Contacts of the strand formed by residues 2428 - 2437 (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 PRO2428 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2097C LEU* 3.9 26.0 - - + -
2098C CYS 4.2 4.5 - - - +
2100C VAL* 3.7 16.2 - - + -
2103C TRP* 3.5 13.2 - - + -
2361C PHE* 3.6 38.6 - - + -
2366C ASN* 5.8 0.4 - - - +
2417C ILE* 4.1 3.1 - - + -
2426C PHE 3.2 7.9 - - - +
2427C ASN* 1.3 98.4 - - - +
2429C CYS* 1.3 58.4 + - - +
2455C CYS* 3.2 2.6 - - - +
2456C GLY 2.9 28.9 + - - -
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Residues in contact with CYS2429 (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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2103C TRP* 4.6 0.7 - - - -
2106C LEU* 4.7 0.2 - - - -
2361C PHE* 3.2 16.7 - - - -
2415C ALA* 3.6 0.2 - - - -
2416C PHE* 3.1 55.9 + - + +
2417C ILE* 4.8 3.6 - - - -
2418C ASP* 4.9 7.2 - - - -
2427C ASN* 3.7 10.5 - - - -
2428C PRO* 1.3 73.3 - - - +
2430C PHE* 1.3 66.2 + - - +
2454C LEU 3.1 6.7 - - - +
2455C CYS* 2.0 47.1 - - - +
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Residues in contact with PHE2430 (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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2103C TRP* 3.5 40.6 - + - -
2359C PHE* 3.4 32.5 - + + -
2381C TYR* 4.4 1.6 - + - -
2383C MET* 3.6 25.4 - - + -
2403C ILE* 3.7 20.6 - - + -
2414C GLY 3.2 16.6 - - - +
2416C PHE* 3.6 9.0 - - - -
2429C CYS* 1.3 75.7 - - - +
2431C TYR* 1.3 71.8 + - - +
2432C VAL* 3.7 21.3 - - + -
2453C ALA* 3.2 4.0 - - - +
2454C LEU* 2.8 58.1 + - + +
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Residues in contact with TYR2431 (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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2126C PRO* 3.0 34.2 + - + -
2127C TYR* 3.4 26.0 - - + -
2128C LEU* 4.1 16.6 - - + -
2234C GLU 3.4 4.2 + - - -
2235C SER* 3.5 3.9 - - - -
2357C LYS* 3.2 31.9 - - - +
2412C TYR* 4.1 8.6 - - + +
2413C SER* 3.3 25.8 - - - -
2414C GLY* 3.3 32.8 + - - -
2415C ALA 4.4 1.8 - - - -
2416C PHE* 4.4 6.7 - + + -
2430C PHE* 1.3 79.4 - - - +
2432C VAL* 1.3 67.8 + - - +
2433C GLU* 3.9 9.6 - - + -
2451C ILE* 4.3 4.9 - - + -
2452C VAL 3.0 12.8 - - - +
2453C ALA* 4.0 9.0 - - + +
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Residues in contact with VAL2432 (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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2381C TYR* 3.8 31.9 - - + -
2403C ILE* 4.1 10.8 - - + -
2404C VAL* 4.3 1.1 - - + -
2410C SER* 4.0 16.4 - - - -
2411C GLY 4.6 0.4 - - - +
2412C TYR 3.7 6.3 - - - +
2413C SER* 4.6 0.9 - - - -
2430C PHE* 3.7 23.6 - - + -
2431C TYR* 1.3 82.1 - - - +
2433C GLU* 1.3 72.5 + - - +
2434C LEU* 3.6 16.3 + - + +
2451C ILE* 3.8 3.3 - - - +
2452C VAL* 2.8 39.9 + - + +
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Residues in contact with GLU2433 (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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2124C ARG* 2.9 42.0 + - - +
2125C GLU 2.8 25.3 + - - -
2126C PRO* 3.2 29.2 - - + +
2410C SER* 2.9 3.3 - - - -
2411C GLY 2.9 28.1 + - - -
2412C TYR* 2.8 41.2 + - + +
2431C TYR* 3.9 3.2 - - + -
2432C VAL* 1.3 71.3 - - - +
2434C LEU* 1.3 59.9 + - - +
2435C ILE* 3.6 10.3 - - + +
2449C ASN* 3.7 12.7 - - + -
2450C SER 3.9 4.0 - - - -
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Residues in contact with LEU2434 (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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2108C LYS* 4.6 4.3 - - - +
2404C VAL* 3.8 30.3 - - + -
2409C TRP 3.8 15.9 - - - +
2410C SER* 4.0 2.2 - - - -
2432C VAL* 3.9 21.5 - - + +
2433C GLU* 1.3 69.7 - - - +
2435C ILE* 1.3 65.7 + - - +
2436C ARG* 3.6 6.2 + - - +
2449C ASN* 3.1 21.1 - - - -
2450C SER* 3.1 34.7 + - - +
2451C ILE 4.4 1.1 - - - -
2452C VAL* 4.2 19.1 - - + +
2466C TRP 3.4 19.7 - - - +
2467C HIS 3.9 0.4 - - - -
2468C ASP* 3.5 24.5 - - + +
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Residues in contact with ILE2435 (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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2124C ARG* 3.7 23.6 - - - +
2378C ARG* 4.5 16.8 - - + +
2409C TRP* 3.4 21.5 - - + +
2410C SER 3.0 14.7 + - - +
2411C GLY* 3.7 14.1 - - - -
2433C GLU* 3.6 33.2 - - + +
2434C LEU* 1.3 70.7 - - - +
2436C ARG* 1.3 78.8 + - - +
2437C GLY 5.3 0.9 - - - +
2438C ARG 4.4 7.4 - - - +
2439C PRO* 5.8 2.0 - - + -
2447C THR* 4.2 15.7 - - + -
2448C SER 3.4 12.6 - - - +
2449C ASN* 4.0 0.2 - - - -
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Residues in contact with ARG2436 (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* 3.9 16.6 - - + -
2408C ASN* 5.6 5.7 - - - +
2409C TRP* 4.4 10.8 - - - +
2434C LEU 4.0 3.1 - - - +
2435C ILE* 1.3 87.2 - - - +
2437C GLY* 1.3 61.8 + - - +
2441C GLU* 2.9 38.9 + - - -
2446C TRP* 3.3 19.6 - - + -
2447C THR* 3.5 2.3 - - - -
2448C SER 2.9 32.2 + - - +
2468C ASP* 2.8 60.4 + - - +
2469C GLY 4.3 1.8 - - - +
2470C ALA* 2.9 33.7 + - - +
2472C ILE* 3.9 20.3 - - + +
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Residues in contact with GLY2437 (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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2435C ILE* 5.3 1.4 - - - +
2436C ARG* 1.3 73.8 - - - +
2438C ARG* 1.3 66.3 + - - -
2440C LYS* 3.5 3.5 + - - +
2441C GLU* 2.9 48.8 + - - +
2444C VAL* 3.8 11.9 - - - -
2446C TRP* 3.4 15.1 - - - -
2472C ILE* 4.7 0.6 - - - +
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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