Contacts of the helix formed by residues 388 - 408 (chain A) in PDB entry 1XV9
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 GLU 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLU 5.5 1.0 - - - +
292A LEU* 4.0 24.8 - - + +
293A PRO* 4.1 19.3 - - - +
296A ASP* 5.5 0.8 - - - +
385A ASN* 2.7 43.2 + - + +
386A PRO 3.5 0.2 - - - -
387A ALA* 1.3 76.0 - - - +
389A VAL* 1.3 60.7 + - + +
391A ALA* 2.9 26.6 + - - +
392A LEU* 3.4 10.2 + - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 5.1 10.3 - - + -
296A ASP* 4.6 7.2 - - + +
300A LEU* 4.0 33.4 - - + -
376A PHE* 4.0 16.0 - - + +
378A PRO* 3.7 23.1 - - + -
383A LEU* 3.7 24.2 - - + -
385A ASN 3.4 15.1 + - - +
386A PRO* 4.9 0.2 - - + -
387A ALA 4.3 0.2 - - - +
388A GLU* 1.3 73.0 - - + +
390A GLU* 1.3 61.7 + - - +
391A ALA 3.0 5.6 + - - -
392A LEU* 3.4 11.9 + - - +
393A ARG* 3.4 19.2 + - - +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A PRO* 3.6 20.9 - - + +
379A ASP* 5.2 2.0 - - - +
386A PRO 3.4 19.7 + - - +
387A ALA* 3.7 8.7 + - - +
388A GLU 3.3 0.6 - - - -
389A VAL* 1.3 76.2 - - - +
391A ALA* 1.3 61.0 + - - +
393A ARG* 3.4 18.7 + - - +
394A GLU* 3.0 31.1 + - + +
248B THR* 6.2 0.2 - - - +
311B LYS* 2.8 36.8 + - - +
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Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA 3.2 12.6 + - - +
388A GLU* 2.9 19.7 - - + +
390A GLU* 1.3 76.7 - - - +
392A LEU* 1.3 64.7 + - + +
394A GLU* 3.2 16.3 + - - +
395A LYS* 3.2 27.8 + - - +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.5 7.9 - - + +
288A HIS* 3.8 36.6 - - + +
292A LEU* 3.5 33.2 - - + -
376A PHE* 3.6 40.8 - - + -
388A GLU* 3.8 12.1 - - + +
389A VAL* 3.4 8.7 + - - +
391A ALA* 1.3 77.7 - - + +
393A ARG* 1.3 57.8 + - - +
395A LYS* 2.9 37.8 + - + +
396A VAL* 3.1 10.7 + - - +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 4.0 22.3 - - + +
376A PHE* 3.2 39.8 - - + +
377A ASN* 5.2 0.2 - - - +
378A PRO* 3.3 29.1 - - - +
379A ASP* 4.9 5.1 + - - -
389A VAL 3.4 8.6 + - - +
390A GLU* 3.4 23.9 + - - +
391A ALA 3.3 0.8 - - - -
392A LEU* 1.3 78.8 - - - +
394A GLU* 1.3 56.9 + - + +
396A VAL* 3.7 4.9 + - - +
397A TYR* 2.8 61.3 + - + -
310B ALA 4.1 0.2 + - - -
311B LYS* 3.3 34.5 + - - +
314B GLY* 4.8 7.9 - - - -
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 4.9 0.7 + - - -
390A GLU* 3.0 26.9 - - + +
391A ALA* 3.2 9.0 + - - +
393A ARG* 1.3 76.7 + - + +
395A LYS* 1.3 63.8 + - + +
397A TYR* 3.3 16.9 - - - +
398A ALA* 3.2 18.2 + - - +
305B ASP* 5.3 4.8 - - - +
306B ARG* 4.6 7.3 + - - +
307B PHE* 3.5 27.2 + - + +
311B LYS* 3.2 42.9 + - - +
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Residues in contact with LYS 395 (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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227A ASN* 3.8 25.5 - - - +
229A ASP* 3.3 28.4 + - + +
230A MET* 3.7 15.3 - - + -
288A HIS* 4.8 5.3 + - + -
391A ALA* 3.2 25.0 + - - +
392A LEU* 2.9 33.2 + - + +
394A GLU* 1.3 78.1 - - + +
