Contacts of the strand formed by residues 266 - 272 (chain B) in PDB entry 4MDH
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 VAL 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG* 3.6 34.3 - - - +
159B HIS* 3.8 11.9 - - + +
180B VAL 5.3 0.9 - - - -
255B ASP* 3.7 3.8 - - + +
260B THR* 3.4 23.5 - - + +
264B GLU* 5.3 5.4 - - + +
265B PHE* 1.4 74.0 - - - +
267B SER* 1.3 70.7 + - - +
268B MET* 5.1 5.4 - - - -
287B PHE 3.4 1.2 - - - +
288B PRO* 3.7 2.4 - - - +
289B VAL* 2.9 37.2 + - + +
291B ILE* 4.0 25.8 - - + -
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 3.6 16.4 + - - -
156B ARG* 4.2 15.4 + - - +
159B HIS* 2.5 38.4 + - - -
180B VAL 3.8 2.6 + - - -
181B ILE* 4.0 1.6 - - - -
182B ILE* 3.2 34.7 + - - -
252B HIS* 5.2 1.9 - - - -
266B VAL* 1.3 79.9 - - - +
268B MET* 1.3 63.0 + - - +
287B PHE 3.3 7.4 - - - -
288B PRO* 4.9 0.2 - - - -
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Residues in contact with MET 268 (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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152B SER* 4.0 11.2 - - - -
153B CYS 4.6 1.1 - - - -
155B THR* 3.7 5.8 - - - -
252B HIS* 3.3 43.1 - - + +
256B ILE* 4.2 18.8 - - + -
266B VAL* 3.8 4.7 + - - -
267B SER* 1.3 76.2 - - - +
269B GLY* 1.3 63.5 + - - +
270B ILE* 3.4 17.4 + - + +
286B SER* 3.9 3.1 + - - -
287B PHE 3.1 23.7 + - - +
289B VAL* 4.3 17.0 - - + +
291B ILE* 4.8 7.2 - - + -
296B TRP* 3.6 41.3 - - + -
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Residues in contact with GLY 269 (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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152B SER* 3.2 9.0 - - - -
153B CYS* 3.0 44.5 + - - -
155B THR* 3.7 7.7 + - - -
268B MET* 1.3 71.7 - - - +
270B ILE* 1.3 60.0 + - - +
284B LEU* 3.6 6.5 - - - -
285B TYR 3.3 12.6 - - - -
286B SER* 3.5 11.4 - - - -
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Residues in contact with ILE 270 (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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151B PHE 3.6 15.5 - - - +
152B SER* 3.8 10.3 - - - -
268B MET* 3.7 20.0 - - + +
269B GLY* 1.3 77.9 - - - +
271B ILE* 1.3 65.8 + - - +
272B SER 3.7 0.2 + - - -
284B LEU* 3.3 11.6 - - - +
285B TYR 2.7 33.8 + - - +
287B PHE* 4.2 9.6 - - + -
289B VAL* 4.0 10.5 - - + -
296B TRP* 3.2 66.6 - - + +
298B ILE* 3.8 22.4 - - + -
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Residues in contact with ILE 271 (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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137B LEU* 3.8 22.4 - - + -
148B LYS* 3.9 44.4 - - + +
149B GLU* 4.8 2.5 - - + +
151B PHE 4.8 0.8 + - - +
270B ILE* 1.3 88.8 - - - +
272B SER* 1.3 63.2 + - - +
273B ASP* 3.2 34.3 + - + +
282B ASP* 3.9 4.9 - - - +
283B LEU 2.8 35.7 - - - +
284B LEU* 4.1 7.7 - - + +
287B PHE* 4.8 0.2 - - - -
296B TRP* 4.1 21.9 - - + -
298B ILE* 4.8 3.3 - - - +
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Residues in contact with SER 272 (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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270B ILE 3.7 1.2 + - - -
271B ILE* 1.3 71.3 - - - +
273B ASP* 1.3 52.0 + - - +
274B GLY 2.9 0.7 + - - -
275B ASN* 2.7 43.2 + - - +
279B VAL* 4.4 2.2 - - - -
280B PRO 2.5 28.9 + - - -
281B ASP* 3.3 4.6 - - - +
283B LEU* 3.0 30.8 + - - +
285B TYR* 4.4 2.9 - - - -
287B PHE* 3.7 29.6 - - - -
298B ILE* 5.2 1.9 - - - +
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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