Contacts of the strand formed by residues 278 - 285 (chain A) in PDB entry 1MHP
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 ILE 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ARG* 3.4 32.8 - - + -
238A PHE* 4.2 18.2 - - + -
250A LYS* 3.2 27.4 - - + +
252A MET* 3.7 36.6 - - + +
273A CYS* 3.0 28.9 + - + +
274A GLU* 5.0 0.6 + - - +
276A GLU* 3.8 15.9 - - + +
277A ASN* 1.3 74.9 - - - +
279A GLN* 1.3 64.4 + - - +
280A ARG* 3.1 26.7 + - + +
308A SER* 3.7 0.5 + - - -
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Residues in contact with GLN 279 (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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249A LYS* 3.0 44.9 - - + +
250A LYS 2.9 9.7 + - - +
251A VAL* 3.4 14.3 - - + +
252A MET* 2.7 33.1 + - - +
277A ASN* 3.6 2.4 + - - +
278A ILE* 1.3 72.3 - - - +
280A ARG* 1.3 55.3 + - - +
281A PHE* 4.2 12.6 - - + -
308A SER* 3.9 8.5 + - - -
309A GLU 5.4 0.9 - - - +
314A HIS* 3.7 21.2 + - + -
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Residues in contact with ARG 280 (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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230A ILE* 5.3 0.2 - - - -
252A MET* 3.4 15.3 - - + +
254A ILE* 4.6 5.2 - - + -
270A ILE* 3.7 26.8 - - - +
273A CYS* 3.8 19.1 - - - +
274A GLU* 3.2 52.9 + - - +
278A ILE* 3.1 37.6 + - + +
279A GLN* 1.3 75.8 - - - +
281A PHE* 1.3 63.4 + - - +
306A ILE* 2.8 31.1 + - - +
307A ALA* 3.4 16.1 + - - -
308A SER* 3.0 44.8 + - - +
314A HIS* 3.4 12.3 + - - +
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Residues in contact with PHE 281 (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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251A VAL* 3.9 30.5 - - + -
252A MET 2.9 8.0 + - - +
253A VAL* 3.3 15.4 - - + +
254A ILE* 2.8 28.4 + - - +
279A GLN* 4.2 14.1 - - + -
280A ARG* 1.3 76.0 - - - +
282A SER* 1.3 60.5 + - - +
283A ILE* 5.2 0.9 - - + -
313A LYS 3.7 11.0 - - - -
314A HIS* 3.2 44.6 - + - +
316A PHE* 4.4 9.4 - + + -
331A LEU* 4.3 20.2 - - + -
334A ARG* 4.0 15.5 - - + -
335A ILE* 3.7 28.7 - - + -
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Residues in contact with SER 282 (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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254A ILE* 3.4 9.0 - - - -
280A ARG 4.1 0.8 + - - -
281A PHE* 1.3 74.6 - - - +
283A ILE* 1.3 67.8 + - - +
303A ILE* 2.9 38.7 + - - +
306A ILE* 4.0 18.8 - - - -
307A ALA* 3.4 14.9 - - - +
314A HIS 3.0 5.0 + - - +
315A PHE* 3.4 7.0 - - - -
316A PHE* 3.0 23.6 + - - -
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Residues in contact with ILE 283 (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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168A PHE* 3.6 33.0 - - + -
253A VAL* 4.2 5.8 - - + -
254A ILE 2.8 15.8 + - - +
255A VAL* 3.7 12.1 - - + -
256A THR* 3.2 28.4 + - - +
281A PHE 5.1 0.7 - - - +
282A SER* 1.3 82.4 - - - +
284A ALA* 1.3 65.8 + - - +
285A ILE* 4.4 1.5 - - + +
303A ILE* 4.0 3.2 - - - +
316A PHE* 3.3 27.6 - - + +
318A VAL* 3.9 24.0 - - + -
324A LEU* 4.0 13.7 - - + -
327A ILE* 4.6 3.6 - - + -
331A LEU* 3.6 17.5 - - + -
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Residues in contact with ALA 284 (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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256A THR 3.4 3.4 - - - -
283A ILE* 1.3 77.0 - - - +
285A ILE* 1.3 64.8 + - - +
286A LEU* 3.4 9.0 + - + -
299A PHE* 3.8 13.0 - - + -
300A VAL* 5.3 0.9 - - - -
303A ILE* 3.7 30.5 - - + -
315A PHE* 3.9 15.7 - - + -
316A PHE 3.0 7.3 + - - -
317A ASN* 3.7 3.9 - - - +
318A VAL 3.0 24.7 + - - -
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Residues in contact with ILE 285 (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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159A ILE* 5.4 2.5 - - + -
165A VAL* 6.3 0.4 - - + -
255A VAL* 3.6 30.3 - - + -
256A THR* 2.9 21.5 + - - +
257A ASP* 3.4 31.6 - - + +
283A ILE* 4.4 1.8 - - + +
284A ALA* 1.3 73.2 - - - +
286A LEU* 1.3 62.6 + - - +
287A GLY* 3.5 13.0 + - - +
299A PHE* 3.6 7.4 - - - -
318A VAL* 3.7 5.8 - - + -
320A ASP* 3.7 5.8 - - - +
321A GLU* 3.5 45.1 - - - +
324A LEU* 3.8 28.0 - - + -
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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