Contacts of the strand formed by residues 314 - 322 (chain A) in PDB entry 5MJ6
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU 3.3 4.5 + - - +
176A ARG* 3.3 16.2 - - - +
177A TYR* 2.9 27.2 + - - -
313A ALA* 1.3 77.4 - - - +
315A PHE* 1.3 67.3 + - - +
350A GLU* 2.7 30.1 + - + +
351A SER* 3.3 25.4 - - - +
352A VAL* 4.6 0.2 - - - -
353A LYS* 3.9 18.6 - - + +
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Residues in contact with PHE 315 (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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177A TYR* 3.4 44.2 - + + -
179A LEU* 6.0 0.9 - - + -
303A PHE* 4.2 11.7 - + - -
311A PHE 5.9 0.4 - - - -
313A ALA* 3.5 22.7 - - + -
314A THR* 1.3 76.7 - - - +
316A ILE* 1.3 63.2 + - - +
317A ILE* 4.0 21.7 + - + +
331A MET* 5.2 0.2 - - - +
349A SER 3.7 2.9 - - - +
350A GLU* 3.5 2.2 - - - -
351A SER* 2.9 41.8 + - - +
354A MET* 3.7 20.9 - - + -
355A SER 4.5 0.4 - - - -
356A THR* 3.6 29.8 - - + -
359A VAL* 3.6 32.3 - - + -
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Residues in contact with ILE 316 (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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176A ARG* 4.3 8.1 - - - +
177A TYR 2.7 13.8 + - - +
178A GLU* 4.2 29.4 - - + +
179A LEU 2.8 28.8 + - - +
315A PHE* 1.3 72.7 - - - +
317A ILE* 1.3 64.2 + - - +
318A LYS* 4.8 9.4 - - + +
347A GLU* 4.3 20.6 - - + +
348A PHE 4.2 12.8 - - - +
350A GLU* 3.7 44.2 - - + +
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Residues in contact with ILE 317 (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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179A LEU* 3.5 29.2 - - + +
315A PHE* 4.1 24.4 + - + +
316A ILE* 1.3 79.9 - - - +
318A LYS* 1.3 67.1 + - - +
319A ILE* 4.0 28.0 - - + -
329A SER* 3.7 25.4 - - - +
330A ASN* 5.3 1.8 - - - +
347A GLU* 4.4 0.2 - - - +
348A PHE* 3.0 43.9 + - + +
349A SER 5.2 0.4 + - - -
359A VAL* 4.3 17.3 - - + -
361A PHE* 4.4 11.0 - - + -
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Residues in contact with LYS 318 (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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178A GLU* 6.5 0.4 - - - -
179A LEU 2.8 10.9 + - - +
180A SER* 3.2 23.7 - - - -
181A LEU 2.7 32.6 + - - -
316A ILE* 4.8 10.8 - - + +
317A ILE* 1.3 78.5 - - - +
319A ILE* 1.3 61.9 + - - +
345A GLN* 3.6 22.9 - - + +
346A ASP 3.2 9.2 - - - +
347A GLU* 3.8 33.6 + - + -
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Residues in contact with ILE 319 (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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181A LEU* 3.6 33.9 - - + -
183A PRO* 4.1 10.1 - - + -
317A ILE* 4.0 12.3 - - + -
318A LYS* 1.3 77.0 - - - +
320A ILE* 1.3 74.7 + - - +
321A ARG* 3.9 5.2 + - + +
327A ALA* 4.5 13.2 - - + -
328A LEU 5.6 0.2 - - - +
344A VAL 3.7 0.9 - - - +
345A GLN* 3.6 4.2 - - - -
346A ASP* 2.8 38.2 + - + +
348A PHE* 4.1 19.1 - - + -
361A PHE* 4.0 20.9 - - + -
362A ILE 6.0 0.2 - - - +
363A VAL* 4.0 24.5 - - + -
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Residues in contact with ILE 320 (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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181A LEU 2.9 14.5 + - - +
182A HIS* 3.6 47.0 - - + +
183A PRO* 3.3 23.6 - - - +
319A ILE* 1.3 73.6 - - - +
321A ARG* 1.3 63.3 + - - +
339A LEU* 4.0 20.4 - - + -
343A LEU* 4.1 20.0 - - + -
344A VAL 3.3 7.2 - - - +
345A GLN* 3.7 28.5 - - + +
363A VAL* 5.7 0.2 - - - +
1141A BR 4.6 13.7 - - + -
1C NAG 4.3 1.2 - - + +
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Residues in contact with ARG 321 (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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319A ILE* 4.6 7.0 - - + +
320A ILE* 1.3 75.6 - - - +
322A ASP* 1.3 69.0 + - - +
323A GLU* 4.3 7.5 + - - +
325A TYR 2.7 29.7 + - - -
326A THR* 4.3 0.9 - - - -
327A ALA* 3.9 16.9 - - + +
333A LYS* 4.9 4.8 - - - +
336A SER* 4.3 3.2 + - - -
343A LEU* 3.6 2.5 - - - -
344A VAL* 2.8 62.7 + - + +
346A ASP* 2.4 56.1 + - - +
363A VAL* 4.2 20.0 - - + -
1C NAG 4.2 8.3 - - - -
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Residues in contact with ASP 322 (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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185A LEU* 5.9 1.0 + - - +
321A ARG* 1.3 80.4 + - - +
323A GLU* 1.3 61.0 + - - +
324A GLN* 3.2 9.6 - - + -
325A TYR* 2.9 54.9 + - + +
342A GLY 3.7 3.8 - - - +
343A LEU* 3.5 9.2 - - - +
1C NAG 2.8 52.6 + - - +
2C NAG 3.1 22.6 + - - -
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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