Contacts of the strand formed by residues 345 - 349 (chain A) in PDB entry 1V2E
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 LEU 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.4 4.7 - - + -
138A PHE* 4.1 9.9 - - + -
302A TYR* 4.2 12.1 - - + -
311A MET* 3.5 35.0 - - + -
312A ALA 3.6 10.5 - - - +
313A GLU* 3.6 28.3 - - + +
332A PRO* 3.8 0.5 - - - +
333A ALA* 2.7 48.2 + - + +
337A TYR* 3.8 24.7 - - + +
342A PRO* 3.1 24.5 + - + +
344A ASP* 1.3 75.9 - - - +
346A PHE* 1.3 55.3 - - - +
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Residues in contact with PHE 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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311A MET* 3.5 9.9 - - - +
312A ALA 2.9 33.4 + - - +
314A LEU* 3.8 35.0 - - + -
317A TRP* 3.2 32.8 - - + -
318A ASP* 3.7 2.0 - - - -
319A ALA* 3.3 28.7 - - + -
322A LEU* 4.3 5.2 - - + -
330A LEU* 4.0 33.2 - - + -
331A ILE 3.6 2.9 - - - +
332A PRO* 4.1 19.5 - - + -
344A ASP* 3.6 24.9 - - - -
345A LEU* 1.3 73.5 - - - +
347A ARG* 1.3 61.3 + - - +
348A PHE* 4.0 6.8 - - + -
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Residues in contact with ARG 347 (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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15A PHE* 3.2 21.3 - - - -
30A LEU 3.8 6.6 - - - +
31A GLY 3.1 20.6 + - - -
163A ASN* 2.7 24.4 + - - -
164A PRO* 3.2 27.6 - - + -
309A PHE* 3.3 24.5 - - + -
310A LEU 3.5 9.4 - - - +
311A MET* 4.3 7.6 - - + -
330A LEU* 3.8 5.4 - - - +
331A ILE* 2.8 39.4 + - + +
336A PHE* 3.6 21.7 - - + -
346A PHE* 1.3 74.5 - - - +
348A PHE* 1.3 68.1 + - - +
520A KMT 2.7 42.4 + - - -
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Residues in contact with PHE 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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30A LEU* 3.6 18.4 - - + -
290A LEU* 3.7 21.8 - - + -
294A LEU* 3.9 16.2 - - + -
309A PHE* 3.3 8.1 - - - +
310A LEU* 2.8 55.7 + - + +
312A ALA* 3.6 18.8 - - + -
314A LEU* 3.8 24.2 - - + -
330A LEU* 3.7 31.6 - - + -
346A PHE* 4.0 11.9 - - + -
347A ARG* 1.3 79.9 - - - +
349A ALA* 1.3 60.9 + - - +
350A PHE 4.2 0.2 + - - -
364A LEU* 3.8 26.5 - - + -
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Residues in contact with ALA 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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30A LEU* 2.9 49.3 + - - +
31A GLY 3.7 16.6 - - - +
32A GLN 4.7 1.6 - - - +
33A GLY* 4.6 2.5 - - - -
290A LEU* 4.9 0.2 - - - +
308A TYR 3.6 5.4 - - - -
309A PHE* 4.2 13.7 - - + -
348A PHE* 1.3 74.4 - - - +
350A PHE* 1.3 61.9 + - - +
351A CYS* 3.5 15.7 + - - -
352A LYS* 4.1 4.5 - - - +
357A LEU* 4.1 1.4 - - - +
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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