Contacts of the helix formed by residues 391 - 404 (chain E) in PDB entry 6XAV
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 GLY 391 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361E ASN* 5.9 1.3 - - - -
389E PRO 3.9 1.0 + - - -
390E MET* 1.3 77.7 - - - +
392E GLU* 1.3 61.5 + - - -
393E ILE 3.4 2.2 - - - -
394E ASP* 3.8 19.6 + - - -
395E ALA* 2.8 27.7 + - - +
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Residues in contact with GLU 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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346E SER* 3.5 23.6 + - - -
348E LYS* 5.4 7.8 + - + +
349E ILE* 3.5 15.9 - - + +
359E ASP* 4.4 20.0 - - - +
361E ASN* 5.4 10.3 - - - +
391E GLY* 1.3 73.7 - - - +
393E ILE* 1.3 64.1 + - + +
395E ALA* 3.7 5.2 - - - +
396E MET* 3.3 27.7 + - - +
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Residues in contact with ILE 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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348E LYS* 4.1 31.0 - - + +
349E ILE* 4.1 24.2 - - + -
352E LYS* 3.4 42.0 - - + +
354E VAL* 5.7 2.5 - - + -
391E GLY 3.4 0.2 - - - -
392E GLU* 1.3 77.9 - - + +
394E ASP* 1.3 66.7 + - - +
396E MET* 3.3 5.4 + - + +
397E GLU* 3.1 32.3 + - + +
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Residues in contact with ASP 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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390E MET* 4.2 12.7 - - + +
391E GLY* 3.5 25.3 + - - +
392E GLU 3.3 0.4 - - - -
393E ILE* 1.3 83.6 - - - +
395E ALA* 1.3 57.4 + - - +
397E GLU* 3.8 14.6 - - - +
398E PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 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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360E TYR* 5.9 0.2 - - + -
361E ASN* 6.0 1.6 - - - +
387E ILE* 3.6 37.2 - - + +
390E MET* 4.4 5.6 - - - +
391E GLY 2.8 19.0 + - - +
392E GLU* 3.7 7.0 - - - +
393E ILE 3.2 0.2 - - - -
394E ASP* 1.3 79.1 - - - +
396E MET* 1.3 67.8 + - + +
398E PHE* 3.3 9.1 + - - +
399E LEU* 2.8 30.1 + - - +
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Residues in contact with MET 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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161E VAL* 6.0 0.9 - - + -
349E ILE* 3.7 23.8 - - + -
354E VAL* 3.8 19.5 - - + -
356E PRO 3.4 25.1 - - - +
357E ALA* 4.4 1.1 - - - -
358E ILE* 3.3 30.1 - - + +
360E TYR* 4.6 13.5 - - + +
387E ILE* 5.9 1.8 - - + -
392E GLU* 3.3 14.6 + - - +
393E ILE 3.3 6.2 + - - +
395E ALA* 1.3 92.4 - - + +
397E GLU* 1.3 57.8 + - - +
399E LEU* 3.2 19.8 + - + +
400E ILE* 2.9 37.5 + - + +
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Residues in contact with GLU 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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352E LYS* 3.3 26.5 + - - +
354E VAL* 5.6 8.3 - - + -
393E ILE* 3.1 25.4 + - + +
394E ASP* 3.9 12.3 - - - +
396E MET* 1.3 75.7 - - + +
398E PHE* 1.3 61.4 + - - +
400E ILE* 4.7 5.2 - - + -
401E ASN* 2.9 37.5 + - - +
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Residues in contact with PHE 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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383E LEU* 4.6 19.3 - - + -
386E ILE* 4.2 24.0 - - + -
387E ILE* 4.5 14.8 - - + -
390E MET* 4.1 31.0 - - + -
394E ASP 2.9 19.0 + - - +
395E ALA* 3.6 5.6 - - - +
397E GLU* 1.3 77.9 - - - +
399E LEU* 1.3 65.8 + - + +
401E ASN* 4.0 3.3 - - - +
402E LYS* 3.1 67.5 + - + +
412E PHE* 5.6 1.3 - + - -
416E MET* 5.0 11.7 - - + -
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Residues in contact with LEU 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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161E VAL* 3.7 36.3 - - + -
164E LEU* 5.3 6.1 - - + -
356E PRO* 5.8 1.6 - - + -
360E TYR* 5.4 8.1 - - + -
383E LEU* 5.2 13.9 - - + -
387E ILE* 5.1 14.8 - - + -
395E ALA 2.8 17.8 + - - +
396E MET* 3.2 22.9 + - + +
398E PHE* 1.3 79.7 - - + +
400E ILE* 1.3 61.8 + - + +
402E LYS* 3.3 5.0 + - + -
403E LEU* 2.9 59.8 + - + +
412E PHE* 5.7 3.8 - - + -
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Residues in contact with ILE 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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157E LEU* 6.4 2.0 - - + -
354E VAL* 3.8 29.8 - - + -
355E PHE 4.2 17.0 - - - +
356E PRO* 5.7 3.1 - - + -
396E MET* 2.9 18.8 + - + +
397E GLU* 4.1 6.1 - - + +
399E LEU* 1.3 78.8 - - + +
401E ASN* 1.3 68.9 + - - +
403E LEU* 3.4 5.9 + - + +
404E ALA* 3.0 28.3 + - + +
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Residues in contact with ASN 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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397E GLU* 2.9 25.2 + - - +
398E PHE* 4.1 4.9 - - - +
400E ILE* 1.3 83.6 - - - +
402E LYS* 1.3 68.9 + - - +
404E ALA* 3.8 8.7 + - - +
405E MET* 3.3 23.0 + - - +
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Residues in contact with LYS 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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398E PHE* 3.1 61.6 + - + +
399E LEU* 3.9 5.8 - - + +
400E ILE 3.2 0.2 - - - -
401E ASN* 1.3 83.4 - - - +
403E LEU* 1.3 64.6 + - + +
404E ALA 3.2 0.4 - - - -
405E MET* 3.3 24.3 + - + +
406E THR* 4.3 3.5 + - - +
412E PHE* 3.5 40.8 - - + -
416E MET* 4.5 15.0 - - - -
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Residues in contact with LEU 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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157E LEU* 4.9 18.7 - - + +
160E ARG* 3.4 40.8 + - + +
161E VAL* 3.9 20.9 - - + +
164E LEU* 4.9 5.8 - - + -
399E LEU* 2.9 48.8 + - + +
400E ILE* 4.2 5.4 - - + +
402E LYS* 1.3 76.6 - - - +
404E ALA* 1.3 58.2 + - - +
405E MET 3.2 0.2 - - - -
406E THR* 2.9 24.3 + - - +
409E ASN* 3.7 10.1 - - - +
412E PHE* 4.7 18.4 - - + -
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Residues in contact with ALA 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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400E ILE* 3.0 22.0 + - + +
401E ASN* 4.1 6.7 - - - +
402E LYS 3.2 0.6 - - - -
403E LEU* 1.3 75.7 - - - +
405E MET* 1.3 66.0 + - - +
406E THR 3.3 3.9 + - - +
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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