Contacts of the helix formed by residues 349 - 363 (chain A) in PDB entry 2XSX
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 SER 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.8 23.9 + - - +
95A ILE* 4.2 4.9 - - - +
103A LYS* 4.6 3.4 - - - -
111A ILE* 4.9 4.3 - - - -
112A LEU* 3.9 9.5 - - - +
115A SER* 3.8 5.4 - - - -
347A ILE* 3.7 1.9 - - - +
348A GLY* 1.3 79.6 - - - +
350A VAL* 1.3 61.4 + - - +
351A THR* 3.8 0.7 + - - -
352A GLU* 2.7 42.8 + - - +
353A SER* 2.9 25.6 + - - -
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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
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87A GLN* 3.7 17.9 - - + +
112A LEU* 4.3 0.9 - - + +
115A SER* 2.9 35.6 + - - +
116A LEU* 3.9 26.2 - - + -
119A CYS* 4.2 16.8 - - + -
134A ILE* 5.6 0.7 - - + -
137A LEU* 4.8 0.2 - - + -
344A VAL* 6.0 2.2 - - + -
349A SER* 1.3 71.5 - - - +
351A THR* 1.3 64.2 + - - +
353A SER* 3.1 8.5 + - - -
354A ILE* 3.0 42.1 + - + +
380A PHE* 3.9 17.0 - - + -
384A LEU* 5.4 4.3 - - + -
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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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87A GLN* 3.4 22.6 + - - +
88A GLU* 3.5 31.1 + - + +
91A ASP* 2.6 34.7 + - + -
349A SER* 3.4 1.1 - - - -
350A VAL* 1.3 78.6 - - - +
352A GLU* 1.3 59.2 + - + +
354A ILE* 3.3 8.8 + - - +
355A GLN* 2.9 52.2 + - + +
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Residues in contact with GLU 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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95A ILE* 3.4 21.0 - - + +
103A LYS* 2.7 34.7 + - - -
347A ILE* 3.6 33.3 - - + +
349A SER* 2.7 25.0 + - - +
351A THR* 1.3 78.6 - - + +
353A SER* 1.3 56.9 + - - +
355A GLN* 3.8 17.6 - - - +
356A ALA* 3.0 29.8 + - - +
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Residues in contact with SER 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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342A LEU* 3.7 20.7 - - - +
344A VAL* 3.4 33.2 - - - +
347A ILE* 3.3 18.1 - - - +
349A SER 2.9 15.7 + - - -
350A VAL* 3.1 11.1 + - - -
352A GLU* 1.3 71.9 - - - +
354A ILE* 1.3 68.5 + - - +
356A ALA* 3.4 3.4 + - - -
357A CYS* 3.0 23.2 + - - +
384A LEU* 5.4 4.0 - - - -
388A LEU* 5.5 0.2 - - - -
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Residues in contact with ILE 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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87A GLN* 5.9 0.2 - - + -
134A ILE* 4.4 13.9 - - + +
137A LEU* 3.7 35.2 - - + +
138A ALA* 3.7 30.7 - - + -
350A VAL* 3.0 35.4 + - + +
351A THR* 3.7 9.6 - - - +
353A SER* 1.3 76.6 - - - +
355A GLN* 1.3 57.9 + - + +
357A CYS* 3.2 4.0 + - - +
358A LYS* 2.9 32.8 + - + +
384A LEU* 4.7 8.5 - - + -
388A LEU* 4.1 18.6 - - + -
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Residues in contact with GLN 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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88A GLU* 4.7 10.9 + - - +
351A THR* 2.9 35.6 + - + +
352A GLU* 3.8 22.8 - - - +
353A SER 3.3 0.2 - - - -
354A ILE* 1.3 76.8 - - + +
356A ALA* 1.3 57.2 + - - +
358A LYS* 3.4 5.8 + - - +
359A LEU* 3.0 30.1 + - - +
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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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323A THR* 4.5 9.2 - - + -
325A PRO* 5.6 4.3 - - + -
