Contacts of the strand formed by residues 2413 - 2417 (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 SER2413 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2357C LYS* 3.2 16.7 + - - +
2358C GLY* 3.2 32.9 - - - -
2359C PHE* 3.7 7.2 - - - -
2381C TYR* 2.7 45.3 + - - -
2412C TYR* 1.3 77.0 - - - +
2414C GLY* 1.3 59.3 + - - +
2431C TYR* 3.3 21.3 - - - -
2432C VAL* 4.5 2.7 - - - -
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Residues in contact with GLY2414 (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* 4.6 0.2 - - - -
2286C SER* 3.3 15.3 - - - -
2357C LYS* 4.3 1.1 - - - -
2359C PHE* 3.8 8.7 - - - -
2413C SER* 1.3 76.6 - - - +
2415C ALA* 1.3 59.3 + - - -
2430C PHE* 3.2 26.3 - - - +
2431C TYR* 3.3 31.7 + - - -
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Residues in contact with ALA2415 (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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2128C LEU 4.9 0.3 - - - +
2235C SER* 4.4 11.3 + - - -
2236C GLU* 3.9 13.2 + - - +
2286C SER* 3.8 12.3 - - - -
2287C CYS 4.0 21.3 + - - +
2288C TYR* 4.6 4.5 - - + -
2359C PHE* 4.3 11.7 - - + -
2360C ALA 5.5 0.9 - - - +
2361C PHE* 3.6 28.7 - - + -
2414C GLY* 1.3 74.0 - - - -
2416C PHE* 1.3 66.0 + - - +
2429C CYS 3.6 5.4 - - - -
2430C PHE* 4.5 1.1 - - - +
2431C TYR* 5.0 0.9 - - - -
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Residues in contact with PHE2416 (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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2106C LEU* 3.5 29.2 - - + -
2128C LEU* 3.2 55.6 - - + +
2130C CYS* 4.1 23.8 - - - -
2135C CYS* 5.0 0.9 - - - -
2236C GLU* 3.3 15.7 - - - +
2287C CYS 5.1 2.0 - - - -
2288C TYR* 5.6 0.2 - - - -
2415C ALA* 1.3 78.6 - - - +
2417C ILE* 1.3 75.8 + - - +
2418C ASP* 5.4 0.4 - - + -
2419C TYR* 5.2 0.4 - - - -
2429C CYS* 3.1 46.8 + - + +
2430C PHE* 3.6 33.7 - - - -
2431C TYR* 4.0 8.7 - + + -
2453C ALA* 4.1 4.7 - - + -
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Residues in contact with ILE2417 (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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2097C LEU* 3.8 28.3 - - + -
2130C CYS* 4.1 14.5 - - - +
2236C GLU* 3.3 9.8 + - - +
2288C TYR* 3.9 13.2 - - + -
2289C GLY 4.1 2.7 - - - +
2361C PHE* 4.1 8.3 - - + -
2416C PHE* 1.3 87.1 - - - +
2418C ASP* 1.3 65.7 + - - +
2419C TYR* 3.0 64.3 + - + +
2420C TRP* 4.5 0.3 - - - -
2426C PHE* 3.9 16.6 - - + -
2427C ASN 3.5 26.0 - - - +
2428C PRO* 4.1 4.9 - - + -
2429C CYS* 4.8 1.1 - - - -
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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