Contacts of the strand formed by residues 234 - 242 (chain A) in PDB entry 3MIB
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 MET 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A TYR* 4.0 11.4 - - + -
229A TYR* 3.4 25.8 - - + +
232A TYR 3.3 1.0 + - - -
233A PRO* 1.3 74.9 - - - +
235A HIS* 1.3 64.0 + - - +
236A VAL* 4.4 10.8 - - + -
281A VAL 3.9 0.2 - - - +
282A ASP* 3.3 5.2 - - - +
283A VAL* 2.9 65.1 + - + -
289A LEU* 3.7 26.7 - - + -
319A ILE* 4.6 2.5 - - + -
321A TYR* 3.4 39.3 - - + -
322A TYR 3.6 4.9 - - - -
323A MET* 3.8 13.2 - - + -
332A MET* 4.1 2.0 - - - -
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A NO2 2.9 4.9 + - - -
233A PRO* 5.1 11.6 + - + -
234A MET* 1.3 75.3 + - - +
236A VAL* 1.3 64.1 + - - +
237A PHE* 3.5 4.0 + - - -
280A PRO* 4.8 13.0 - - + -
281A VAL 3.6 2.5 - - - -
282A ASP* 3.4 21.2 - - + +
321A TYR* 3.0 5.2 - - - -
322A TYR* 2.8 78.8 + + + -
323A MET* 6.2 0.2 - - - -
359A NI 2.0 45.4 - - + +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A MET* 4.4 7.2 - - + -
235A HIS* 1.3 71.9 - - - +
237A PHE* 1.3 61.8 + - - +
238A ALA 3.8 8.5 - - - +
263A ILE* 3.6 19.1 - - + -
277A VAL* 3.5 24.4 - - + +
280A PRO* 3.6 10.1 - - - +
281A VAL* 2.9 41.3 + - + +
283A VAL* 4.3 18.2 - - + -
319A ILE* 3.4 35.9 - - + -
320A MET 3.5 4.7 - - - +
321A TYR* 4.1 2.5 - - + +
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Residues in contact with PHE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG 5.2 2.2 - - - -
150A LEU* 3.8 18.8 - - + -
151A PRO* 3.7 31.9 - - + -
154A VAL* 4.4 5.4 - - + -
202A ALA* 4.5 1.3 - - + -
235A HIS 4.7 0.2 - - - +
236A VAL* 1.3 74.2 - - - +
238A ALA* 1.3 67.0 + - + +
276A PRO* 3.5 7.1 - - - +
277A VAL* 3.1 23.3 + - - -
280A PRO* 5.5 4.0 - - + -
320A MET* 3.0 42.7 + - + -
321A TYR* 3.3 31.0 - - - -
322A TYR* 3.6 33.0 - + + -
360A GOL 4.7 5.4 - - - -
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 6.4 0.4 - - - -
236A VAL* 3.8 5.0 - - - +
237A PHE* 1.3 89.8 - - + +
239A TYR* 1.3 61.5 + - - +
274A PHE* 4.2 8.3 - - + -
275A TYR 3.3 15.0 - - - +
276A PRO* 4.5 1.3 - - + -
277A VAL* 3.8 5.0 - - - +
319A ILE 3.7 0.5 - - - -
320A MET* 2.8 43.4 + - + +
360A GOL 3.8 22.0 - - - +
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Residues in contact with TYR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ALA* 1.3 76.3 - - - +
240A ARG* 1.3 63.2 + - - +
241A VAL* 4.1 13.9 - - + -
263A ILE* 4.0 19.7 - - + -
264A GLY* 3.7 30.9 - - - -
265A ARG 3.6 21.8 + - - -
266A GLN* 4.1 23.8 + - + -
273A ALA 3.7 0.7 - - - +
274A PHE* 3.4 5.3 - - - -
275A TYR* 2.8 60.5 + + + +
276A PRO 3.8 12.8 - - - -
277A VAL* 4.0 7.6 - - + -
317A LEU* 4.3 10.8 - - + -
318A TYR 3.0 12.8 - - - +
319A ILE* 4.6 3.6 - - - -
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A HIS* 5.3 4.9 + - - -
110A LEU* 3.7 32.2 - - - +
137A ILE* 3.8 13.9 - - - +
140A ALA* 4.1 5.2 - - - -
239A TYR* 1.3 75.1 - - - +
241A VAL* 1.3 69.6 + - - +
242A HIS* 4.1 13.6 + - - +
272A GLN* 2.7 51.3 + - - +
273A ALA 3.6 10.5 - - - +
274A PHE* 3.6 36.1 - - + -
275A TYR* 5.6 0.4 - - - -
317A LEU* 3.5 4.2 - - - +
318A TYR* 2.8 70.5 + - + -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TYR* 4.1 9.0 - - + -
240A ARG* 1.3 81.1 - - - +
242A HIS* 1.3 62.7 + - - +
250A VAL* 3.7 36.1 - - + +
265A ARG* 5.7 0.7 - - - +
266A GLN* 4.0 33.7 - - + -
268A PRO* 3.7 30.3 - - + -
272A GLN* 3.3 26.7 - - + +
273A ALA 4.9 0.8 + - - -
275A TYR* 6.0 1.6 - - + -
316A ASN 3.5 3.8 - - - -
317A LEU* 3.9 12.6 - - + -
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A NO2 2.8 11.6 + - - -
240A ARG* 4.1 22.6 + - - +
241A VAL* 1.3 77.2 - - - +
243A THR* 1.3 76.3 + - - +
244A HIS* 3.3 4.7 + + - -
250A VAL* 5.1 1.7 - - - +
272A GLN* 2.7 25.7 + - - +
314A MET* 3.5 21.5 - - + +
316A ASN* 2.9 55.7 + - + +
318A TYR* 4.1 3.1 - - + -
358A CU 2.0 31.4 - - - -
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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