Contacts of the strand formed by residues 2224 - 2231 (chain B) in PDB entry 4YNM
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 CYS2224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2166B ILE* 3.8 16.6 - - - -
2222B PRO* 3.5 4.7 - - - +
2223B ASN* 1.3 96.3 - - - +
2225B GLU* 1.3 64.0 + - - +
2239B LEU* 3.7 22.4 - - + -
2240B TYR 3.2 11.2 - - - +
2242B LEU* 3.7 12.0 - - - +
2245B MET* 3.7 18.4 - - - -
2251B LEU* 3.9 13.2 - - - -
2252B THR 3.0 17.6 + - - +
2253B TYR* 3.5 10.2 - - - +
2254B ASP 4.6 0.5 + - - -
2258B HIS* 5.2 0.2 + - - -
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Residues in contact with GLU2225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2114B PHE* 5.4 1.6 - - - -
2224B CYS* 1.3 76.5 - - - +
2226B MET* 1.3 66.5 + - - +
2227B GLN* 3.1 33.8 + - - +
2238B GLY 3.6 0.2 - - - +
2239B LEU* 3.3 6.5 - - - -
2240B TYR* 2.9 37.7 + - + +
2241B ALA 5.5 0.2 - - - +
2242B LEU* 3.5 30.6 - - + +
2253B TYR* 4.3 3.4 - - - -
2258B HIS* 3.8 18.1 + - - +
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Residues in contact with MET2226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2169B TYR* 3.8 26.2 - - + -
2196B LEU* 4.0 9.6 - - + -
2213B ALA* 5.3 0.9 - - + -
2216B ILE* 5.3 3.6 - - + -
2225B GLU* 1.3 79.5 - - - +
2227B GLN* 1.3 63.3 + - - +
2237B ILE* 3.8 21.1 - - + -
2238B GLY 3.2 17.0 - - - +
2239B LEU* 3.4 33.9 - - + -
2253B TYR* 3.7 28.7 - - + -
2258B HIS* 3.4 50.2 + - + +
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Residues in contact with GLN2227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2114B PHE* 3.3 30.9 - - + -
2163B GLY* 5.5 3.0 + - - -
2225B GLU* 3.1 28.6 + - + +
2226B MET* 1.3 76.2 - - - +
2228B LYS* 1.3 59.2 + - - +
2229B TRP* 2.8 36.7 + - + +
2237B ILE* 3.5 5.4 - - - -
2238B GLY 2.8 30.8 + - - -
2240B TYR* 3.3 41.2 - - + +
2241B ALA 5.8 0.4 + - - -
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Residues in contact with LYS2228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2114B PHE* 3.6 21.5 - - - +
2198B LEU* 4.4 13.0 - - + -
2199B ASP* 2.0 41.2 + - - +
2227B GLN* 1.3 70.2 - - - +
2229B TRP* 1.3 62.8 + - - +
2235B TYR* 3.6 61.1 - - + -
2236B ARG 3.6 6.3 - - - +
2237B ILE* 4.5 13.9 - - + -
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Residues in contact with TRP2229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2111B ARG* 4.0 24.0 - - + -
2114B PHE* 3.1 48.1 - + + -
2115B ALA 3.5 16.8 - - - -
2116B GLU* 3.6 20.4 - - + -
2130B ASN* 3.3 25.6 - - - -
2132B ARG* 5.5 4.3 - - - -
2133B ILE* 3.7 21.1 - - + -
2227B GLN* 2.8 44.9 + - + +
2228B LYS* 1.3 78.1 - - - +
2230B SER* 1.3 58.7 + - - +
2231B VAL* 3.7 6.9 + - + +
2235B TYR* 3.3 6.8 - - - -
2236B ARG 2.9 31.1 + - - +
2240B TYR* 3.4 24.1 + + - -
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Residues in contact with SER2230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2084B SER* 2.6 31.6 + - - -
2086B TYR* 3.7 36.3 + - - +
2114B PHE 2.9 8.4 + - - -
2115B ALA* 3.4 3.0 - - - +
2116B GLU 3.0 25.3 + - - +
2228B LYS 4.3 0.4 + - - -
2229B TRP* 1.3 71.6 - - - +
2231B VAL* 1.3 62.3 + - - +
2232B ASN 4.0 0.8 + - - -
2233B GLY* 3.9 6.8 + - - -
2234B VAL 3.7 3.8 - - - -
2235B TYR* 4.0 8.2 - - - -
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Residues in contact with VAL2231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2116B GLU* 3.9 20.2 - - + +
2133B ILE* 4.2 13.9 - - + -
2134B GLN* 3.5 34.3 - - + +
2229B TRP* 3.9 22.9 - - + +
2230B SER* 1.3 81.1 + - - +
2232B ASN* 1.3 71.4 + - + +
2234B VAL* 2.7 27.7 + - - +
2236B ARG* 3.9 31.7 + - + +
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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
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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