Contacts of the strand formed by residues 345 - 350 (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 GLY 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASN 3.2 12.3 - - - -
336A ALA* 4.2 0.2 - - - -
343A SER 3.5 1.8 - - - -
344A GLN* 1.3 72.3 - - - +
346A THR* 1.3 58.0 + - - -
362A VAL* 3.3 5.2 - - - +
363A PHE* 2.8 46.1 + - - -
364A GLN 2.8 16.5 + - - -
368A MET* 3.9 14.1 - - - +
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Residues in contact with THR 346 (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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333A PHE 3.6 1.0 - - - +
334A SER* 3.4 4.3 - - - -
335A ASN* 2.9 29.9 + - - +
337A ALA* 3.4 22.0 - - + -
344A GLN* 2.9 23.3 - - + +
345A GLY* 1.3 74.4 - - - +
347A ILE* 1.3 70.4 + - - +
348A ARG* 3.1 24.0 + - - +
360A SER* 4.2 4.9 - - - -
361A LYS 3.3 14.1 - - - -
362A VAL* 3.9 16.6 - - + -
363A PHE* 3.5 3.3 - - - -
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 4.5 9.4 - - + -
333A PHE 3.2 8.3 - - - +
334A SER* 4.4 10.5 - - - -
346A THR* 1.3 77.2 - - - +
348A ARG* 1.3 69.6 + - - +
360A SER* 3.2 3.3 - - - -
361A LYS 2.9 33.2 + - - +
363A PHE* 3.8 25.8 - - + -
373A LEU* 5.0 2.9 - - + -
383A LEU* 4.3 5.6 - - + -
396A PHE* 3.6 42.8 - - + -
400A TRP* 3.9 20.2 - - + -
401A LEU* 3.8 24.5 - - + +
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Residues in contact with ARG 348 (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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304A ASP 3.8 10.8 + - - -
305A LEU* 3.8 23.1 - - - -
306A PRO* 3.6 31.3 + - - +
332A LEU* 3.3 4.7 - - - -
333A PHE* 2.8 40.8 + - + +
335A ASN* 3.5 22.6 + - - -
337A ALA* 3.7 16.0 - - - +
346A THR* 3.1 23.2 + - - +
347A ILE* 1.3 80.2 - - - +
349A MET* 1.3 60.5 + - - +
357A TRP* 3.8 25.0 - - + -
359A VAL 3.2 7.4 - - - +
360A SER* 3.7 18.8 + - - -
401A LEU* 5.3 0.4 - - - -
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Residues in contact with MET 349 (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 VAL* 3.9 18.8 - - + -
331A LEU 3.3 11.4 - - - +
332A LEU* 3.9 9.0 - - + -
348A ARG* 1.3 75.8 - - - +
350A SER* 1.3 70.7 + - - +
351A CYS* 4.4 14.4 - - - -
357A TRP* 3.4 21.6 - - - -
358A PRO* 3.4 10.1 - - - +
359A VAL* 2.9 42.2 + - + +
398A LEU* 4.0 25.6 - - + -
401A LEU* 4.1 12.8 - - + -
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Residues in contact with SER 350 (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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329A LYS 4.1 0.2 - - - -
330A VAL* 3.2 8.1 - - - +
331A LEU* 2.9 32.2 + - - +
349A MET* 1.3 74.5 - - - +
351A CYS* 1.3 61.6 + - - +
352A ASP* 2.8 24.3 + - - -
354A GLY* 2.9 23.6 + - - -
356A THR 2.8 16.5 + - - -
357A TRP* 3.5 22.8 - - - -
358A PRO* 4.3 0.9 - - - -
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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