Contacts of the helix formed by residues 2335 - 2356 (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 ASN2335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2327C LEU* 4.5 2.8 - - - +
2330C VAL* 2.7 48.3 + - + +
2331C MET* 3.0 21.6 + - - +
2333C ARG 3.0 21.6 + - - -
2334C LYS* 1.3 74.2 - - - +
2336C ILE* 1.3 69.6 + - + +
2338C GLU* 3.4 1.6 - - - +
2339C GLU* 3.0 33.2 - - - +
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Residues in contact with ILE2336 (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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2334C LYS* 3.3 14.0 - - + +
2335C ASN* 1.3 82.5 - - + +
2337C LEU* 1.3 91.3 + - + +
2339C GLU* 2.6 49.6 + - - +
2340C SER 4.0 1.9 + - - -
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Residues in contact with LEU2337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2293C GLY* 6.0 2.7 - - - -
2294C ILE* 5.5 11.4 - - + -
2300C PHE* 4.6 25.5 - - + -
2330C VAL* 5.1 0.2 - - - +
2334C LYS 5.0 1.0 + - - -
2335C ASN 3.6 0.2 - - - -
2336C ILE* 1.3 106.1 - - + +
2338C GLU* 1.3 64.0 + - - +
2339C GLU 3.3 0.3 + - - -
2340C SER* 4.2 1.7 + - - +
2341C LEU* 3.5 18.9 + - - +
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Residues in contact with GLU2338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2300C PHE* 5.5 2.8 - - - -
2326C ILE* 3.1 54.0 - - + +
2327C LEU* 3.1 26.7 - - - +
2330C VAL* 2.9 44.0 - - + +
2337C LEU* 1.3 77.2 - - - +
2339C GLU* 1.3 86.5 + - - +
2341C LEU* 3.2 20.9 - - - +
2342C CYS* 3.2 9.4 + - - +
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Residues in contact with GLU2339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2327C LEU* 5.2 4.8 - - + +
2330C VAL* 4.7 0.9 - - + -
2335C ASN* 3.0 41.5 - - - +
2336C ILE* 2.6 30.7 + - - +
2338C GLU* 1.3 82.3 - - - +
2340C SER* 1.3 68.1 + - - +
2342C CYS* 2.8 25.3 + - - +
2343C GLU* 3.4 8.8 + - - +
2374C LEU* 6.4 2.7 - - + -
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Residues in contact with SER2340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2336C ILE 4.0 2.8 + - - -
2337C LEU* 4.2 1.7 + - - -
2339C GLU* 1.3 78.2 - - - +
2341C LEU* 1.3 55.1 + - - +
2343C GLU* 2.6 54.6 + - - +
2344C LEU* 2.9 14.9 + - - +
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Residues in contact with LEU2341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2298C GLU* 5.2 0.9 - - - +
2300C PHE* 3.4 52.5 - - + -
2301C GLN* 4.5 1.6 - - - +
2304C VAL* 3.5 26.7 - - + -
2323C LEU* 5.7 2.0 - - + -
2326C ILE* 4.4 21.1 - - + -
2337C LEU 3.5 13.7 + - - +
2338C GLU* 3.2 10.3 - - - +
2339C GLU 3.1 0.2 + - - -
2340C SER* 1.3 76.1 - - - +
2342C CYS* 1.3 67.7 + - - +
2344C LEU* 2.9 38.6 - - + +
2345C VAL* 3.0 11.6 + - + +
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Residues in contact with CYS2342 (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* 5.6 8.2 - - + +
2326C ILE* 5.8 5.1 - - + +
2338C GLU* 3.2 12.1 + - - +
2339C GLU* 2.8 19.5 + - - +
2341C LEU* 1.3 71.8 - - - +
2343C GLU* 1.3 58.5 + - + +
2345C VAL* 2.1 46.7 + - - -
2346C ALA* 2.7 14.8 + - - -
2371C PHE* 3.7 32.3 - - - -
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Residues in contact with GLU2343 (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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2339C GLU* 3.7 7.3 - - - +
2340C SER* 2.6 48.9 + - - +
2342C CYS* 1.3 73.7 - - + +
2344C LEU* 1.3 60.9 + - + +
2346C ALA* 3.0 12.8 - - - +
2347C LYS* 2.9 34.1 + - - +
2377C ARG* 6.2 2.2 - - - +
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Residues in contact with LEU2344 (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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2298C GLU* 5.5 2.7 - - - +
2301C GLN* 4.7 15.3 - - - +
2304C VAL* 4.7 9.2 - - + -
2340C SER* 2.9 9.2 + - - +
2341C LEU* 2.9 38.8 - - + +
2342C CYS 2.6 2.9 + - - -
2343C GLU* 1.3 71.9 - - + +
2345C VAL* 1.3 56.2 + - - +
2347C LYS* 2.6 43.8 + - + +
2348C GLN* 2.8 12.0 + - - +
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Residues in contact with VAL2345 (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* 3.6 23.8 - - + -
2307C MET* 3.7 22.2 - - + +
2323C LEU* 3.9 27.1 - - + -
2341C LEU* 3.2 15.5 - - + +
2342C CYS* 2.1 30.9 + - - +
2344C LEU* 1.3 68.3 - - - +
2346C ALA* 1.3 54.6 - - - -
2348C GLN* 3.0 27.4 - - - +
2349C LEU* 2.8 25.3 + - - +
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Residues in contact with ALA2346 (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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2342C CYS* 2.7 16.9 + - - -
2343C GLU* 3.0 20.6 - - - +
2344C LEU 2.8 0.2 + - - -
