Contacts of the strand formed by residues 378 - 384 (chain A) in PDB entry 1MD9
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 THR 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A VAL* 4.2 1.1 - - - -
367A ASP* 6.0 0.5 - - - +
373A VAL* 4.0 12.8 - - - +
377A GLU* 1.3 81.2 + - - +
379A GLY* 1.3 61.9 + - - +
414A ILE* 3.3 26.7 - - + -
415A VAL* 3.2 10.5 - - - +
416A ARG* 3.9 14.6 - - + +
426A GLU* 3.4 17.4 + - + +
439A LYS* 3.5 13.0 + - - +
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Residues in contact with GLY 379 (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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365A VAL* 3.4 13.5 - - - +
366A TRP 3.4 6.7 - - - -
367A ASP* 5.2 2.2 - - - -
373A VAL* 5.0 1.1 - - - -
378A THR* 1.3 79.8 - - - +
380A HIS* 1.3 66.9 + - - -
381A LEU 3.4 0.5 + - - -
414A ILE* 3.4 9.8 - - - -
415A VAL 2.7 34.7 + - - +
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Residues in contact with HIS 380 (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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364A ARG 3.3 2.6 - - - +
365A VAL* 3.1 3.7 - - - -
366A TRP* 2.7 41.7 + - + +
367A ASP* 3.5 32.3 - - - +
368A ASP* 3.1 31.1 + - - -
379A GLY* 1.3 70.5 - - - -
381A LEU* 1.3 62.0 + - - +
382A LEU* 3.5 8.7 - - + +
410A ARG* 6.3 2.2 - - + -
412A GLY* 5.6 4.2 + - - -
413A ASP 3.9 4.8 + - - -
414A ILE* 4.3 23.1 - - + +
429A ALA* 4.5 12.4 - - + +
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Residues in contact with LEU 381 (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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330A PHE* 3.6 35.0 - - + -
332A MSE 5.0 1.8 - - + -
336A LEU* 5.0 5.4 - - + -
363A SER* 4.1 16.4 - - - -
364A ARG 4.0 3.6 - - - +
365A VAL* 4.6 7.9 - - + +
379A GLY 3.4 1.4 + - - -
380A HIS* 1.3 71.7 - - - +
382A LEU* 1.3 81.6 + - - +
383A THR* 5.2 1.6 - - - -
410A ARG* 3.7 2.8 - - - +
411A THR* 2.9 50.0 + - + +
412A GLY 4.2 2.6 + - - +
413A ASP* 3.0 17.6 + - - +
415A VAL* 3.6 24.5 - - + -
417A LEU* 5.2 0.4 - - + -
423A ILE* 4.2 12.3 - - + -
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Residues in contact with LEU 382 (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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363A SER* 3.3 3.6 - - - -
364A ARG* 2.9 47.3 + - + +
366A TRP* 3.6 41.1 - - + -
380A HIS* 3.5 17.5 - - + +
381A LEU* 1.3 81.8 - - - +
383A THR* 1.3 64.7 + - - +
404A THR* 3.4 32.5 - - + -
408A PHE* 4.0 17.0 - - + -
409A TYR 3.3 7.0 - - - +
410A ARG* 4.0 25.1 - - + +
411A THR* 5.1 0.2 - - - -
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Residues in contact with THR 383 (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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332A MSE 4.7 1.6 - - - -
336A LEU* 3.0 48.4 - - + +
361A ASP* 4.8 2.4 + - - +
362A GLU 2.9 20.9 + - - -
363A SER* 4.2 0.8 - - - +
381A LEU* 5.2 0.7 - - - -
382A LEU* 1.3 78.2 - - - +
384A ARG* 1.3 62.1 + - - +
388A THR* 4.1 15.7 + - + +
408A PHE* 4.1 3.1 - - - -
409A TYR* 2.9 42.2 + - + +
411A THR* 4.2 14.4 - - + -
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Residues in contact with ARG 384 (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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9A PRO* 6.2 0.2 - - - +
12A LEU* 4.4 20.2 - - + +
360A TYR 3.6 1.2 - - - +
361A ASP* 3.6 1.5 - - - -
362A GLU* 2.6 79.6 + - - +
364A ARG* 4.9 1.6 - - - +
383A THR* 1.3 79.6 + - - +
385A GLY* 1.3 60.8 + - - +
388A THR* 4.3 9.0 - - - -
390A ARG* 3.3 25.0 - - - +
406A ASP* 3.2 27.8 + - - +
407A GLY 3.6 17.3 - - - +
408A PHE* 3.1 40.6 - - + +
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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