Contacts of the helix formed by residues 388 - 406 (chain E) in PDB entry 7V3X
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 388 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387E VAL* 1.3 77.6 - - - +
389E ASN* 1.3 58.9 + - - +
390E ASN* 4.0 7.0 + - - +
391E ALA* 3.1 23.9 + - - +
392E PHE* 3.0 27.8 + - - +
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Residues in contact with ASN 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E VAL 4.0 0.4 + - - -
388E SER* 1.3 72.0 - - - +
390E ASN* 1.3 64.1 + - - +
392E PHE* 3.6 7.3 + - - +
393E ARG* 2.9 30.8 + - - +
427E ASP 5.0 1.0 + - - -
428E SER* 3.3 40.8 + - - +
429E HIS* 4.7 9.6 - - - +
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Residues in contact with ASN 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E SER* 3.3 7.2 - - - +
389E ASN* 1.3 79.3 + - - +
391E ALA* 1.3 53.9 + - - +
393E ARG* 3.2 8.0 + - - +
394E GLN* 2.7 36.2 + - - +
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Residues in contact with ALA 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E ARG* 4.9 16.6 + - - +
356E LEU* 4.0 8.1 - - + +
387E VAL* 3.5 22.7 - - + -
388E SER* 3.1 20.1 + - - +
390E ASN* 1.3 73.6 - - - +
392E PHE* 1.3 56.7 + - - +
394E GLN* 3.2 10.4 + - - +
395E PHE* 2.9 33.1 + - - +
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Residues in contact with PHE 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E LEU* 4.0 11.3 - - + +
380E LEU* 3.2 43.7 - - + -
381E SER* 4.6 1.6 - - - -
383E LEU* 4.1 10.5 - - + -
384E ALA* 3.4 34.8 - - + +
387E VAL* 5.3 1.8 - - + +
388E SER 3.0 17.2 + - - +
389E ASN* 3.6 9.6 - - - +
391E ALA* 1.3 76.0 - - - +
393E ARG* 1.3 59.4 + - - +
395E PHE* 3.1 11.4 + + - +
396E VAL* 2.9 52.7 + - + +
414E ASN* 5.6 0.7 - - - -
428E SER* 3.4 37.7 - - - -
430E ILE* 4.4 9.0 - - + -
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Residues in contact with ARG 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E ASN* 2.9 22.8 + - - +
390E ASN* 3.4 7.0 - - - +
392E PHE* 1.3 77.9 - - + +
394E GLN* 1.3 57.2 - - - +
396E VAL* 3.1 9.7 + - - +
397E ILE* 2.9 38.5 + - + +
428E SER 5.7 0.4 - - - +
430E ILE* 4.7 13.9 - - + -
433E ILE* 5.6 2.0 - - + -
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Residues in contact with GLN 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ARG* 3.3 29.3 + - - +
234E GLU 5.6 3.2 + - - -
236E PRO* 3.9 14.9 - - - +
249E LEU* 4.2 25.6 - - + +
360E LEU* 5.8 0.5 - - - +
390E ASN 2.7 17.2 + - - +
391E ALA* 3.2 11.9 + - - +
393E ARG* 1.3 71.3 - - - +
395E PHE* 1.3 60.6 + - - +
397E ILE* 3.8 8.1 + - + +
398E GLY* 3.2 17.7 + - - -
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Residues in contact with PHE 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E LEU* 3.9 32.8 - - + -
359E HIS* 4.1 7.2 - - + -
360E LEU* 3.7 42.6 - - + +
363E ILE* 4.0 13.2 - - + -
377E ILE* 5.3 0.7 - - + -
380E LEU* 4.3 10.5 - - + -
383E LEU* 3.4 34.5 - - + -
391E ALA 2.9 12.3 + - - +
392E PHE* 3.1 16.4 + + - +
394E GLN* 1.3 73.2 + - - +
396E VAL* 1.3 63.2 + - + +
398E GLY* 2.9 5.4 + - - -
399E VAL* 2.9 59.1 + - + +
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Residues in contact with VAL 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E LEU* 4.3 17.0 - - + -
392E PHE* 2.9 54.2 + - + +
393E ARG* 3.6 8.1 - - - +
395E PHE* 1.3 81.5 - - + +
397E ILE* 1.3 54.4 + - - +
399E VAL* 3.2 4.1 + - - +
400E THR* 2.7 52.6 + - - +
430E ILE* 4.5 19.3 - - + -
433E ILE* 4.4 21.1 - - + -
434E THR* 6.4 1.1 - - + -
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Residues in contact with ILE 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E LEU 6.0 1.6 - - - +
252E MET* 6.5 0.9 - - + -
393E ARG* 2.9 24.9 + - + +
394E GLN* 3.9 8.3 - - + +
396E VAL* 1.3 74.3 - - - +