396A VAL* 1.3 56.3 + - - +
398A ALA* 3.1 6.4 + - - +
399A SER* 3.0 28.7 + - - -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.5 32.1 - - + -
235A ILE* 5.2 5.4 - - + -
286A ILE* 6.4 0.2 - - + -
369A CYS* 3.8 27.6 - - + +
372A ALA* 4.7 8.7 - - + -
373A ILE* 3.7 27.1 - - + -
376A PHE* 4.3 16.4 - - + -
392A LEU 3.1 6.1 + - - +
393A ARG* 4.0 7.0 - - - +
395A LYS* 1.3 71.4 - - - +
397A TYR* 1.3 66.0 + - - +
398A ALA 3.0 1.8 - - - -
399A SER* 4.3 7.0 - - - +
400A LEU* 2.9 23.9 + - - +
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 4.0 30.0 - - + +
393A ARG* 2.8 54.0 + - + +
394A GLU* 3.3 21.1 - - - +
396A VAL* 1.3 76.5 - - - +
398A ALA* 1.3 60.0 + - - +
400A LEU* 4.8 0.7 - - - -
401A GLU* 3.3 21.0 + - - +
415A PHE* 3.7 11.7 - + - -
419A LEU* 5.0 5.6 - - + -
422A LEU* 5.9 0.7 - - - +
307B PHE* 3.3 46.7 - + + -
310B ALA* 2.6 47.3 + - + -
311B LYS* 3.7 14.6 - - + -
314B GLY* 5.2 0.5 + - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 3.4 29.8 - - + +
394A GLU 3.2 8.0 + - - +
395A LYS 3.1 10.5 + - - +
396A VAL 3.0 0.2 - - - -
397A TYR* 1.3 77.2 - - - +
399A SER* 1.3 67.8 + - - +
400A LEU 3.1 0.3 + - - -
401A GLU* 3.2 4.3 + - - +
402A ALA* 3.0 24.0 + - - +
306B ARG* 4.2 13.5 - - - +
307B PHE* 3.6 13.9 - - + -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 3.5 13.2 + - - +
230A MET* 2.8 44.0 + - - +
232A VAL* 4.1 17.9 - - - +
235A ILE* 5.4 4.3 - - - -
369A CYS* 5.5 0.7 - - - -
395A LYS 3.0 6.6 + - - -
396A VAL* 3.4 8.3 + - - -
398A ALA* 1.3 76.8 - - - +
400A LEU* 1.3 57.4 + - - +
402A ALA* 3.0 8.2 - - - +
403A TYR* 2.8 30.0 + - - +
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Residues in contact with LEU 400 (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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366A GLU* 4.4 10.3 - - + -
369A CYS* 3.3 41.9 - - + -
370A LEU* 3.9 23.1 - - + -
373A ILE* 4.0 11.4 - - + -
396A VAL 2.9 17.8 + - - +
399A SER* 1.3 73.0 - - - +
401A GLU* 1.3 61.0 + - - +
402A ALA 2.9 4.9 - - - -
403A TYR* 3.3 5.8 + - + -
404A CYS* 3.0 42.6 + - - -
415A PHE* 3.6 24.5 - - + -
418A LEU* 4.3 12.3 - - + -
419A LEU* 4.6 2.5 - - + -
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Residues in contact with GLU 401 (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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397A TYR 3.3 13.0 + - - +
398A ALA* 3.2 4.6 + - - +
400A LEU* 1.3 78.2 - - - +
402A ALA* 1.3 57.2 + - - +
404A CYS 4.0 0.4 - - - -
405A LYS* 3.0 41.9 + - + +
415A PHE* 3.4 40.1 - - + -
297B LYS* 4.4 17.8 + - - -
306B ARG* 3.8 10.6 + - - -
307B PHE* 3.1 27.3 - - - -
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Residues in contact with ALA 402 (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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227A ASN 5.7 5.4 - - - +
398A ALA 3.0 13.3 + - - +
399A SER* 3.0 15.7 - - - +
401A GLU* 1.3 75.0 - - - +
403A TYR* 1.3 54.5 + - - +
404A CYS 3.1 1.1 - - - -
