Contacts of the strand formed by residues 333 - 340 (chain A) in PDB entry 3RCZ
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A HIS* 3.6 7.7 - - - +
332A LYS* 1.3 88.4 - - + +
334A ILE* 1.3 62.3 + - - +
349A SER* 3.8 33.4 - - - +
350A ILE 3.5 4.9 - - - +
351A PRO* 3.5 35.4 - - + -
352A VAL* 4.4 3.4 - - - +
397A ASP* 4.8 1.7 - - - +
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Residues in contact with ILE 334 (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 LEU* 1.3 76.3 - - - +
335A THR* 1.3 67.0 + - - +
336A LEU* 4.0 14.1 - - + -
348A LEU 3.6 0.7 - - - +
349A SER* 3.3 1.9 - - - -
350A ILE* 2.9 54.4 + - + +
352A VAL* 3.6 21.3 - - + -
390A VAL* 4.0 15.9 - - + -
395A LEU* 4.0 17.3 - - + +
396A GLU* 3.7 24.0 - - - +
397A ASP* 3.8 20.0 - - + +
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Residues in contact with THR 335 (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 LEU* 6.0 0.2 - - - +
334A ILE* 1.3 73.5 - - - +
336A LEU* 1.3 71.6 + - - +
347A ARG* 4.6 13.7 - - + +
348A LEU 3.3 13.0 - - - +
349A SER* 3.8 13.7 - - - -
397A ASP* 2.8 20.7 + - - -
398A GLU* 2.7 59.1 + - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 4.0 22.4 - - + +
335A THR* 1.3 86.1 - - - +
337A LEU* 1.3 61.3 + - - +
338A LEU* 3.7 14.4 - - + +
347A ARG* 3.3 7.6 - - - +
348A LEU* 2.9 32.7 + - + +
350A ILE* 4.3 16.8 - - + -
359A LEU* 3.7 32.1 - - + -
390A VAL* 4.9 1.3 - - + -
395A LEU* 4.3 25.1 - - + -
396A GLU 3.9 17.0 - - - +
398A GLU* 4.8 0.7 - - - +
399A ASP* 3.5 13.9 - - + +
401A VAL* 4.5 5.2 - - + -
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 1.3 72.1 - - - +
338A LEU* 1.3 61.7 + - - +
339A ARG* 3.8 20.6 + - + +
345A ASP* 3.7 32.5 - - + +
346A LEU 3.8 3.4 - - - +
347A ARG* 3.9 44.1 - - + +
398A GLU 4.8 1.5 + - - +
399A ASP 2.9 14.1 + - - +
400A GLN* 3.2 25.0 - - + +
401A VAL 2.7 32.9 + - - +
18B ARG 3.5 22.9 - - - +
19B ASP* 4.8 0.9 - - + -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.7 28.3 - - + +
337A LEU* 1.3 78.1 - - - +
339A ARG* 1.3 61.9 + - - +
340A SER 4.2 0.3 + - - -
344A GLU 4.5 1.4 - - - +
345A ASP* 4.0 2.3 - - - -
346A LEU* 2.8 40.7 + - + +
348A LEU* 4.5 10.5 - - + -
359A LEU* 4.0 30.1 - - + +
363A TYR* 3.6 46.7 + - + -
377A LEU* 4.6 8.1 - - + -
401A VAL* 3.3 12.6 - - + +
403A VAL* 3.8 15.9 - - + -
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Residues in contact with ARG 339 (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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337A LEU* 3.8 13.3 + - + +
338A LEU* 1.3 73.6 - - - +
340A SER* 1.3 67.6 + - - +
345A ASP* 2.8 41.0 + - - +
400A GLN* 3.2 29.1 + - + +
401A VAL 2.9 6.8 + - - +
402A SER* 3.4 4.9 - - - +
403A VAL* 2.8 23.9 + - - +
19B ASP* 2.7 32.1 + - - -
20B HIS 2.9 29.6 + - - -
21B PRO* 4.8 1.6 - - - +
22B PHE* 3.5 23.8 - - + +
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Residues in contact with SER 340 (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 LEU 4.2 0.6 + - - -
339A ARG* 1.3 80.8 - - - +
341A SER* 1.3 65.5 + - - +
342A LYS 4.2 0.9 - - - -
343A SER* 2.8 49.3 + - - +
344A GLU 4.6 0.7 + - - -
345A ASP* 5.0 0.2 + - - -
363A TYR* 3.5 17.4 + - - -
403A VAL* 4.0 13.2 - - - -
22B PHE* 3.6 15.9 - - - +
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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