398E GLY* 1.3 58.1 + - - +
400E THR* 4.2 3.3 - - - -
401E GLY* 2.9 27.7 + - - -
433E ILE* 3.8 36.1 - - + -
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Residues in contact with GLY 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E LEU* 4.4 18.7 - - - +
364E LYS* 4.8 2.9 - - - -
394E GLN 3.2 8.6 + - - -
395E PHE 2.9 8.9 + - - -
397E ILE* 1.3 76.7 - - - +
399E VAL* 1.3 58.2 + - - +
401E GLY* 3.9 0.7 - - - -
402E TYR* 3.0 29.5 + - - +
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Residues in contact with VAL 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E LEU* 4.2 14.3 - - + +
363E ILE* 4.8 12.6 - - + -
367E ILE* 6.2 1.7 - - + +
377E ILE* 3.7 13.7 - - + -
380E LEU* 5.9 0.4 - - + -
395E PHE* 2.9 61.9 + - + +
396E VAL* 3.7 6.1 - - - +
398E GLY* 1.3 69.4 - - - +
400E THR* 1.3 55.8 + - - +
402E TYR* 3.1 7.5 + - - +
403E ALA* 2.9 32.8 + - + +
412E PHE* 3.6 28.9 - - + -
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Residues in contact with THR 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E ILE* 3.3 49.0 - - + +
380E LEU* 5.8 0.2 - - - +
396E VAL* 2.7 40.1 + - - +
397E ILE 4.2 1.3 - - - -
399E VAL* 1.3 73.4 - - - +
401E GLY* 1.3 52.2 + - - +
403E ALA* 3.6 2.2 - - - +
404E LYS* 2.9 41.8 + - + +
412E PHE* 4.3 14.1 - - - -
433E ILE* 4.0 23.6 - - + +
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Residues in contact with GLY 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLN* 4.7 11.2 - - - +
397E ILE 2.9 19.3 + - - -
398E GLY 3.9 0.9 - - - -
400E THR* 1.3 73.6 - - - +
402E TYR* 1.3 53.5 + - - +
404E LYS* 3.2 8.4 + - - +
405E GLN* 2.7 39.3 + - - +
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Residues in contact with TYR 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E LEU* 5.5 0.2 - - + -
363E ILE* 6.1 0.2 - - + -
364E LYS* 3.8 52.3 + - + +
367E ILE* 3.8 42.8 - - + +
368E ASN* 4.3 13.2 - - - +
398E GLY 3.0 15.7 + - - +
399E VAL* 3.4 8.7 - - - +
401E GLY* 1.3 69.5 - - - +
403E ALA* 1.3 60.7 + - - +
405E GLN* 3.2 24.0 + - + +
406E GLU* 2.9 58.8 + - + +
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Residues in contact with ALA 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E ILE* 4.1 11.4 - - + -
367E ILE* 5.7 4.9 - - + +
375E ILE* 5.8 4.5 - - + -
399E VAL* 2.9 13.1 + - + +
400E THR* 3.6 10.5 - - - +
402E TYR* 1.3 75.9 - - - +
404E LYS* 1.3 57.4 + - - +
406E GLU* 3.4 3.5 + - - -
407E GLU 3.1 8.0 + - - -
408E ILE* 2.9 56.9 + - + +
410E GLY* 5.1 3.1 - - - -
412E PHE* 4.8 9.0 - - + -
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Residues in contact with LYS 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLN* 3.6 43.1 - - + +
257E ARG 4.5 5.2 + - - +
281E ASP* 5.5 8.1 - - - +
282E SER* 5.3 5.6 - - - +
283E ILE* 3.5 18.8 - - + -
400E THR* 2.9 26.7 + - - +
401E GLY 3.2 5.6 + - - +
403E ALA* 1.3 75.9 - - - +
405E GLN* 1.3 60.9 + - - +
407E GLU* 3.3 16.7 + - - +
408E ILE 5.2 0.7 - - - -
433E ILE 4.6 8.6 + - - -
435E ASP* 3.1 39.1 + - - -
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Residues in contact with GLN 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E MET* 5.7 5.4 - - - +
255E THR 6.0 0.4 - - - -
256E GLN* 3.8 22.2 - - + +
257E ARG 5.5 1.3 + - - +
401E GLY 2.7 19.3 + - - +
402E TYR* 3.4 33.5 - - + +
404E LYS* 1.3 73.2 - - - +
406E GLU* 1.3 67.8 + - - +
407E GLU* 3.4 5.2 + - - +
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Residues in contact with GLU 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ILE* 5.1 3.1 - - + -
402E TYR* 2.9 49.0 + - + +
403E ALA 4.0 0.2 - - - +
405E GLN* 1.3 84.5 + - - +
407E GLU* 1.3 72.4 - - - +
408E ILE* 3.3 28.9 + - + +
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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