Contacts of the helix formed by residues 346 - 360 (chain A) in PDB entry 2I91
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 ASP 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A THR* 4.8 6.1 - - + +
294A LEU* 4.5 3.5 - - + +
296A PRO* 3.8 28.2 - - - +
297A ALA 4.8 0.7 + - - -
301A VAL* 3.7 14.6 - - - +
331A TYR* 3.2 20.6 + - - +
344A ILE 3.2 5.9 + - - +
345A PRO* 1.3 70.7 - - - +
347A THR* 1.3 62.9 + - - +
348A SER* 2.8 39.0 + - - -
349A ILE* 3.3 17.0 + - + +
350A VAL* 3.2 24.2 + - - +
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Residues in contact with THR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO 3.5 5.9 + - - -
346A ASP* 1.3 70.8 + - - +
348A SER* 1.3 63.8 + - - +
349A ILE 3.3 0.2 - - - -
350A VAL* 3.9 10.8 - - + +
351A GLU* 3.3 22.6 + - + +
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 4.2 7.8 - - - +
305A CYS* 3.5 19.7 - - - -
346A ASP* 2.8 14.8 + - - -
347A THR* 1.3 78.5 - - - +
349A ILE* 1.3 56.0 + - - +
351A GLU* 3.3 15.4 + - - +
352A ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 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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285A LEU* 3.7 33.2 - - + -
294A LEU* 5.2 4.9 - - + -
301A VAL* 3.6 18.6 - - + -
304A VAL* 3.8 20.0 - - + -
305A CYS* 3.4 24.2 - - - -
308A LEU* 4.5 4.3 - - + -
331A TYR* 3.5 29.6 - - + +
346A ASP* 3.3 23.3 + - + +
348A SER* 1.3 73.6 - - - +
350A VAL* 1.3 59.3 + - - +
351A GLU 3.1 1.8 - - - -
352A ALA* 3.0 1.6 + - - -
353A LEU* 2.8 34.0 + - + +
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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
----------------------------------------------------------
328A LEU* 3.7 13.1 - - + +
331A TYR* 4.0 18.6 - - + -
332A LYS* 4.4 16.4 - - + -
345A PRO* 4.6 6.7 - - + -
346A ASP 3.2 20.1 + - - +
347A THR* 4.0 11.4 - - + +
348A SER 3.4 0.2 - - - -
349A ILE* 1.3 76.7 - - - +
351A GLU* 1.3 56.4 + - - +
353A LEU* 4.7 4.5 - - - -
354A ASP* 3.1 29.0 + - + +
429A LEU* 6.6 0.4 - - + -
431A HIS* 4.2 25.8 - - + +
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Residues in contact with GLU 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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305A CYS* 5.9 0.3 - - - +
347A THR* 3.3 18.6 + - + +
348A SER* 3.7 16.0 + - - +
349A ILE 3.1 0.6 - - - -
350A VAL* 1.3 79.1 - - - +
352A ALA* 1.3 61.5 + - - +
354A ASP* 3.9 12.1 - - - +
355A ASN* 3.2 32.2 + - - +
429A LEU* 5.4 7.4 - - + -
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Residues in contact with ALA 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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305A CYS* 3.8 33.4 - - + +
308A LEU* 4.6 8.1 - - + -
309A THR* 3.3 25.0 - - + +
348A SER 3.0 15.8 + - - +
349A ILE* 3.0 6.3 + - - +
351A GLU* 1.3 79.6 - - - +
353A LEU* 1.3 54.4 + - - +
355A ASN* 3.3 0.6 + - - -
356A ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 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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282A LEU* 3.3 32.3 - - + -
285A LEU* 3.7 26.0 - - + -
308A LEU* 3.8 13.9 - - + -
324A ILE* 3.4 17.1 - - + +
327A ALA* 4.2 6.3 - - + +
328A LEU* 3.7 41.1 - - + +
331A TYR* 4.3 9.9 - - + -
349A ILE* 2.8 23.5 + - + +
350A VAL* 4.2 1.3 - - - +
352A ALA* 1.3 73.3 - - - +
354A ASP* 1.3 58.1 + - - +
355A ASN 2.9 4.3 - - - -
356A ALA* 2.9 19.9 + - + +
357A PHE 2.9 12.8 + - - -
