Contacts of the strand formed by residues 2238 - 2245 (chain B) in PDB entry 4NF9
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 GLU2238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2233B ASP 3.5 1.2 - - - +
2234B ILE* 3.4 6.6 - - - +
2235B ASN* 3.0 48.9 + - - +
2236B ASN* 2.9 11.5 + - - +
2237B ASN* 1.3 80.6 - - - +
2239B LEU* 1.3 60.9 + - - +
2240B ARG* 2.9 34.7 + - - +
2255B THR* 4.1 7.6 - - + +
2256B LEU 3.4 5.4 - - - +
2257B PHE* 3.4 40.1 - - + -
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Residues in contact with LEU2239 (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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2171B LEU* 4.7 0.2 - - + -
2217B ILE* 4.0 16.2 - - + -
2232B ILE* 4.1 11.2 - - + -
2233B ASP 3.5 0.4 - - - -
2234B ILE* 3.8 32.8 - - + -
2237B ASN 4.0 0.2 - - - -
2238B GLU* 1.3 76.1 - - - +
2240B ARG* 1.3 61.0 + - - +
2241B LEU* 4.4 11.4 - - + +
2254B ILE 3.4 1.7 - - - +
2255B THR* 3.2 4.9 - - - +
2256B LEU* 2.7 46.7 + - + +
2258B LEU* 3.3 33.9 - - + -
2297B LEU* 3.7 39.9 - - + -
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Residues in contact with ARG2240 (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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2231B ASN* 3.7 1.2 + - - +
2232B ILE* 3.5 3.8 - - - -
2233B ASP* 2.7 59.7 + - + +
2235B ASN* 4.1 22.8 - - - +
2238B GLU* 2.9 38.6 + - - +
2239B LEU* 1.3 74.3 - - - +
2241B LEU* 1.3 63.3 + - - +
2242B LEU* 3.9 0.9 + - - +
2253B GLU* 4.0 29.3 + - - +
2254B ILE 3.4 4.3 - - - -
2255B THR* 3.0 23.2 + - + +
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Residues in contact with LEU2241 (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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2229B LEU* 3.3 14.1 - - + -
2231B ASN 3.7 0.9 - - - -
2232B ILE* 3.2 40.2 - - + -
2239B LEU* 4.4 13.2 - - + +
2240B ARG* 1.3 74.0 - - - +
2242B LEU* 1.3 60.2 + - - +
2243B PHE* 3.7 16.9 + - + -
2252B PHE 3.8 0.2 - - - +
2253B GLU* 3.1 4.1 - - - +
2254B ILE* 2.6 48.1 + - + +
2256B LEU* 3.7 29.8 - - + -
2297B LEU* 4.8 3.1 - - + -
2300B VAL* 5.5 0.7 - - + -
2301B VAL* 3.9 25.8 - - + -
2304B ILE* 5.3 3.6 - - + -
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Residues in contact with LEU2242 (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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2229B LEU* 3.4 6.5 - - - +
2230B MSE 2.6 56.4 + - + -
2231B ASN* 3.1 26.0 + - + +
2240B ARG 3.9 1.8 + - - +
2241B LEU* 1.3 70.4 - - - +
2243B PHE* 1.3 58.7 + - - +
2251B LYS* 4.1 29.6 - - + +
2252B PHE 3.6 19.1 - - - +
2253B GLU* 4.3 16.2 - - + +
2274B HIS* 4.6 8.3 - - + +
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Residues in contact with PHE2243 (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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2227B TYR 3.6 17.5 - - - -
2228B ASN 2.8 22.9 - - - -
2229B LEU* 3.9 26.0 - - + -
2241B LEU* 3.9 15.9 - - + -
2242B LEU* 1.3 74.7 - - - +
2244B SER* 1.3 65.8 + - - +
2251B LYS* 3.2 6.6 - - - +
2252B PHE* 2.8 63.6 + + + +
2254B ILE* 3.6 22.0 - - + -
2301B VAL* 4.3 19.1 - - + -
2304B ILE* 3.6 31.6 - - + -
2309B PHE* 3.9 10.1 - + + -
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Residues in contact with SER2244 (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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2228B ASN* 3.1 25.4 + - - +
2230B MSE 3.5 34.8 - - - +
2242B LEU* 5.4 0.2 - - - -
2243B PHE* 1.3 76.0 - - - +
2245B SER* 1.3 60.3 + - - +
2246B SER 4.2 0.8 + - - -
2250B ALA 3.5 4.6 + - - -
2251B LYS* 3.6 30.1 + - - +
2309B PHE* 4.4 1.4 - - - -
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Residues in contact with SER2245 (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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2228B ASN* 3.7 12.8 + - - +
2244B SER* 1.3 72.9 - - - +
2246B SER* 1.3 61.8 + - - +
2247B ALA* 3.3 12.0 + - - +
2248B ALA* 3.1 19.6 + - - +
2249B PHE* 3.1 19.1 + - - -
2250B ALA 2.9 18.9 + - - +
2309B PHE* 2.9 37.9 + - - +
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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