Contacts of the helix formed by residues 339 - 352 (chain A) in PDB entry 3SPZ
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 GLN 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASP* 2.8 31.2 + - - +
336A ALA* 3.8 11.2 - - - +
337A LYS 3.8 8.9 - - - +
338A ARG* 1.3 77.2 - - - +
340A PHE* 1.3 58.7 + - - +
341A ILE 3.4 2.5 - - - -
342A ASN* 3.6 25.9 + - + +
343A LEU* 3.2 25.5 + - - +
551A ALA* 3.6 32.9 + - + +
554A THR* 4.0 4.9 - - + +
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Residues in contact with PHE 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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273A TYR* 3.3 31.2 - + + +
276A LEU* 4.1 18.4 - - + -
277A TYR* 4.0 24.0 - + - -
280A PHE* 3.5 38.2 - + + -
281A SER* 3.7 23.8 - - - -
335A ASP* 3.0 4.0 + - - -
338A ARG* 3.5 34.3 - - + -
339A GLN* 1.3 74.6 - - - +
341A ILE* 1.3 60.2 + - - +
343A LEU* 3.7 4.7 - - + +
344A SER* 2.8 34.8 + - - -
554A THR* 3.6 31.0 - - + -
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 4.6 23.6 - - + -
212A ILE* 4.5 15.7 - - + -
214A THR* 4.2 27.4 - - + -
271A LEU* 4.6 5.2 - - + -
273A TYR* 4.1 4.7 - - + -
276A LEU* 3.8 22.4 - - + -
335A ASP* 3.1 29.0 + - + +
340A PHE* 1.3 76.2 - - - +
342A ASN* 1.3 58.3 + - - +
344A SER* 3.7 5.0 - - - -
345A LEU* 3.0 45.9 + - + +
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Residues in contact with ASN 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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103A TYR* 3.7 11.1 + - - -
335A ASP* 4.9 1.0 + - - -
339A GLN* 3.6 32.4 + - + +
340A PHE 3.3 0.4 - - - -
341A ILE* 1.3 79.5 - - - +
343A LEU* 1.3 60.1 + - - +
345A LEU* 3.3 10.5 + - - +
346A ASP* 2.8 41.7 + - - +
555A ALA* 6.2 1.4 - - - +
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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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280A PHE* 3.6 38.4 - - + -
339A GLN 3.2 15.1 + - - +
340A PHE* 3.7 3.1 - - + +
342A ASN* 1.3 78.2 - - - +
344A SER* 1.3 67.2 + - - +
346A ASP* 3.0 8.9 + - - +
347A MET* 2.9 47.6 + - + +
554A THR* 3.9 16.4 - - + +
555A ALA* 4.8 2.0 - - - +
558A ASN* 3.6 30.1 - - + +
559A ARG* 4.0 26.7 - - + +
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Residues in contact with SER 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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271A LEU* 4.1 20.8 - - - +
276A LEU* 3.3 25.1 - - - +
280A PHE* 3.6 7.6 - - - -
340A PHE 2.8 26.6 + - - -
341A ILE* 3.7 4.9 - - - -
343A LEU* 1.3 73.9 - - - +
345A LEU* 1.3 58.9 + - - +
347A MET* 4.8 0.9 - - - -
348A GLY* 2.9 26.5 + - - -
355A ILE* 4.2 5.6 - - - +
358A VAL* 3.4 25.1 - - - +
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Residues in contact with LEU 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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103A TYR* 3.6 20.9 - - + +
105A HIS* 4.6 11.4 - - + -
108A ILE* 3.9 25.6 - - + -
110A VAL* 5.3 4.5 - - + -
212A ILE* 4.1 27.8 - - + -
341A ILE* 3.0 37.1 + - + +
342A ASN* 3.6 6.5 - - - +
343A LEU 3.2 0.4 - - - -
344A SER* 1.3 75.4 - - - +
346A ASP* 1.3 66.0 + - - +
348A GLY* 3.3 0.5 + - - -
349A TYR* 3.1 50.2 + - + +
355A ILE* 4.4 10.3 - - + -
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.6 36.3 + - - -
342A ASN* 2.8 33.2 + - - +
343A LEU* 3.4 9.1 - - - +
