Contacts of the strand formed by residues 2447 - 2457 (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 THR2447 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2122C VAL* 3.1 21.1 - - - +
2123C THR 4.0 2.1 - - - +
2124C ARG* 3.8 28.8 - - + +
2142C GLN* 5.2 0.3 + - - +
2154C THR* 3.0 24.5 + - - +
2155C ILE* 3.3 24.8 - - + +
2435C ILE* 4.2 6.1 - - + -
2436C ARG 3.5 8.3 - - - +
2438C ARG* 2.9 28.7 + - - +
2446C TRP* 1.3 77.0 + - - +
2448C SER* 1.3 64.8 + - - +
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Residues in contact with SER2448 (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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2112C ILE* 3.8 12.3 - - - +
2121C LEU 4.4 1.9 + - - -
2122C VAL* 3.5 9.9 - - - -
2123C THR* 3.2 29.3 + - - -
2124C ARG* 4.4 1.8 - - - +
2146C LEU* 3.7 27.5 - - - +
2435C ILE* 3.4 7.8 - - - +
2436C ARG 2.9 28.2 + - - +
2446C TRP* 3.5 1.9 - - - -
2447C THR* 1.3 77.3 - - - +
2449C ASN* 1.3 73.6 + - - +
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Residues in contact with ASN2449 (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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2111C ALA* 3.9 9.2 - - - +
2112C ILE* 3.6 18.1 - - - +
2123C THR* 2.8 35.8 + - - -
2124C ARG* 3.1 27.2 - - + +
2126C PRO* 3.6 16.8 - - - +
2433C GLU* 3.7 24.7 - - + +
2434C LEU 3.1 15.9 - - - +
2435C ILE* 4.0 1.3 - - + -
2436C ARG 4.3 0.2 - - - +
2448C SER* 1.3 84.4 + - - +
2450C SER* 1.3 78.1 + - - +
2451C ILE* 3.8 4.2 - - - +
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Residues in contact with SER2450 (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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2108C LYS* 4.8 0.9 + - - -
2109C ASP* 3.5 12.3 - - - -
2110C ASN* 4.4 4.7 - - - -
2111C ALA* 3.7 19.7 - - - -
2112C ILE* 4.1 1.5 - - - +
2433C GLU* 3.9 1.0 - - - -
2434C LEU* 3.1 43.9 + - - +
2449C ASN* 1.3 84.7 - - - +
2451C ILE* 1.3 67.7 + - - +
2468C ASP* 2.7 28.3 + - - -
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Residues in contact with ILE2451 (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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2108C LYS* 3.3 9.7 - - - +
2109C ASP* 2.8 42.2 + - - +
2110C ASN 4.6 0.2 + - - -
2126C PRO* 3.7 32.5 - - + -
2128C LEU* 4.0 16.4 - - + -
2137C MET* 3.9 27.1 - - + -
2138C PHE 4.5 1.1 - - - +
2167C TRP* 3.8 31.4 - - + -
2431C TYR* 4.3 7.6 - - + -
2432C VAL 3.8 4.5 - - - +
2434C LEU* 4.4 3.8 - - - +
2449C ASN* 3.8 4.0 - - - +
2450C SER* 1.3 81.8 + - - +
2452C VAL* 1.3 75.9 + - - +
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Residues in contact with VAL2452 (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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2105C ILE* 3.6 21.1 - - + -
2107C SER 3.5 5.8 - - - +
2108C LYS* 4.4 8.3 - - + -
2403C ILE* 4.6 4.3 - - + -
2404C VAL* 4.8 0.7 - - + -
2431C TYR* 3.0 4.9 - - - +
2432C VAL* 2.8 56.8 + - + +
2434C LEU* 4.2 9.6 - - + +
2451C ILE* 1.3 76.6 - - - +
2453C ALA* 1.3 63.8 + - - +
2454C LEU* 4.1 10.2 - - + +
2466C TRP* 3.6 43.1 - - + +
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Residues in contact with ALA2453 (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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2105C ILE* 3.6 1.9 - - - +
2106C LEU* 2.8 31.2 + - + -
2107C SER* 2.9 20.3 + - - +
2128C LEU* 4.3 13.7 - - + -
2137C MET* 5.5 0.2 - - + -
2416C PHE* 4.1 21.3 - - + -
2430C PHE 3.2 11.7 - - - +
2431C TYR* 4.2 4.9 - - + -
2451C ILE* 4.9 0.9 - - + -
2452C VAL* 1.3 76.7 - - - +
2454C LEU* 1.3 66.9 + - - +
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Residues in contact with LEU2454 (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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2103C TRP* 4.0 21.3 - - + +
2104C HIS 3.1 22.0 - - - +
2105C ILE* 4.1 4.9 - - + +
2106C LEU 4.0 2.0 - - - +
2401C GLN* 4.3 2.7 - - - +
2403C ILE* 3.9 41.1 - - + -
2429C CYS* 3.1 2.3 - - - +
2430C PHE* 2.8 54.4 + - + -
2452C VAL* 4.1 16.8 - - + -
2453C ALA* 1.3 83.9 - - - +
2455C CYS* 1.3 62.4 + - - +
2466C TRP* 4.1 21.8 - - + +
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Residues in contact with CYS2455 (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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218A PRO* 5.3 4.0 - - + -
2103C TRP* 3.4 8.1 - - - -
2104C HIS* 2.9 48.3 + - - +
2106C LEU* 3.8 31.1 - - - +
2427C ASN* 3.7 8.5 - - - +
2428C PRO 3.2 6.1 - - - +
2429C CYS* 2.0 46.7 - - - +
2454C LEU* 1.3 74.6 - - - +
2456C GLY* 1.3 63.1 + - - +
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Residues in contact with GLY2456 (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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221A GLU* 4.7 3.1 - - - +
2100C VAL* 3.6 17.5 - - - -
2102C SER 3.5 8.1 - - - -
2103C TRP* 3.4 5.4 - - - -
2104C HIS* 3.5 9.9 + - - -
2423C LYS* 5.7 0.7 + - - -
2427C ASN* 2.9 29.9 + - - +
2428C PRO 2.9 13.7 + - - -
2455C CYS* 1.3 76.6 - - - +
2457C SER* 1.3 58.3 + - - -
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Residues in contact with SER2457 (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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221A GLU* 2.7 28.3 + - - -
2099C GLU 4.3 4.3 - - - -
2100C VAL* 4.0 0.8 - - - +
2101C ASN 2.8 30.5 + - - -
2102C SER* 2.7 24.9 + - - -
2104C HIS* 4.7 2.5 - - - -
2456C GLY* 1.3 73.9 - - - -
2458C LYS* 1.3 54.1 + - - +
2459C LYS* 3.0 23.5 + - - +
2461C LEU* 3.6 23.3 - - - +
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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
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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