Contacts of the helix formed by residues 400 - 418 (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 ARG 400 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER 2.9 16.7 + - - -
207A VAL* 3.6 24.9 - - - +
399A CYS* 3.7 11.7 - - - -
400A ARG* 3.7 34.3 - - + +
402A GLU* 3.8 6.5 - - - +
502A EDO 5.2 0.8 - - - -
14B SER* 3.1 29.3 + - - -
15B ARG* 5.0 1.8 - - - +
207B VAL* 4.3 2.2 - - - -
208B GLY 2.9 23.1 + - - -
209B ASP* 3.1 22.8 + - - +
210B GLU 4.1 0.4 - - - -
211B GLY* 3.5 26.2 - - - +
399B CYS* 1.3 76.6 - - - +
401B SER* 1.3 61.0 + - - +
402B GLU* 2.7 34.6 + - - +
403B ARG* 2.9 19.8 + - + -
404B LEU* 3.0 12.9 + - - +
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 4.5 1.2 - - - -
14A SER* 3.2 27.7 + - - -
375A GLU 3.9 3.1 + - - -
376A THR* 3.9 4.5 - - - -
377A GLU* 4.3 21.7 + - - +
401A SER* 4.6 3.1 - - - -
402A GLU* 3.0 33.7 + - - +
377B GLU* 5.2 0.8 - - - -
400B ARG* 1.3 67.6 - - - +
402B GLU* 1.3 57.2 + - - +
403B ARG 3.0 5.2 - - - -
404B LEU* 4.0 8.9 - - - +
405B ALA* 2.8 32.3 + - - +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 3.8 0.7 - - - -
401A SER* 3.0 40.6 + - - +
14B SER* 3.2 21.9 - - - +
209B ASP 3.4 0.3 - - - +
375B GLU* 3.6 9.7 - - + +
376B THR 3.5 18.6 - - - +
377B GLU 4.8 0.4 - - - +
395B THR* 4.6 0.2 + - - -
400B ARG* 2.7 40.2 + - - +
401B SER* 1.3 76.4 + - - +
403B ARG* 1.3 92.8 + - - +
405B ALA* 4.8 0.2 - - - -
406B LYS* 2.8 33.5 + - - +
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Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 3.5 8.9 + - - -
209B ASP 2.9 22.7 + - - -
210B GLU* 3.8 16.2 - - - +
371B HIS* 2.9 25.3 + - - -
372B ARG 3.0 17.4 + - - -
373B SER 2.9 25.1 + - - -
375B GLU* 3.4 8.2 - - - +
395B THR* 3.2 24.8 - - - +
396B GLY* 3.8 7.6 - - - -
397B ALA 3.6 15.9 - - - +
399B CYS 3.4 16.8 - - - +
400B ARG* 2.9 11.1 + - + +
402B GLU* 1.3 102.5 + - - +
404B LEU* 1.3 64.3 + - - +
405B ALA 3.2 1.3 - - - -
406B LYS* 3.0 18.0 + - - +
407B TYR* 3.4 15.7 + - + -
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 30.1 - - + +
13A ASP 3.5 25.1 - - - +
14A SER* 4.2 2.0 - - - -
377A GLU* 5.4 0.4 - - - +
182B MET* 4.5 0.2 - - + -
398B PRO* 3.5 24.9 - - + +
399B CYS* 3.3 31.9 - - - +
400B ARG 3.0 23.4 + - - +
401B SER* 4.2 8.3 - - - +
403B ARG* 1.3 74.0 - - - +
405B ALA* 1.3 60.0 + - - +
407B TYR* 4.1 15.5 - - + -
408B ASN* 2.7 44.7 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 3.8 29.8 + - + +
377B GLU* 3.9 17.9 - - - +
379B THR* 3.3 30.2 - - + +
401B SER* 2.8 21.3 + - - +
402B GLU 4.8 0.7 - - - +
403B ARG 3.2 0.4 + - - -
404B LEU* 1.3 75.7 - - - +
406B LYS* 1.3 61.9 + - + +
408B ASN* 3.9 1.4 - - - +
409B GLN* 3.1 22.3 + - - +
412B ARG* 4.6 1.0 + - - -
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Residues in contact with LYS 406 (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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375B GLU* 2.9 26.7 + - - -
376B THR 2.7 29.3 + - - -
377B GLU 4.8 0.2 - - - -
378B ASP 2.8 23.1 + - - +
379B THR* 4.4 7.6 - - - -
381B ILE* 3.8 26.7 - - + -
382B ALA* 3.7 12.6 - - + +
393B ILE* 5.3 1.3 - - + -
395B THR* 3.6 32.5 - - + +
