Contacts of the helix formed by residues 339 - 351 (chain A) in PDB entry 3SA0
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 PRO 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLN* 4.7 1.8 - - - +
337A ASP 3.9 6.3 - - - +
338A LEU* 1.3 89.3 - - + +
340A LYS* 1.3 67.3 + - + +
341A GLU* 3.5 15.7 - - + +
342A LYS* 2.9 36.4 + - + +
343A LEU* 3.1 10.3 + - - +
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Residues in contact with LYS 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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59A PHE 5.9 2.9 - - - +
62A GLN* 3.9 19.7 + - + +
65A CYS* 5.7 2.5 - - - -
338A LEU 3.8 0.4 + - - -
339A PRO* 1.3 70.9 - - + +
341A GLU* 1.3 84.8 + - + +
343A LEU* 3.4 9.3 + - - +
344A LYS* 3.1 23.7 + - - +
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Residues in contact with GLU 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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339A PRO* 2.9 17.2 + - + +
340A LYS* 1.3 96.2 - - + +
342A LYS* 1.3 69.1 + - + +
344A LYS* 3.5 5.2 + - - +
345A GLU* 3.1 23.4 + - - +
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Residues in contact with LYS 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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338A LEU* 4.4 16.8 - - + -
339A PRO* 2.9 33.2 + - + +
341A GLU* 1.3 80.3 - - + +
343A LEU* 1.3 58.7 + - - +
345A GLU* 3.3 26.5 + - - +
346A LEU* 2.9 39.3 + - + +
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Residues in contact with LEU 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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62A GLN* 3.8 35.4 - - + +
65A CYS* 4.1 24.2 - - + +
66A GLN* 3.8 25.1 - - + +
69A LEU* 4.2 17.2 - - + +
335A LEU* 4.2 9.2 - - + +
338A LEU* 3.8 31.4 - - + +
339A PRO 3.1 10.0 + - - +
340A LYS* 3.8 9.0 - - - +
341A GLU 3.3 0.2 - - - -
342A LYS* 1.3 76.0 - - - +
344A LYS* 1.3 63.9 + - - +
346A LEU* 3.2 4.5 + - - +
347A ILE* 3.0 29.2 + - + +
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Residues in contact with LYS 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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59A PHE* 3.7 34.9 - - + +
65A CYS* 5.4 1.3 - - - -
95A ILE* 3.0 33.8 + - + +
96A GLU* 4.7 4.8 + - - +
98A MET* 3.0 47.9 + - + +
99A LYS* 6.0 0.4 - - - +
340A LYS 3.1 18.1 + - - +
341A GLU* 3.9 5.6 - - - +
343A LEU* 1.3 76.5 - - - +
345A GLU* 1.3 58.5 + - - +
347A ILE* 3.2 3.7 + - - +
348A PHE* 2.9 27.5 + - - +
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Residues in contact with GLU 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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95A ILE* 3.9 28.4 - - + +
341A GLU 3.1 17.5 + - - +
342A LYS* 3.6 33.7 + - - +
343A LEU 3.2 0.2 - - - -
344A LYS* 1.3 77.0 - - - +
346A LEU* 1.3 57.8 + - + +
348A PHE* 3.3 3.3 + - - +
349A GLU* 3.0 50.2 + - + +
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Residues in contact with LEU 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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69A LEU* 3.7 27.4 - - + -
73A LYS* 6.2 0.9 - - - +
335A LEU* 4.9 2.0 - - + -
338A LEU* 3.7 30.7 - - + -
342A LYS* 2.9 25.2 + - + +
343A LEU* 3.2 2.2 + - - +
345A GLU* 1.3 78.6 - - + +
347A ILE* 1.3 58.7 + - - +
349A GLU* 3.3 20.9 + - + +
350A GLU* 2.9 34.8 + - + +
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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
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58A PRO* 5.0 0.4 - - + -
59A PHE* 4.0 33.9 - - + -
65A CYS* 3.8 35.2 - - + +
68A THR* 4.3 12.3 - - + -
69A LEU* 3.9 25.6 - - + +
72A ILE* 4.6 9.2 - - + -
98A MET* 4.6 2.0 - - - -
101A VAL* 4.3 15.0 - - + -
343A LEU* 3.0 17.5 + - + +
344A LYS* 3.2 6.9 + - - +
346A LEU* 1.3 74.2 - - - +
348A PHE* 1.3 63.2 + - - +
350A GLU* 3.4 1.7 + - - -
351A THR* 2.7 36.9 + - + +
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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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91A ARG* 2.9 60.8 + - - -
92A ALA 4.0 0.7 - - - -
93A PRO 3.4 16.8 - - - -
94A THR* 3.4 22.9 - - - -
95A ILE* 3.4 35.2 - - + -
98A MET* 3.7 18.8 - - + +
344A LYS 2.9 12.7 + - - +
345A GLU 3.4 8.7 - - - +
347A ILE* 1.3 77.4 - - - +
349A GLU* 1.3 70.9 + - + +
351A THR* 3.0 10.3 + - - -
352A ALA* 3.4 2.8 + - + -
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Residues in contact with GLU 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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345A GLU* 3.0 41.7 + - + +
346A LEU* 3.8 21.3 - - + +
348A PHE* 1.3 85.0 - - + +
350A GLU* 1.3 65.7 + - + +
351A THR 3.3 0.7 + - - -
352A ALA* 3.4 19.2 + - - +
353A ARG 5.1 0.3 + - - -
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Residues in contact with GLU 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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69A LEU* 3.7 10.1 - - + -
72A ILE* 4.2 14.1 - - + -
73A LYS* 3.4 34.9 - - + +
76A LEU* 3.4 26.4 - - - +
77A ARG* 3.1 38.0 + - - -
346A LEU* 2.9 20.7 + - + +
347A ILE* 4.0 3.8 - - - +
348A PHE 3.3 0.2 - - - -
349A GLU* 1.3 79.6 - - + +
351A THR* 1.3 60.0 + - - +
352A ALA 3.4 0.4 + - - -
353A ARG* 4.6 10.6 + - - +
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Residues in contact with THR 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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72A ILE* 4.2 20.0 - - + -
89A ILE* 3.6 44.9 - - + +
91A ARG* 2.9 34.3 + - - +
101A VAL* 4.7 3.8 - - + -
347A ILE* 2.7 27.4 + - + +
348A PHE* 3.0 1.9 + - - -
349A GLU 3.2 0.2 - - - -
350A GLU* 1.3 78.1 - - - +
352A ALA* 1.3 61.4 + - - +
353A ARG 3.2 4.4 + - - -
354A PHE* 3.4 19.4 + - - +
355A GLN* 4.4 3.6 + - - +
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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