRO* 4.7 3.8 - - - +
2373C PRO* 6.1 6.7 - - + -
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Residues in contact with TYR2329 (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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2281C MET* 2.0 53.0 + - + -
2282C ALA* 3.3 8.1 + - - -
2284C ASP* 4.3 1.6 - - - -
2285C LEU* 3.2 43.9 - - + +
2286C PRO* 3.2 24.5 - - + -
2321C GLU 4.9 1.1 - - - -
2322C VAL* 4.6 3.8 - - - -
2325C LEU* 2.2 63.0 + - + +
2326C ILE* 3.1 17.7 - - + +
2328C ARG* 1.3 70.5 - - - +
2330C VAL* 1.3 57.1 + - - +
2331C MET 2.6 13.8 + - - -
2332C GLU* 3.1 15.9 + - - +
2333C ARG* 4.3 7.9 + - - +
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Residues in contact with VAL2330 (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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2326C ILE 2.9 8.0 + - - +
2327C LEU* 2.8 18.8 + - + -
2329C TYR* 1.3 75.5 - - + +
2331C MET* 1.3 51.8 + - - +
2332C GLU 3.5 0.4 - - - -
2333C ARG* 2.7 32.4 - - + +
2334C LYS 3.0 27.1 - - - +
2335C ASN* 2.7 45.6 - - + +
2338C GLU* 2.9 42.4 - - + +
2339C GLU* 4.7 0.4 - - + -
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Residues in contact with MET2331 (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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2327C LEU* 3.1 24.8 + - + +
2328C ARG* 3.4 33.2 - - + +
2329C TYR 2.6 6.1 + - - -
2330C VAL* 1.3 72.7 - - - +
2332C GLU* 1.3 63.0 + - + +
2333C ARG 2.9 14.2 + - - +
2335C ASN* 3.0 19.7 + - - +
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Residues in contact with GLU2332 (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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2285C LEU* 3.0 45.6 - - + +
2328C ARG 4.8 5.4 - - - +
2329C TYR 3.1 4.7 + - - +
2331C MET* 1.3 82.9 - - + +
2333C ARG* 1.3 63.0 + - - +
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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