2345C VAL* 1.3 67.9 - - - +
2347C LYS* 1.3 58.0 + - + +
2349C LEU* 2.1 43.7 + - + -
2350C LYS* 2.7 35.0 + - - +
2377C ARG* 4.7 9.9 - - + -
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Residues in contact with LYS2347 (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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2343C GLU* 2.9 21.1 + - - +
2344C LEU* 2.6 25.0 + - + +
2346C ALA* 1.3 74.1 - - + +
2348C GLN* 1.3 65.3 + - - +
2350C LYS* 3.9 15.2 - - + +
2351C GLN* 2.9 31.8 + - + +
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Residues in contact with GLN2348 (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* 2.2 58.7 + - + +
2305C ASN* 3.6 2.6 - - - +
2307C MET* 3.1 21.0 - - - +
2308C SER* 2.7 26.9 - - - +
2344C LEU 2.8 7.3 + - - +
2345C VAL* 3.0 19.8 - - - +
2346C ALA 2.6 1.4 + - - -
2347C LYS* 1.3 77.4 - - - +
2349C LEU* 1.3 61.2 + - - +
2351C GLN* 3.0 11.7 + - - +
2352C HIS* 2.7 48.9 + - + +
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Residues in contact with LEU2349 (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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2345C VAL 2.8 14.6 + - - +
2346C ALA* 2.1 25.3 + - + +
2348C GLN* 1.3 68.2 - - - +
2350C LYS* 1.3 80.6 + - + +
2352C HIS* 2.4 40.8 + - - +
2353C GLN* 2.9 35.8 + - - +
2361C ILE* 4.7 1.1 - - + -
2364C LEU* 3.4 38.1 - - + +
2365C ASN* 5.0 0.4 - - - +
2368C THR* 4.6 8.7 - - + +
2377C ARG* 4.1 10.3 - - + +
2378C PHE* 4.4 15.9 - - + +
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Residues in contact with LYS2350 (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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2346C ALA* 2.7 33.2 + - - +
2347C LYS* 3.9 16.1 - - + +
2349C LEU* 1.3 77.7 - - + +
2351C GLN* 1.3 66.9 + - - +
2353C GLN* 3.0 15.1 - - - +
2354C ASN* 2.7 34.9 + - - +
2377C ARG* 3.2 56.3 - - - +
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Residues in contact with GLN2351 (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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2308C SER* 6.0 0.3 - - - -
2347C LYS* 2.9 27.0 + - + +
2348C GLN* 3.0 17.6 - - - +
2350C LYS* 1.3 71.9 - - - +
2352C HIS* 1.3 62.6 + - + +
2354C ASN* 2.3 36.3 + - - +
2355C THR* 2.7 26.2 + - + -
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Residues in contact with HIS2352 (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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2307C MET* 3.3 15.3 - - + -
2308C SER* 3.7 20.5 - - - -
2348C GLN* 2.7 58.3 + - + +
2349C LEU* 2.4 17.9 + - - +
2351C GLN* 1.3 74.8 + - + +
2353C GLN* 1.3 62.9 + - - +
2355C THR* 2.4 25.9 + - + -
2356C MET 2.8 13.7 - - - +
2360C PHE* 2.8 29.2 - + + -
2364C LEU* 3.0 29.9 - - + +
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Residues in contact with GLN2353 (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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2349C LEU* 2.9 35.6 + - - +
2350C LYS* 3.0 23.5 - - - +
2351C GLN 2.7 1.8 + - - -
2352C HIS* 1.3 78.5 - - - +
2354C ASN* 1.3 72.1 + - - +
2356C MET 2.8 18.4 - - - +
2357C GLU* 4.5 2.6 - - - +
2361C ILE* 3.3 42.7 - - + +
2364C LEU* 3.6 3.3 - - + +
2377C ARG 4.6 1.2 - - - +
2378C PHE* 4.1 9.1 + - - +
2381C ALA* 4.0 26.7 - - + +
2385C LEU* 4.3 7.8 - - + +
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Residues in contact with ASN2354 (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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195A ASP 4.8 12.4 + - - +
196A THR 6.0 1.8 - - - -
197A GLY* 6.5 0.7 - - - -
2350C LYS* 2.7 33.7 + - - +
2351C GLN* 2.3 19.0 + - - +
2353C GLN* 1.3 82.1 + - - +
2355C THR* 1.3 62.7 + - + +
2356C MET* 4.3 0.7 - - - -
2381C ALA* 5.9 1.2 - - - +
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Residues in contact with THR2355 (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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2351C GLN* 2.7 38.2 + - + +
2352C HIS* 2.4 28.3 + - + +
2354C ASN* 1.3 76.0 - - + +
2356C MET* 1.3 63.3 + - - +
2360C PHE* 2.9 17.8 - - - -
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Residues in contact with MET2356 (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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160A LYS* 5.0 8.3 - - - +
2352C HIS 2.8 16.1 - - - +
2353C GLN 2.8 9.5 - - - +
2354C ASN 4.3 0.9 - - - -
2355C THR* 1.3 83.6 + - - +
2357C GLU* 1.3 80.7 + - + +
2358C ASP* 3.9 3.1 - - - +
2359C LYS* 3.6 26.7 - - + +
2360C PHE* 3.1 24.8 - - + +
40E T 3.9 8.7 - - - +
41E A 3.1 41.7 - - - +
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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