328A ILE* 4.4 15.5 - - + +
340A LEU* 3.9 12.5 - - + +
342A LEU* 4.2 12.1 - - + -
347A ILE* 4.6 7.0 - - + -
352A GLU 3.0 18.7 + - - +
353A SER 3.7 4.7 - - - +
354A ILE 3.3 0.2 - - - -
355A GLN* 1.3 75.6 - - - +
357A CYS* 1.3 63.1 + - - +
359A LEU* 3.4 4.6 + - - +
360A ALA* 3.1 23.6 + - - +
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Residues in contact with CYS 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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340A LEU* 4.7 3.1 - - - -
342A LEU* 4.3 6.4 - - + +
353A SER 3.0 13.2 + - - +
354A ILE 3.4 8.3 - - - +
356A ALA* 1.3 77.4 - - - +
358A LYS* 1.3 57.0 + - - +
360A ALA* 3.3 3.9 + - - +
361A GLN* 2.9 58.4 + - - +
367A VAL* 3.8 21.3 - - + -
388A LEU* 3.8 39.0 - - + -
390A THR* 4.1 5.6 - - - -
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Residues in contact with LYS 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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138A ALA* 2.7 36.1 + - + +
139A GLY* 4.1 6.3 + - - -
140A ASN* 2.9 23.3 + - - +
354A ILE* 2.9 29.5 + - + +
355A GLN* 3.9 6.3 - - - +
357A CYS* 1.3 77.9 - - - +
359A LEU* 1.3 58.0 + - - +
361A GLN* 3.4 21.4 + - - +
362A SER* 2.9 31.7 + - - -
388A LEU* 5.6 0.9 - - + -
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Residues in contact with LEU 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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325A PRO* 5.8 9.9 - - + +
328A ILE* 5.8 10.1 - - + -
329A ALA* 6.1 5.6 - - + -
332A VAL* 6.2 0.9 - - + -
355A GLN 3.0 17.8 + - - +
356A ALA* 3.9 5.6 - - - +
358A LYS* 1.3 75.5 - - - +
360A ALA* 1.3 63.3 + - - +
362A SER* 2.7 31.3 + - - +
363A ASN* 3.1 25.6 + - - +
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Residues in contact with ALA 360 (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 ILE* 5.4 7.4 - - + +
332A VAL* 5.7 1.1 - - - -
340A LEU* 4.1 12.3 - - + -
356A ALA 3.1 13.2 + - - +
357A CYS 3.5 8.1 - - - +
359A LEU* 1.3 74.9 - - - +
361A GLN* 1.3 62.6 + - - +
363A ASN* 3.1 15.5 + - - +
364A GLY 3.5 0.2 + - - -
365A TRP* 3.1 45.0 + - + +
367A VAL* 3.9 17.5 - - + -
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Residues in contact with GLN 361 (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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140A ASN* 5.2 2.2 + - - +
357A CYS* 2.9 35.8 + - - +
358A LYS* 3.6 35.2 - - + +
360A ALA* 1.3 71.5 - - - +
362A SER* 1.3 58.5 + - - +
364A GLY* 3.0 18.9 + - - -
365A TRP 3.6 13.0 - - - +
366A GLY* 5.7 0.2 - - - -
367A VAL* 4.0 13.2 - - + +
388A LEU 3.3 22.1 + - - +
389A CYS* 4.3 2.9 - - - +
390A THR* 4.2 12.1 - - - +
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Residues in contact with SER 362 (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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358A LYS 2.9 15.0 + - - -
359A LEU* 2.7 33.5 + - - +
361A GLN* 1.3 77.3 - - - +
363A ASN* 1.3 62.2 + - - +
364A GLY 3.4 1.4 + - - -
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Residues in contact with ASN 363 (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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332A VAL* 3.6 42.5 - - + +
359A LEU* 3.1 32.1 + - - +
360A ALA 3.1 9.4 + - - +
362A SER* 1.3 85.1 + - - +
364A GLY* 1.3 59.3 + - - +
365A TRP* 3.3 13.5 + - + -
510A EDO 3.9 10.7 + - - -
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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