405A LYS* 3.9 1.6 - - - +
406A HIS* 2.7 40.0 + - - +
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Residues in contact with TYR 403 (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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232A VAL* 3.6 22.6 - - + +
236A LEU* 6.0 0.2 - - - +
363A ASP* 2.9 37.8 + - - +
365A THR* 3.2 34.0 + - + -
366A GLU* 4.2 10.8 - - + -
369A CYS* 5.8 0.2 - - - -
399A SER 2.8 18.4 + - - +
400A LEU* 3.3 8.3 + - + +
402A ALA* 1.3 72.6 - - - +
404A CYS* 1.3 61.1 + - - +
406A HIS* 3.9 13.2 - + - -
407A LYS* 2.9 52.1 + - + +
408A TYR* 4.0 11.9 - + - -
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Residues in contact with CYS 404 (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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366A GLU* 4.2 10.5 - - - -
400A LEU* 3.0 35.3 + - - +
401A GLU 4.1 0.4 - - - +
403A TYR* 1.3 75.8 - - - +
405A LYS* 1.3 59.1 + - - +
406A HIS 2.9 4.5 - - - -
408A TYR* 2.8 38.1 + - - +
414A ARG* 4.2 11.9 - - + +
415A PHE* 3.9 31.0 - - + +
418A LEU* 3.7 30.5 - - - -
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Residues in contact with LYS 405 (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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401A GLU* 3.0 41.7 + - + +
402A ALA* 4.4 1.3 - - - +
404A CYS* 1.3 75.3 - - + +
406A HIS* 1.3 61.2 + - - +
408A TYR 4.5 4.7 - - - -
409A PRO* 3.8 17.2 - - - +
411A GLN 5.2 0.2 - - - -
412A PRO* 2.9 51.0 + - + +
413A GLY* 3.7 5.6 - - - +
415A PHE* 4.4 9.0 - - + -
297B LYS* 4.8 11.7 - - - +
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Residues in contact with HIS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ALA 2.7 21.7 + - - +
403A TYR* 3.6 16.8 - + - +
404A CYS 2.9 0.6 - - - -
405A LYS* 1.3 76.7 - - - +
407A LYS* 1.3 78.9 + - + +
409A PRO* 3.1 17.0 - - - +
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Residues in contact with LYS 407 (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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363A ASP* 5.3 0.8 + - - -
403A TYR* 2.9 42.8 + - + +
406A HIS* 1.3 89.5 - - + +
408A TYR* 1.3 88.3 + - + +
409A PRO* 3.0 8.9 - - - +
410A GLU* 4.6 1.7 - - - +
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Residues in contact with TYR 408 (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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360A MET 5.6 0.2 - - - -
361A GLN* 3.8 25.9 + - + -
363A ASP* 2.8 26.3 + - - +
366A GLU* 3.4 14.1 - - - -
403A TYR* 4.0 4.5 - + - -
404A CYS* 2.8 20.9 + - - +
405A LYS* 4.5 0.7 - - - -
407A LYS* 1.3 101.7 + - + +
409A PRO* 1.3 53.9 - - - +
410A GLU* 2.9 20.0 - - - +
411A GLN* 2.6 48.7 - - - +
414A ARG* 3.3 38.8 - - - -
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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
------------------------------------------------------------
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