Contacts of the strand formed by residues 340 - 345 (chain A) in PDB entry 3SRG
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU 5.6 1.1 - - - +
92A GLU 6.0 0.7 - - - -
93A LYS 5.2 7.2 - - - -
335A ALA 3.8 0.2 - - - +
336A VAL* 3.0 8.5 - - - +
337A TYR* 2.8 41.7 + - + +
338A LYS 4.0 6.3 - - - +
339A GLY* 1.3 83.8 - - - +
341A LEU* 1.3 61.2 + - - +
352A TYR* 3.5 45.5 - - + +
353A CYS 3.2 9.6 - - - +
354A ASP* 3.2 28.0 - - - +
355A LEU* 4.0 1.8 - - - -
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Residues in contact with LEU 341 (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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39A LEU* 3.6 27.8 - - + -
281A TRP* 4.0 13.0 - - + -
304A VAL* 4.4 3.6 - - + -
320A VAL* 4.4 7.0 - - + -
321A TYR* 4.5 3.8 - - + -
334A ALA* 4.0 22.9 - - + -
335A ALA 3.5 9.2 - - - +
336A VAL* 3.6 20.0 - - + -
340A LYS* 1.3 74.6 - - - +
342A LEU* 1.3 58.8 + - - +
343A ILE* 3.8 25.8 - - + -
351A LEU 3.6 1.7 - - - +
352A TYR* 3.3 6.5 - - - -
353A CYS* 2.8 38.8 + - + +
355A LEU* 3.9 17.0 - - + -
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Residues in contact with LEU 342 (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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45A VAL* 4.1 20.2 - - + -
55A LEU* 3.7 32.5 - - + +
57A ILE* 5.0 1.6 - - + -
63A ALA* 4.1 25.4 - - + -
65A ILE* 4.3 6.5 - - + -
88A MET* 4.2 18.4 - - - -
90A LEU* 4.3 13.7 - - + -
334A ALA* 3.2 4.5 - - - +
335A ALA 2.9 35.2 + - - +
340A LYS 4.2 0.4 - - - -
341A LEU* 1.3 74.1 - - - +
343A ILE* 1.3 60.0 + - - +
350A ALA* 4.8 7.2 - - + -
351A LEU 3.4 13.5 - - - +
352A TYR* 3.9 20.4 - - + -
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Residues in contact with ILE 343 (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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55A LEU* 4.3 2.9 - - - -
302A SER* 5.5 0.2 - - - -
304A VAL* 3.8 20.0 - - + -
321A TYR* 3.6 34.5 - - + -
328A LEU* 3.7 20.3 - - + +
331A SER* 3.7 20.4 - - - -
333A VAL 3.3 15.3 - - - +
334A ALA* 4.6 0.2 - - + -
341A LEU* 3.8 27.6 - - + +
342A LEU* 1.3 79.3 - - - +
344A GLY* 1.4 59.0 + - - +
350A ALA* 3.2 7.5 - - - +
351A LEU* 2.9 47.8 + - + +
353A CYS* 4.4 3.8 - - - -
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Residues in contact with GLY 344 (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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52A SER* 3.0 29.4 - - - -
55A LEU* 3.9 4.3 - - - +
331A SER* 3.2 8.8 - - - -
332A THR* 2.9 24.7 + - - -
333A VAL* 2.9 17.8 + - - +
343A ILE* 1.4 73.3 - - - +
345A THR* 1.3 63.5 + - - +
350A ALA* 4.6 0.2 - - - -
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Residues in contact with THR 345 (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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51A GLY* 4.0 0.2 - - - -
52A SER* 2.7 31.6 + - - -
53A GLU 3.1 6.1 + - - -
328A LEU* 3.4 29.2 - - + -
329A GLN 3.2 26.9 - - - +
330A GLY 3.1 11.4 - - - +
332A THR* 3.5 7.2 - - - -
344A GLY* 1.3 79.1 - - - +
346A VAL* 1.3 61.2 + - - +
348A HIS 3.0 21.2 + - - -
349A LYS 2.7 26.8 + - - +
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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