Contacts of the helix formed by residues 357 - 371 (chain B) in PDB entry 1X11
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 ALA 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B ARG 2.8 12.1 + - - +
354B MSE 3.3 14.1 - - - +
355B MSE 3.0 0.2 - - - -
356B GLN* 1.3 76.6 - - - +
358B GLN* 1.3 60.2 + - - +
359B GLU 3.2 0.2 - - - -
360B ALA* 2.9 2.4 + - - +
361B VAL* 2.8 35.1 + - - +
418B TYR* 4.3 0.2 - - + -
420B ALA* 4.3 8.7 - - + -
422B ILE* 4.0 11.4 - - + -
427B VAL* 4.0 19.0 - - + +
429B MSE 3.6 17.7 - - + -
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Residues in contact with GLN 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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354B MSE 3.0 14.5 + - - +
355B MSE 2.8 13.1 + - - +
357B ALA* 1.3 75.4 - - - +
359B GLU* 1.3 58.9 + - - +
361B VAL* 2.9 10.0 + - - +
362B SER* 2.9 36.3 + - - +
422B ILE* 4.1 20.7 - - + +
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Residues in contact with GLU 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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355B MSE 2.8 14.2 + - - +
356B GLN* 4.1 8.3 - - - +
358B GLN* 1.3 78.1 - - - +
360B ALA* 1.3 59.3 + - - +
362B SER* 3.1 12.6 + - - -
363B ARG* 2.8 75.3 + - + +
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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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340B THR* 3.7 22.9 - - - +
342B LEU* 6.1 0.4 - - + -
356B GLN 3.1 17.8 + - - +
357B ALA 2.9 6.4 + - - +
359B GLU* 1.3 76.2 - - - +
361B VAL* 1.3 62.6 + - - +
363B ARG* 3.8 3.3 - - - +
364B ILE* 2.9 31.9 + - - +
427B VAL* 4.0 11.4 - - + -
460B CYS* 3.9 17.9 - - + -
462B VAL* 4.0 6.5 - - + -
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Residues in contact with VAL 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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357B ALA 2.8 19.2 + - - +
358B GLN* 2.9 13.0 + - - +
360B ALA* 1.3 79.3 - - - +
362B SER* 1.3 56.5 + - - +
364B ILE* 3.5 3.1 + - - +
365B LYS* 3.0 52.3 + - + +
422B ILE* 3.7 20.0 - - + +
425B ILE* 3.5 25.6 - - + -
427B VAL* 3.4 25.1 - - + -
462B VAL* 4.5 6.4 - - + +
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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 GLN* 2.9 22.1 + - - +
359B GLU* 3.1 30.7 + - - -
361B VAL* 1.3 75.8 - - - +
363B ARG* 1.3 56.3 + - - -
365B LYS* 2.7 28.8 + - - +
366B MSE 2.7 20.2 + - - +
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Residues in contact with ARG 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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340B THR* 3.7 28.2 - - + +
359B GLU* 2.8 50.9 + - + +
360B ALA* 3.8 0.9 - - - +
361B VAL 3.5 0.2 - - - -
362B SER* 1.3 79.7 + - - +
364B ILE* 1.3 64.7 + - - +
366B MSE 3.3 8.5 + - - +
367B ALA* 3.2 20.4 + - - +
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Residues in contact with ILE 364 (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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337B LEU* 3.5 41.5 - - + +
338B GLY* 3.7 3.4 - - - -
339B SER* 3.6 29.6 - - - +
340B THR* 3.8 18.8 - - + -
360B ALA 2.9 22.6 + - - +
361B VAL 3.6 4.7 - - - +
362B SER 3.1 0.4 - - - -
363B ARG* 1.3 74.6 - - - +
365B LYS* 1.3 61.1 + - + +
367B ALA* 3.1 7.8 + - + +
368B GLN* 2.9 36.0 + - + +
462B VAL* 3.3 24.0 - - + -
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Residues in contact with LYS 365 (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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337B LEU* 5.9 5.2 - - + -
361B VAL* 3.0 37.4 + - + +
362B SER* 2.7 18.0 + - - +
364B ILE* 1.3 75.4 - - + +
366B MSE 1.3 54.5 + - - -
368B GLN* 3.5 7.9 - - + +
369B LYS* 2.8 32.4 + - - +
424B ASN* 5.3 4.9 + - - +
425B ILE* 4.7 18.0 - - + +
464B GLU* 5.5 2.5 - - - -
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Residues in contact with MSE 366 (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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362B SER 2.7 15.1 + - - +
363B ARG* 3.7 10.8 - - - +
364B ILE 3.2 0.2 - - - -
365B LYS* 1.3 72.1 - - - +
367B ALA* 1.3 63.3 + - - +
369B LYS* 3.3 8.1 + - - +
370B LEU* 3.0 56.8 + - + +
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Residues in contact with ALA 367 (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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363B ARG 3.2 8.9 + - - +
364B ILE* 3.1 9.8 + - + +
366B MSE 1.3 79.9 - - - +
368B GLN* 1.3 58.6 + - + +
370B LEU* 3.0 11.7 + - - +
371B ALA* 2.8 32.0 + - - +
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Residues in contact with GLN 368 (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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337B LEU* 3.0 40.4 + - + +
364B ILE* 2.9 31.6 + - + +
365B LYS* 3.5 9.0 - - + +
367B ALA* 1.3 76.8 - - + +
369B LYS* 1.3 57.9 + - - +
370B LEU 3.1 0.3 + - - -
371B ALA* 3.2 4.7 + - - +
372B LYS* 2.8 35.6 + - - +
385B MSE 3.7 34.7 + - - +
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Residues in contact with LYS 369 (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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365B LYS 2.8 22.5 + - - +
366B MSE 3.5 10.5 - - - +
368B GLN* 1.3 72.4 - - - +
370B LEU* 1.3 65.4 + - + +
372B LYS* 4.0 13.9 + - - +
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Residues in contact with LEU 370 (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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366B MSE 3.0 48.3 + - + +
367B ALA* 3.0 10.1 + - - +
369B LYS* 1.3 80.9 - - + +
371B ALA* 1.3 64.0 + - - +
372B LYS 3.1 7.9 + - - +
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Residues in contact with ALA 371 (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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367B ALA 2.8 18.6 + - - +
368B GLN* 4.0 4.5 - - - +
370B LEU* 1.3 73.7 - - - +
372B LYS* 1.3 62.7 + - - +
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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