Contacts of the strand formed by residues 374 - 380 (chain A) in PDB entry 5MLG
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 ARG 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.3 56.9 + - + +
233A VAL 3.4 19.1 - - - +
234A SER* 4.2 5.8 - - - +
235A ILE* 3.9 4.8 - - - +
241A TRP* 3.7 2.0 - - - -
367A GLU* 5.1 0.6 + - - -
369A ASP* 3.0 57.6 + - + +
372A ASN* 3.5 29.6 - - + +
373A ASN* 1.3 77.1 - - - +
375A ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 375 (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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231A HIS 4.0 0.9 - - - +
232A TYR* 3.4 3.9 - - - -
233A VAL* 2.9 36.3 + - - +
235A ILE* 4.7 2.2 - - + -
241A TRP* 3.7 55.4 - - + +
242A GLN 4.5 0.2 - - - +
243A ILE* 3.9 19.5 - - + -
265A VAL* 3.9 13.0 - - + -
366A THR* 3.6 29.2 - - + -
367A GLU 3.4 4.7 - - - +
368A PHE* 4.4 4.3 - - + -
374A ARG* 1.3 79.2 - - - +
376A GLY* 1.3 62.1 + - - +
377A PHE* 3.6 20.8 - - + -
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Residues in contact with GLY 376 (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 PHE* 3.6 9.0 - - - -
231A HIS 3.4 5.2 - - - -
232A TYR* 3.4 27.4 - - - -
366A THR* 3.3 7.1 - - - +
367A GLU 2.8 35.9 + - - +
375A ILE* 1.3 73.9 - - - +
377A PHE* 1.3 64.8 + - - -
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Residues in contact with PHE 377 (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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229A ASN 3.9 1.6 - - - +
230A PHE* 3.4 3.5 - - - -
231A HIS* 3.0 30.2 + - - +
233A VAL* 4.2 16.4 - - + -
243A ILE* 3.9 20.9 - - + -
265A VAL* 3.9 19.5 - - + -
313A LEU* 4.1 10.5 - - + -
318A TYR* 3.8 43.9 + + + +
360A PHE* 3.7 26.0 - + - -
364A PHE* 4.5 5.4 - - + -
365A TYR 3.6 2.5 - - - -
366A THR* 3.4 36.1 - - + -
375A ILE* 3.6 17.9 - - + -
376A GLY* 1.3 76.3 - - - -
378A ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 378 (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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226A TYR* 4.0 22.2 - - + -
227A GLN 4.8 1.3 - - - +
229A ASN 3.9 15.7 - - - +
230A PHE* 3.8 27.4 - - + -
318A TYR* 5.8 1.3 - - - -
364A PHE* 3.2 9.1 - - - +
365A TYR* 2.7 38.2 + - - +
377A PHE* 1.3 76.4 - - - +
379A LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 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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226A TYR* 3.4 2.1 - - - -
227A GLN* 3.0 67.9 + - + +
229A ASN 5.3 0.2 + - - -
363A LYS* 4.0 25.1 - - - +
364A PHE* 3.8 27.4 - - + -
378A ALA* 1.3 69.1 - - - +
380A ALA* 1.3 70.4 + - - +
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Residues in contact with ALA 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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204A TYR* 4.3 13.5 - - + -
225A HIS 3.5 12.6 - - - +
361A ILE 4.8 0.4 - - - +
362A ARG 3.5 17.7 - - - +
363A LYS 2.9 23.1 + - - +
365A TYR* 3.7 16.6 - - + +
378A ALA 3.1 3.5 + - - -
379A LEU* 1.3 84.2 - - - +
381A ARG* 1.3 62.1 + - - +
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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