Contacts of the strand formed by residues 346 - 353 (chain A) in PDB entry 3CS0
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 LYS 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.5 4.4 - - - -
343A ARG* 3.1 33.6 + - + +
344A ASP 2.7 11.5 + - - +
345A GLY* 1.3 74.8 - - - +
347A GLN* 1.3 77.9 + - + +
348A VAL* 3.5 6.7 - - + +
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Residues in contact with GLN 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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311A THR* 3.6 24.7 - - - +
340A GLY* 4.8 2.4 - - - -
341A LEU 3.5 14.2 + - - +
342A LEU* 4.3 12.8 - - + +
345A GLY 3.9 2.2 + - - -
346A LYS* 1.3 89.1 - - + +
348A VAL* 1.3 84.3 + - - +
349A ASN* 3.7 10.4 - - - +
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Residues in contact with VAL 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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340A GLY 3.6 0.2 - - - -
341A LEU* 2.7 58.0 + - + +
343A ARG* 3.6 42.2 - - + +
346A LYS* 3.5 16.2 - - + +
347A GLN* 1.3 83.4 + - - +
349A ASN* 1.3 80.6 + - - +
350A VAL* 5.2 2.7 - - + -
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Residues in contact with ASN 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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338A THR* 5.7 5.4 + - - -
339A LEU 3.6 5.6 - - - -
340A GLY* 4.4 5.6 - - - -
347A GLN* 3.7 10.0 - - - +
348A VAL* 1.3 90.3 - - - +
350A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 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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302A ALA* 3.0 45.8 - - + +
303A GLY* 5.2 1.1 - - - -
304A ILE* 4.3 22.4 - - + -
338A THR* 3.1 7.2 - - - -
339A LEU* 2.9 56.0 + - + +
341A LEU* 4.7 11.0 - - + -
348A VAL* 4.3 3.1 - - + -
349A ASN* 1.3 76.1 - - - +
351A ASN* 1.3 66.7 + - - +
352A LEU* 4.6 4.9 - - + -
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Residues in contact with ASN 351 (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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302A ALA* 3.7 15.2 - - - +
336A LYS* 4.3 15.2 + - + +
337A LEU 3.7 2.9 - - - +
338A THR* 2.7 35.5 - - - +
350A VAL* 1.3 76.8 - - - +
352A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 352 (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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265A LEU* 3.7 23.1 - - + -
298A SER* 2.9 46.2 - - - +
299A ALA* 3.5 1.6 - - - +
302A ALA* 3.2 19.3 - - + -
304A ILE* 4.0 11.2 - - + -
336A LYS* 3.6 8.9 - - - +
337A LEU* 3.0 46.3 + - + +
339A LEU* 3.6 31.6 - - + -
350A VAL* 4.1 4.5 + - + -
351A ASN* 1.3 74.2 - - - +
353A GLU* 1.3 61.8 + - - +
354A LEU* 4.1 0.9 - - - +
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Residues in contact with GLU 353 (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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298A SER* 3.6 7.8 - - - -
334A GLY* 4.0 23.6 - - - +
335A SER 3.5 4.5 - - - -
336A LYS* 5.4 5.0 - - + +
352A LEU* 1.3 79.3 - - - +
354A LEU* 1.3 76.6 + - - +
355A GLN* 3.1 24.4 + - + +
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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