345A LEU* 1.3 72.0 - - - +
347A MET* 1.3 58.9 + - + +
349A TYR* 4.2 1.2 - - - +
350A TYR* 3.1 29.2 + - - +
485A HIS* 6.0 0.5 - - - -
559A ARG* 3.2 30.9 + - - +
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Residues in contact with MET 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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279A LYS* 5.3 2.5 - - - -
280A PHE* 4.8 12.8 - - + -
343A LEU* 2.9 43.5 + - + +
344A SER 3.9 2.7 - - - +
346A ASP* 1.3 76.0 - - + +
348A GLY* 1.3 66.4 + - - +
350A TYR* 3.4 7.5 + - + +
351A ALA* 3.0 26.9 + - - +
353A ILE* 5.2 0.7 - - - -
358A VAL* 4.0 33.7 - - + +
364A THR* 4.9 7.4 - - + +
558A ASN 4.5 13.2 - - - +
559A ARG* 5.4 9.4 - - + +
562A LEU* 4.2 39.5 - - + -
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Residues in contact with GLY 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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5A TYR* 3.1 5.6 + - - -
344A SER 2.9 17.7 + - - -
345A LEU 3.3 0.2 + - - -
347A MET* 1.3 78.0 - - - +
349A TYR* 1.3 55.4 + - - +
352A LYS 3.0 20.4 + - - -
353A ILE* 3.1 28.2 + - - +
355A ILE* 3.7 17.9 - - - -
358A VAL* 3.8 6.0 - - - +
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Residues in contact with TYR 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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4A PHE* 3.8 14.2 - + + -
5A TYR* 2.7 59.2 + + - -
6A LEU* 4.1 9.0 + - - +
101A ILE* 3.5 41.3 + - + +
103A TYR* 3.5 31.9 - + + -
108A ILE* 3.5 16.6 - - + +
211A VAL* 5.8 0.3 - - - +
345A LEU* 3.1 47.4 + - + +
346A ASP 4.3 1.3 - - - +
348A GLY* 1.3 72.8 - - - +
350A TYR* 1.3 67.1 + - - +
351A ALA 3.2 0.4 - - - -
352A LYS* 3.3 18.2 + - - +
355A ILE* 4.2 8.9 - - + +
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Residues in contact with TYR 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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100A GLU* 6.0 7.4 - - + -
346A ASP 3.1 20.7 + - - +
347A MET* 3.6 10.3 - - + +
349A TYR* 1.3 78.0 - - - +
351A ALA* 1.3 60.6 + - - +
352A LYS* 4.6 6.1 - - - +
368A ILE* 4.2 28.3 - - + +
474A GLU* 4.3 4.8 + - - -
477A LYS* 3.3 37.6 - - + +
478A VAL* 3.8 25.7 + - + +
481A GLN* 3.5 29.8 - - - -
562A LEU* 5.7 3.8 - - + -
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Residues in contact with ALA 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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347A MET 3.0 16.6 + - - +
350A TYR* 1.3 76.3 - - + +
352A LYS* 1.3 68.5 + - - +
353A ILE* 4.0 18.6 - - + -
364A THR* 3.9 20.6 - - + +
367A ALA* 3.3 17.8 - - - +
368A ILE* 3.8 27.0 - - + +
371A ASN* 3.5 8.2 + - - -
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Residues in contact with LYS 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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5A TYR* 3.4 14.1 - - + -
90A LEU* 3.7 12.7 - - - +
93A LEU* 3.7 32.6 - - + +
94A SER* 4.7 1.3 + - - +
97A TYR 2.8 22.3 + - - +
98A ASN* 4.3 3.2 + - - +
99A TYR 2.8 37.9 + - - +
100A GLU* 4.8 2.0 - - - +
101A ILE* 3.8 21.5 - - + +
348A GLY 3.0 4.0 + - - -
349A TYR 3.3 12.9 + - - +
350A TYR 4.6 3.8 - - - +
351A ALA* 1.3 82.8 - - - +
353A ILE* 1.3 57.7 + - - +
367A ALA* 4.4 1.9 - - - +
371A ASN* 3.8 31.3 + - - +
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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