Contacts of the helix formed by residues 349 - 363 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ASP* 3.8 23.3 + - - -
95B ILE* 4.3 4.6 - - - +
103B LYS* 4.6 2.9 - - - -
111B ILE* 4.8 4.7 - - - -
112B LEU* 4.0 8.8 - - - +
115B SER* 3.8 5.8 - - - -
344B VAL 4.3 0.2 + - - -
347B ILE* 3.7 2.2 - - - +
348B GLY* 1.3 78.3 - - - +
350B VAL* 1.3 63.0 + - - +
351B THR* 3.7 1.7 + - - -
352B GLU* 2.8 42.9 + - - +
353B SER* 2.9 26.1 + - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN* 3.6 18.4 - - + +
112B LEU* 4.9 1.3 - - + -
115B SER* 3.0 41.5 + - - +
116B LEU* 3.9 22.7 - - + -
119B CYS* 4.2 15.9 - - + -
134B ILE* 5.6 0.4 - - + -
137B LEU* 4.9 0.2 - - + -
344B VAL* 6.0 2.5 - - + -
349B SER* 1.3 73.1 - - - +
351B THR* 1.3 64.6 + - - +
353B SER* 3.2 5.8 + - - -
354B ILE* 3.0 42.7 + - + +
380B PHE* 4.0 15.5 - - + -
384B LEU* 5.4 3.4 - - + -
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Residues in contact with THR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN* 3.4 20.4 + - - +
88B GLU* 3.5 31.0 + - + +
91B ASP* 2.7 32.1 + - + -
349B SER* 3.3 0.8 - - - -
350B VAL* 1.3 77.5 - - - +
352B GLU* 1.3 60.2 + - + +
354B ILE* 3.3 9.6 + - - +
355B GLN* 2.9 49.4 + - + +
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.4 20.4 - - + +
103B LYS* 2.6 36.4 + - - -
347B ILE* 3.7 33.4 - - + +
349B SER* 2.8 25.0 + - - +
351B THR* 1.3 76.1 - - + +
353B SER* 1.3 60.5 + - - +
355B GLN* 3.7 18.8 - - - +
356B ALA* 3.0 29.5 + - - +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B LEU* 3.7 17.7 - - - +
344B VAL* 3.4 34.0 - - - +
347B ILE* 3.3 18.9 - - - +
349B SER 2.9 22.2 + - - -
350B VAL* 3.5 6.7 - - - -
352B GLU* 1.3 76.5 - - - +
354B ILE* 1.3 63.6 + - - +
356B ALA* 3.3 6.4 + - - +
357B CYS* 3.1 22.5 + - - +
384B LEU* 5.5 4.3 - - - -
388B LEU* 5.7 0.2 - - - -
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLN* 5.9 0.4 - - + -
134B ILE* 4.4 14.4 - - + +
137B LEU* 3.9 32.5 - - + +
138B ALA* 3.8 29.8 - - + -
350B VAL* 3.0 36.7 + - + +
351B THR* 3.6 9.2 - - - +
353B SER* 1.3 72.4 - - - +
355B GLN* 1.3 66.8 + - + +
357B CYS* 3.3 2.9 + - - +
358B LYS* 3.0 28.8 + - + +
384B LEU* 4.7 8.1 - - + -
388B LEU* 4.0 20.4 - - + -
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 6.2 1.2 - - - -
351B THR* 2.9 37.7 + - + +
352B GLU* 3.7 24.7 - - - +
354B ILE* 1.3 74.8 - - + +
356B ALA* 1.3 56.6 + - - +
358B LYS* 3.4 6.1 + - - +
359B LEU* 3.0 30.0 + - - +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B THR* 4.6 8.1 - - + -
325B PRO* 5.9 3.8 - - + -
328B ILE* 4.6 15.3 - - + +
340B LEU* 3.9 12.7 - - + +
342B LEU* 4.2 12.1 - - + -
347B ILE* 4.7 7.4 - - + -
352B GLU 3.0 17.2 + - - +
353B SER* 3.7 5.6 - - - +
355B GLN* 1.3 73.5 - - - +
357B CYS* 1.3 66.1 + - - +
359B LEU* 3.4 6.7 + - - +
360B ALA* 3.0 23.7 + - - +
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Residues in contact with CYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 4.7 0.4 - - - -
342B LEU* 4.2 9.5 - - + +
353B SER 3.1 13.8 + - - +
354B ILE 3.5 8.3 - - - +
356B ALA* 1.3 78.3 - - - +
358B LYS* 1.3 58.0 + - - +
360B ALA* 3.3 2.4 + - - +
361B GLN* 2.9 58.2 + - - +
367B VAL* 3.9 25.0 - - + +
388B LEU* 3.9 35.9 - - + -
390B THR* 4.0 4.7 - - - -
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ALA* 2.9 29.7 + - + +
139B GLY 4.2 5.3 + - - -
140B ASN* 2.9 27.2 + - - +
354B ILE* 3.0 30.7 + - + +
355B GLN* 3.8 6.3 - - - +
356B ALA 3.4 0.2 - - - -
357B CYS* 1.3 77.9 - - + +
359B LEU* 1.3 57.6 + - - +
361B GLN* 3.3 21.0 + - - +
362B SER* 2.9 30.0 + - - -
388B LEU* 5.6 1.3 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B PRO* 6.0 7.4 - - + +
328B ILE* 5.7 10.5 - - + -
329B ALA* 6.4 2.7 - - + -
355B GLN 3.0 18.4 + - - +
356B ALA* 3.9 5.6 - - - +
357B CYS 3.3 0.2 - - - -
358B LYS* 1.3 73.3 - - - +
360B ALA* 1.3 64.0 + - - +
362B SER* 2.7 30.3 + - - +
363B ASN* 3.0 23.8 + - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 5.4 7.4 - - + +
332B VAL* 5.8 0.9 - - - -
340B LEU* 4.2 9.2 - - + -
356B ALA 3.0 13.9 + - - +
357B CYS 3.7 6.7 - - - +
359B LEU* 1.3 74.8 - - - +
361B GLN* 1.3 64.4 + - - +
363B ASN* 3.0 14.8 + - - +
364B GLY 3.3 0.2 + - - -
365B TRP* 3.2 49.3 + - + +
367B VAL* 3.9 17.3 - - + -
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ASN* 5.3 1.4 + - - +
357B CYS* 2.9 37.0 + - - +
358B LYS* 3.6 25.6 + - + +
360B ALA* 1.3 76.1 - - - +
362B SER* 1.3 60.4 + - - +
364B GLY* 3.1 14.2 + - - -
365B TRP 3.8 11.8 - - - +
367B VAL* 4.2 12.4 - - + +
388B LEU* 3.4 24.0 + - - +
389B CYS* 4.4 3.6 + - - +
390B THR* 4.3 14.5 - - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B LYS 2.9 17.3 + - - -
359B LEU* 2.7 32.4 + - - +
361B GLN* 1.3 71.2 - - - +
363B ASN* 1.3 63.6 + - - +
364B GLY 3.3 1.8 + - - -
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B VAL* 3.5 43.3 - - + +
359B LEU* 3.0 31.5 + - - +
360B ALA 3.0 10.0 + - - +
362B SER* 1.3 86.2 + - - +
364B GLY* 1.3 58.3 + - - +
365B TRP* 3.4 12.6 + - + -
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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