Contacts of the strand formed by residues 371 - 375 (chain A) in PDB entry 1EUR
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 SER 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 4.5 1.3 - - - -
262A LYS* 4.8 1.6 + - - -
311A ASN* 4.7 5.4 + - - -
312A ALA* 3.9 10.6 + - - +
313A SER* 3.5 11.6 - - - -
334A SER* 2.9 31.3 + - - -
335A ASN* 4.1 5.4 + - - -
363A PHE* 4.5 1.5 - - - -
368A MET* 4.0 11.0 - - - -
369A SER 3.8 0.9 + - - -
370A TYR* 1.3 78.3 - - - +
372A THR* 1.3 63.9 + - - +
383A LEU* 3.7 12.8 - - - -
384A LEU 3.2 7.4 - - - -
385A TYR* 3.7 15.5 - - - -
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Residues in contact with THR 372 (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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70A PRO* 3.3 25.8 + - - +
71A ALA* 4.0 1.6 + - - -
72A LEU* 4.4 14.8 - - - +
207A GLY* 3.4 35.4 - - - -
208A GLU* 3.9 7.4 - - + +
262A LYS* 4.7 3.1 - - - +
313A SER* 3.6 11.0 - - - +
371A SER* 1.3 76.8 - - - +
373A LEU* 1.3 70.2 + - - +
382A GLY 3.8 0.2 - - - +
383A LEU* 3.3 5.6 - - - +
384A LEU* 2.9 35.6 + - - +
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Residues in contact with LEU 373 (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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208A GLU* 3.7 9.7 - - - +
313A SER* 3.0 15.9 + - - +
315A ILE* 3.5 28.1 - - + +
332A LEU* 4.1 29.4 - - + +
333A PHE 4.1 2.7 - - - +
334A SER* 3.7 37.9 - - - +
347A ILE* 5.0 4.0 - - + -
372A THR* 1.3 78.8 - - - +
374A THR* 1.3 66.7 + - - +
381A TYR* 4.9 3.4 - - + -
382A GLY 3.3 9.4 - - - +
383A LEU* 3.8 14.6 - - + -
396A PHE* 3.7 34.5 - - + -
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Residues in contact with THR 374 (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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72A LEU* 3.0 36.8 + - - +
73A THR* 4.0 11.9 - - - -
74A VAL* 4.4 11.9 - - + +
138A ARG* 5.3 3.6 - - - +
208A GLU* 2.9 31.6 - - - +
315A ILE* 3.9 9.0 - - - -
373A LEU* 1.3 74.6 + - - +
375A ALA* 1.3 70.3 + - - +
376A LEU* 4.1 2.4 - - - +
381A TYR* 3.5 4.7 - - - +
382A GLY 2.9 30.4 + - - -
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Residues in contact with ALA 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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74A VAL* 3.8 14.6 - - - +
138A ARG* 5.9 0.3 + - - -
315A ILE* 3.9 4.5 - - + +
316A ARG 4.5 5.6 - - - +
317A ALA 4.5 0.7 - - - +
319A PRO* 4.2 29.6 - - + -
374A THR* 1.3 76.4 - - - +
376A LEU* 1.3 64.0 + - - +
377A PRO* 4.6 0.2 - - - +
380A THR 4.9 0.2 - - - +
381A TYR* 3.8 25.1 - - + -
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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