402B GLU 2.8 21.9 + - - +
403B ARG 3.0 7.8 + - - +
405B ALA* 1.3 75.1 - - + +
407B TYR* 1.3 60.4 + - - +
409B GLN* 3.2 4.7 + - - +
410B LEU* 2.9 32.8 + - - +
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Residues in contact with TYR 407 (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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148B PRO* 3.7 20.9 - - + -
149B ALA 3.7 7.1 + - - -
150B PHE* 3.6 18.8 - + - -
178B PHE* 3.5 20.4 - + - -
182B MET* 3.5 34.8 - - + -
393B ILE* 4.8 3.8 - - + -
395B THR* 3.2 48.2 + - + -
396B GLY 2.7 28.3 + - - -
397B ALA 3.9 7.0 - - - -
403B ARG 3.4 17.4 + - - -
404B LEU* 3.2 16.7 + - + +
406B LYS* 1.3 75.3 - - - +
408B ASN* 1.3 63.0 + - - +
410B LEU* 3.3 5.4 + - + -
411B MET* 3.1 22.3 + - - +
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Residues in contact with ASN 408 (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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11A ILE* 3.6 14.2 - - + +
12A LEU* 2.9 48.5 + - - +
377A GLU* 3.1 30.7 + - - +
404B LEU* 2.7 26.4 + - - +
405B ALA 3.9 1.1 - - - +
407B TYR* 1.3 72.0 - - - +
409B GLN* 1.3 58.6 + - - +
411B MET* 3.1 20.5 + - - +
412B ARG* 2.9 42.5 + - - +
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Residues in contact with GLN 409 (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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32A ARG* 4.7 3.5 + - - -
379B THR* 3.9 21.7 + - - +
382B ALA* 3.8 11.4 - - + -
383B ASP* 3.1 34.3 + - - +
405B ALA 3.1 20.2 + - - +
406B LYS 3.2 5.1 + - - +
408B ASN* 1.3 77.8 - - - +
410B LEU* 1.3 57.3 + - - +
412B ARG* 3.1 31.5 + - - +
413B ILE* 2.9 42.0 + - + +
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Residues in contact with LEU 410 (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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145B LEU* 3.7 6.2 - - + +
146B PRO* 4.0 12.6 - - + -
178B PHE* 3.4 42.3 - - + -
382B ALA* 3.5 22.9 - - + +
385B VAL* 4.2 0.4 - - + -
386B VAL* 3.5 32.5 - - + -
393B ILE* 4.1 27.6 - - + -
406B LYS* 2.9 21.6 + - + +
407B TYR* 3.6 6.3 - - + +
408B ASN 3.3 0.2 - - - -
409B GLN* 1.3 75.6 - - - +
411B MET* 1.3 63.4 + - - +
413B ILE* 3.3 5.6 + - + +
414B GLU* 3.0 24.3 + - - +
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Residues in contact with MET 411 (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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10A GLU 4.1 14.8 - - - +
11A ILE* 4.2 7.6 - - + -
12A LEU* 4.3 13.2 - - + +
57A TYR* 5.3 3.6 - - - +
178B PHE* 3.8 17.0 - - + -
179B LYS* 4.1 17.0 - - + +
182B MET* 3.9 22.7 - - + -
407B TYR 3.1 14.4 + - - +
408B ASN* 3.1 35.0 + - - +
410B LEU* 1.3 77.8 - - - +
412B ARG* 1.3 57.1 + - + +
414B GLU* 3.4 6.5 + - - +
415B GLU* 3.0 27.2 + - - +
505B EDO 4.0 31.6 - - - -
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Residues in contact with ARG 412 (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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9A ARG* 3.9 20.8 - - - +
11A ILE* 4.3 4.1 - - + +
21A GLU* 2.8 39.3 + - - -
32A ARG* 3.4 38.7 - - - +
377A GLU* 3.5 22.8 + - - +
