Contacts of the strand formed by residues 2283 - 2290 (chain C) in PDB entry 1W21
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 GLU2283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2231C ARG* 2.6 41.5 + - - +
2249C THR* 4.1 5.9 - - - +
2253C ALA* 4.3 0.7 - - - -
2281C HIS* 3.6 20.3 + - + +
2282C ILE* 1.3 85.7 - - - +
2284C GLU* 1.4 75.1 + - + +
2285C CYS 3.2 3.3 + - - -
2298C CYS* 3.4 2.2 - - - +
2299C ARG* 2.9 50.0 + - - +
2301C ASN* 3.8 9.1 - - + +
3477C SIA 2.6 34.5 + - - +
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Residues in contact with GLU2284 (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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2231C ARG* 6.4 1.8 - - - -
2232C THR* 3.8 14.8 + - - +
2233C GLN* 3.2 19.2 - - - +
2234C GLU* 3.9 17.0 - - + +
2283C GLU* 1.4 79.2 + - + +
2285C CYS* 1.4 60.8 + - - +
2286C SER* 3.6 1.6 + - - -
2297C ILE 4.3 2.8 - - - +
2298C CYS* 4.3 2.4 - - - -
2299C ARG* 2.7 30.8 + - - -
2357C LYS* 3.1 35.0 + - + +
2358C GLY 4.7 0.7 - - - +
2412C TYR* 2.5 40.3 + - - -
3477C SIA 3.5 20.5 + - - +
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Residues in contact with CYS2285 (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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2233C GLN* 3.0 39.1 - - + +
2235C SER* 3.4 2.4 + - - -
2247C VAL* 3.7 19.5 - - + -
2282C ILE* 3.4 20.4 - - - -
2283C GLU 3.2 1.4 + - - -
2284C GLU* 1.4 73.6 - - - +
2286C SER* 1.3 58.6 + - - +
2287C CYS* 3.9 3.6 - - - -
2296C CYS* 3.8 13.5 - - + -
2297C ILE 3.7 0.9 - - - -
2298C CYS* 2.1 48.9 - - - -
2310C ILE* 4.2 1.3 - - - -
2357C LYS* 3.1 9.1 + - - -
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Residues in contact with SER2286 (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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2235C SER* 3.6 5.6 - - - -
2285C CYS* 1.3 73.8 - - - +
2287C CYS* 1.3 59.3 + - - +
2288C TYR* 5.2 1.0 - - - -
2295C LYS 3.7 1.2 - - - +
2296C CYS* 3.3 0.5 - - - -
2297C ILE* 2.9 33.8 + - - +
2357C LYS* 3.0 17.5 + - - -
2358C GLY 2.6 28.0 + - - -
2359C PHE* 3.5 18.1 - - - +
2360C ALA 5.5 0.3 - - - +
2414C GLY* 3.3 11.4 - - - -
2415C ALA* 3.8 14.4 - - - +
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Residues in contact with CYS2287 (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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2233C GLN* 3.6 28.9 - - - +
2235C SER* 4.5 1.2 + - - -
2236C GLU* 4.1 17.5 + - - +
2237C CYS* 5.3 2.0 - - - -
2238C VAL* 3.6 20.2 - - + +
2245C PRO 6.0 0.9 - - - -
2285C CYS* 3.9 4.4 + - - -
2286C SER* 1.3 75.8 - - - +
2288C TYR* 1.3 66.0 + - - +
2294C ILE* 4.3 3.8 - - + -
2295C LYS 3.2 4.9 - - - +
2296C CYS* 2.1 48.2 - - - -
2415C ALA* 4.0 17.9 + - - +
2419C TYR* 4.7 0.3 + - - -
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Residues in contact with TYR2288 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2097C LEU* 3.7 25.9 - - + +
2238C VAL* 3.6 9.0 - - - -
2286C SER 5.2 0.7 - - - -
2287C CYS* 1.3 79.1 - - - +
2289C GLY* 1.3 72.2 + - - +
2290C ALA* 4.6 6.3 - - + -
2293C VAL 3.9 0.6 - - - +
2294C ILE* 3.4 3.0 - - - +
2295C LYS* 3.0 60.4 + - + +
2297C ILE* 4.3 3.1 - - + -
2360C ALA 3.5 23.1 - - - -
2361C PHE* 3.6 34.1 - + + -
2362C LEU* 2.8 35.8 + - - -
2415C ALA* 4.6 6.1 - - + -
2416C PHE 5.6 0.7 - - - -
2417C ILE* 3.9 6.3 - - + -
2419C TYR* 3.3 13.7 - - - +
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Residues in contact with GLY2289 (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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2093C LEU* 3.8 24.9 - - - -
2097C LEU* 4.3 0.3 - - - +
2238C VAL* 3.8 2.7 - - - +
2288C TYR* 1.3 84.3 - - - +
2290C ALA* 1.3 64.6 + - - +
2293C VAL 3.2 9.0 - - - -
2294C ILE* 4.2 0.9 - - - -
2417C ILE* 4.1 3.8 - - - +
2419C TYR* 2.9 18.1 + - - -
2426C PHE* 3.6 13.7 - - - -
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Residues in contact with ALA2290 (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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2093C LEU* 3.9 3.2 - - - +
2095C LYS 3.4 13.2 - - - +
2096C PRO* 4.5 1.6 - - + -
2097C LEU* 4.0 31.4 - - + +
2288C TYR* 4.6 5.6 - - + -
2289C GLY* 1.3 76.3 - - - +
2291C GLY* 1.3 69.4 + - - +
2292C GLY 3.1 2.2 - - - -
2293C VAL* 2.8 25.3 + - - +
2426C PHE* 4.1 3.4 - - + -
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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