Contacts of the strand formed by residues 2236 - 2245 (chain B) in PDB entry 4D0N
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 LEU2236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2201B LYS* 3.5 56.6 + - + +
2202B LYS* 6.2 0.2 - - - +
2204B ARG* 3.7 27.1 - - + -
2205B LEU* 3.9 19.0 - - + +
2208B ILE* 4.8 2.7 - - + -
2234B LYS 4.2 1.0 + - - -
2235B LYS* 1.3 85.9 + - - +
2237B VAL* 1.3 61.6 + - - +
2238B ARG* 3.8 21.1 - - - +
2239B ASP* 4.1 10.5 - - + +
2257B VAL* 4.0 21.3 - - + -
2258B LEU 3.5 17.0 - - - +
2259B LEU* 3.9 8.7 - - + +
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Residues in contact with VAL2237 (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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2201B LYS* 3.3 22.4 + - - +
2235B LYS* 6.1 0.2 - - - +
2236B LEU* 1.3 75.7 - - - +
2238B ARG* 1.3 60.4 + - - +
2258B LEU* 2.9 20.8 + - + +
2259B LEU 3.7 22.9 - - - +
2260B THR* 3.8 21.1 - - + -
2331B ILE* 3.5 30.8 - - + +
2335B THR* 3.7 21.3 - - + +
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Residues in contact with ARG2238 (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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2201B LYS* 4.9 7.0 - - - +
2236B LEU* 3.8 6.0 - - - +
2237B VAL* 1.3 83.4 - - + +
2239B ASP* 1.3 71.4 + - - +
2257B VAL 3.8 0.2 - - - -
2258B LEU* 2.8 31.5 + - + +
2327B SER* 3.5 41.4 + - - -
2328B TRP* 3.7 33.7 - - + +
2331B ILE* 3.2 37.7 - - + +
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Residues in contact with ASP2239 (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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2201B LYS* 5.6 3.3 + - - +
2204B ARG* 2.7 57.0 + - - +
2208B ILE* 4.2 4.2 - - + +
2236B LEU* 4.1 14.4 - - + +
2238B ARG* 1.3 82.7 - - - +
2240B GLY* 1.3 58.4 + - - +
2255B GLN* 3.6 6.1 + - - +
2256B ALA 3.1 12.3 - - - +
2257B VAL* 4.3 11.0 - - + -
2328B TRP* 4.2 6.0 - - - -
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Residues in contact with GLY2240 (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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2239B ASP* 1.3 76.1 - - - +
2241B SER* 1.3 61.4 + - - -
2242B VAL* 4.6 0.2 - - - -
2255B GLN* 3.2 13.4 + - - +
2256B ALA* 2.8 37.9 + - - +
2324B GLU* 5.7 2.0 - - - -
2328B TRP* 4.0 11.2 - - - -
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Residues in contact with SER2241 (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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2240B GLY* 1.3 70.7 - - - -
2242B VAL* 1.3 67.1 + - - +
2243B PHE* 5.7 1.4 - - - -
2253B GLU* 2.8 32.1 + - - +
2254B VAL 3.4 6.5 + - - -
2255B GLN* 3.2 19.9 + - - +
2320B SER* 5.4 4.3 + - - -
2324B GLU* 3.8 12.9 + - - +
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Residues in contact with VAL2242 (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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2240B GLY 4.2 0.4 - - - +
2241B SER* 1.3 81.6 + - - +
2243B PHE* 1.3 71.2 + - - +
2253B GLU* 3.6 4.5 - - - +
2254B VAL* 2.8 50.7 + - + +
2256B ALA* 3.8 24.5 - - + -
2265B PHE* 4.0 2.5 - - + -
2317B VAL* 3.6 24.7 - - + -
2318B HIS 3.8 11.2 - - - +
2319B ALA* 4.8 7.2 - - - +
2324B GLU* 4.6 2.0 - - - +
2328B TRP* 3.7 30.3 - - + +
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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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2241B SER 5.7 1.3 - - - -
2242B VAL* 1.3 77.4 - - - +
2244B LEU* 1.3 62.5 + - - +
2251B LEU* 4.0 33.2 - - + -
2252B LYS 3.4 3.6 - - - +
2253B GLU* 3.8 50.7 - - + -
2317B VAL* 3.3 4.4 - - - +
2318B HIS* 2.6 58.4 + - + +
2319B ALA 4.9 9.0 - - - -
2320B SER* 5.6 5.4 - - - -
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Residues in contact with LEU2244 (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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2243B PHE* 1.3 73.2 - - - +
2245B LYS* 1.3 59.9 + - - +
2246B ASN 4.0 0.8 + - - -
2250B ARG 3.2 5.5 - - - +
2251B LEU* 3.3 3.1 - - - -
2252B LYS* 2.9 41.6 + - + +
2254B VAL* 4.0 14.6 - - + -
2265B PHE* 3.8 38.6 - - + -
2276B ALA* 4.0 26.9 - - + -
2278B LEU* 3.9 28.3 - - + -
2283B THR* 4.8 2.5 - - + -
2315B VAL* 3.8 26.7 - - + -
2316B GLU 3.5 5.6 - - - +
2317B VAL* 4.3 5.4 - - + -
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Residues in contact with LYS2245 (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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2243B PHE 4.0 0.8 + - - -
2244B LEU* 1.3 72.3 - - - +
2246B ASN* 1.3 70.2 + - - +
2249B GLY* 3.8 29.6 + - - -
2250B ARG 3.5 2.9 - - - -
2251B LEU* 3.9 15.2 - - + +
2278B LEU* 4.1 6.3 - - - +
2298B GLU* 4.0 21.2 + - - -
2316B GLU* 2.9 55.7 + - + +
2318B HIS* 3.8 21.2 - - + +
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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