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Residues in contact with ASP 354 (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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328A LEU* 3.2 18.0 - - + +
350A VAL* 3.1 18.6 + - + +
351A GLU* 3.9 12.5 - - - +
353A LEU* 1.3 79.3 - - - +
355A ASN* 1.3 59.0 + - - +
357A PHE* 3.8 9.1 - - - +
358A TYR* 3.6 23.6 - - - -
405A ARG* 5.3 2.8 + - - -
428A MET 5.2 0.2 - - - +
429A LEU* 3.0 31.4 - - + +
430A LEU* 3.3 34.2 + - + +
431A HIS 5.4 0.7 - - - +
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Residues in contact with ASN 355 (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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309A THR* 4.1 10.0 - - + +
351A GLU* 3.2 27.3 + - - +
352A ALA* 3.3 5.8 + - - +
353A LEU 2.9 0.6 - - - -
354A ASP* 1.3 78.6 - - - +
356A ALA* 1.3 64.8 - - - +
357A PHE 3.1 2.3 + - - -
358A TYR* 3.3 18.0 + - - +
359A LYS* 3.7 29.7 + - - +
405A ARG* 6.0 1.4 - - - +
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Residues in contact with ALA 356 (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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308A LEU* 3.0 32.8 - - + +
309A THR* 4.4 2.9 - - - +
314A LEU* 4.0 9.7 - - + +
324A ILE* 4.5 15.0 - - + +
352A ALA 2.8 16.3 + - - +
353A LEU* 3.4 9.6 - - + +
355A ASN* 1.3 75.1 - - - +
357A PHE* 1.3 64.3 + - - +
359A LYS* 2.9 16.5 + - - +
360A SER* 3.1 15.3 + - - -
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Residues in contact with PHE 357 (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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321A PRO* 3.5 33.2 - - + -
324A ILE* 3.8 13.9 - - + +
325A LEU* 4.1 15.3 - - + -
328A LEU* 6.2 0.2 - - + -
353A LEU 2.9 10.1 + - - +
354A ASP* 3.8 7.2 - - - +
356A ALA* 1.3 76.9 - - - +
358A TYR* 1.3 77.6 + + - +
360A SER* 2.7 20.5 + - - -
361A PHE* 3.4 37.8 - + - -
398A ALA* 3.4 33.4 - - + -
402A LEU* 5.2 0.2 - - + -
430A LEU* 3.2 37.2 - - + -
522A PHE* 4.1 11.4 - + - -
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Residues in contact with TYR 358 (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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354A ASP* 3.6 17.7 - - - -
355A ASN* 3.3 13.3 + - - +
356A ALA 3.2 0.4 - - - -
357A PHE* 1.3 91.3 - + - +
359A LYS* 1.3 61.2 + - + +
360A SER 3.7 0.2 + - - -
361A PHE* 4.0 5.0 + - - -
363A LEU* 3.0 27.5 - - - +
401A MET* 3.1 36.1 - - + +
402A LEU* 3.8 44.9 - - + +
405A ARG* 3.6 37.9 + - + -
428A MET 4.9 0.3 + - - -
430A LEU* 3.3 30.1 - - + +
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Residues in contact with LYS 359 (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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309A THR* 3.3 42.9 + - - +
311A GLU* 3.0 50.7 - - + +
314A LEU* 3.9 9.9 - - + +
315A LYS* 5.4 1.9 - - - +
355A ASN* 3.8 31.0 - - - +
356A ALA 2.9 7.8 + - - +
358A TYR* 1.3 79.3 - - + +
360A SER* 1.3 63.5 + - - +
361A PHE 3.3 3.4 + - - +
363A LEU* 4.3 9.6 - - + -
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 4.5 11.9 - - - +
315A LYS* 5.7 8.1 - - - +
319A ILE* 3.3 29.5 - - - +
320A HIS 4.3 0.4 - - - -
321A PRO* 3.5 22.3 - - - +
324A ILE* 4.0 5.4 - - - +
356A ALA 3.1 10.7 + - - -
357A PHE* 2.7 20.8 + - - -
358A TYR 3.4 0.2 - - - -
359A LYS* 1.3 74.3 - - - +
361A PHE* 1.3 61.8 + - - +
362A LYS* 5.6 0.7 - - - +
524A SER* 4.1 11.3 - - - -
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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