511A EDO 3.9 4.8 + - - -
379B THR* 5.5 3.0 - - - +
405B ALA 4.6 2.4 + - - -
408B ASN* 2.9 21.9 + - - +
409B GLN* 3.1 50.5 + - - +
411B MET* 1.3 72.7 - - + +
413B ILE* 1.3 61.4 + - + +
415B GLU* 3.4 12.5 + - - +
416B ALA* 3.0 28.8 + - - +
505B EDO 5.1 0.2 - - - -
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Residues in contact with ILE 413 (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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131B TYR* 3.7 31.9 - - + -
145B LEU* 4.5 3.8 - - + -
382B ALA 4.2 5.6 - - - +
383B ASP* 3.9 40.6 - - - +
386B VAL* 4.2 22.2 - - + -
409B GLN* 2.9 35.6 + - + +
410B LEU* 3.7 6.3 - - + +
411B MET 3.3 0.2 - - - -
412B ARG* 1.3 73.7 - - - +
414B GLU* 1.3 65.3 + - - +
416B ALA* 3.1 7.2 + - - +
417B LEU* 3.1 38.0 + - + +
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Residues in contact with GLU 414 (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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145B LEU* 4.0 24.2 - - + +
177B SER* 3.5 12.6 - - - -
178B PHE* 2.8 29.9 + - + +
179B LYS* 2.9 34.5 + - - +
410B LEU 3.0 15.9 + - - +
411B MET* 3.7 5.8 - - - +
413B ILE* 1.3 76.4 - - - +
415B GLU* 1.3 63.6 + - - +
417B LEU* 3.2 12.4 + - - +
418B GLY* 3.2 11.1 + - - +
421B ALA* 4.0 19.7 - - + +
422B ILE 5.9 0.2 - - - -
423B PHE* 4.7 3.6 + - - +
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Residues in contact with GLU 415 (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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7A PHE* 3.5 24.9 - - + -
9A ARG* 2.9 40.4 + - - -
411B MET 3.0 17.4 + - - +
412B ARG* 3.5 7.5 - - - +
414B GLU* 1.3 77.0 - - - +
416B ALA* 1.3 63.9 + - - +
418B GLY* 3.3 14.3 + - - -
505B EDO 2.6 30.1 + - - +
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Residues in contact with ALA 416 (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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131B TYR* 3.9 18.2 - - + +
412B ARG 3.0 17.3 + - - +
413B ILE* 3.1 6.7 + - - +
415B GLU* 1.3 78.2 - - - +
417B LEU* 1.3 63.4 + - - +
418B GLY* 3.6 0.5 + - - -
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Residues in contact with LEU 417 (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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131B TYR* 3.7 27.6 - - + +
132B ARG* 5.7 0.7 - - - +
143B LEU* 3.9 29.6 - - + +
145B LEU* 4.0 24.2 - - + -
386B VAL* 5.1 0.2 - - + -
413B ILE* 3.1 25.0 + - + +
414B GLU 3.2 5.1 + - - +
416B ALA* 1.3 80.0 - - - +
418B GLY* 1.3 63.2 + - - +
419B ASP* 3.6 0.5 + - - +
420B LYS* 3.2 25.8 + - + +
421B ALA* 4.0 17.0 - - + +
422B ILE 5.7 0.2 - - - +
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Residues in contact with GLY 418 (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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414B GLU 3.2 9.7 + - - +
415B GLU 3.3 11.2 + - - -
416B ALA 3.4 0.8 - - - -
417B LEU* 1.3 76.5 - - - +
419B ASP* 1.3 59.4 + - - -
420B LYS 3.1 5.1 + - - -
421B ALA* 3.2 18.7 + - - +
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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