Contacts of the helix formed by residues 391 - 404 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ASN* 5.2 2.4 + - - -
389A PRO 3.9 0.6 + - - -
390A MET* 1.3 77.9 - - - +
392A GLU* 1.3 61.6 + - - -
393A ILE 3.5 2.0 - - - -
394A ASP* 3.9 19.8 + - - +
395A ALA* 2.9 26.7 + - - +
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Residues in contact with GLU 392 (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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346A SER* 3.1 23.5 + - - -
348A LYS* 5.1 9.4 + - + +
349A ILE* 3.9 14.8 - - + +
359A ASP* 3.6 30.2 - - - +
361A ASN* 4.9 10.1 - - - +
391A GLY* 1.3 73.4 - - - +
393A ILE* 1.3 65.8 + - + +
395A ALA* 3.4 4.1 + - - +
396A MET* 3.3 27.5 + - - +
283F LYS* 5.8 2.4 + - - -
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Residues in contact with ILE 393 (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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348A LYS* 3.8 34.3 - - + +
349A ILE* 4.5 16.4 - - + -
352A LYS* 3.4 42.2 - - + +
354A VAL* 6.1 2.2 - - + -
392A GLU* 1.3 74.7 - - + +
394A ASP* 1.3 71.4 + - - +
396A MET* 3.3 6.3 + - + +
397A GLU* 3.0 37.2 + - + +
295F HIS* 6.1 0.4 - - + -
298F LYS* 5.9 4.5 - - - +
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Residues in contact with ASP 394 (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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390A MET* 4.3 13.0 - - + +
391A GLY* 3.6 24.7 + - - +
392A GLU 3.3 0.2 - - - -
393A ILE* 1.3 82.6 - - - +
395A ALA* 1.3 58.4 + - - +
397A GLU* 4.0 12.3 - - - +
398A PHE* 3.0 28.9 + - - +
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Residues in contact with ALA 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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360A TYR* 5.6 3.1 - - + -
361A ASN* 5.9 1.6 - - - +
387A ILE* 3.7 37.0 - - + +
390A MET* 4.0 14.3 - - + +
391A GLY 2.9 19.3 + - - +
392A GLU* 3.8 4.9 - - - +
393A ILE 3.2 0.4 - - - -
394A ASP* 1.3 76.1 - - - +
396A MET* 1.3 64.8 + - + +
398A PHE* 3.3 3.1 + - - +
399A LEU* 2.8 30.5 + - - +
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Residues in contact with MET 396 (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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161A VAL* 5.1 10.1 - - + -
349A ILE* 3.8 21.8 - - + -
354A VAL* 4.5 15.7 - - + -
356A PRO* 3.2 30.5 - - + +
357A ALA* 5.1 0.2 - - - -
358A ILE* 3.4 22.7 - - - +
360A TYR* 5.3 9.2 - - - -
392A GLU 3.3 17.3 + - - +
393A ILE* 3.3 5.6 + - + +
395A ALA* 1.3 78.1 - - - +
397A GLU* 1.3 60.0 + - + +
399A LEU* 3.2 19.1 + - + +
400A ILE* 2.8 48.4 + - + +
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Residues in contact with GLU 397 (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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352A LYS* 3.6 12.8 + - - -
354A VAL* 6.2 5.2 - - + -
393A ILE* 3.0 36.5 + - + +
394A ASP* 4.0 11.2 - - - +
396A MET* 1.3 76.1 - - + +
398A PHE* 1.3 61.4 + - - +
400A ILE* 4.7 4.3 - - + -
401A ASN* 3.0 39.5 + - - +
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Residues in contact with PHE 398 (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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383A LEU* 4.9 13.0 - - + -
386A ILE* 4.9 12.1 - - + -
387A ILE* 4.9 6.5 - - + -
390A MET* 3.8 30.3 - - + -
394A ASP 3.0 19.8 + - - +
395A ALA 3.6 3.6 - - - +
397A GLU* 1.3 77.2 - - - +
399A LEU* 1.3 66.0 + - + +
401A ASN* 4.1 3.5 - - - +
402A LYS* 3.2 75.0 + - + +
412A PHE* 5.4 1.8 - + - -
416A MET* 4.6 23.8 - - + -
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Residues in contact with LEU 399 (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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161A VAL* 3.7 37.9 - - + -
164A LEU* 4.7 9.2 - - + -
360A TYR* 4.6 16.2 - - + -
383A LEU* 5.0 7.6 - - + -
387A ILE* 5.1 10.1 - - + -
395A ALA 2.8 19.1 + - - +
396A MET* 3.8 15.9 - - + +
398A PHE* 1.3 80.1 - - + +
400A ILE* 1.3 61.4 + - + +
402A LYS* 3.4 2.0 + - - -
403A LEU* 3.0 59.7 + - + +
412A PHE* 4.6 16.6 - - + -
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Residues in contact with ILE 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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157A LEU* 5.2 17.5 - - + +
354A VAL* 3.8 28.5 - - + -
355A PHE 4.7 11.7 - - - +
356A PRO* 5.8 2.9 - - + -
396A MET* 2.8 36.0 + - + +
397A GLU* 4.2 4.7 - - - +
399A LEU* 1.3 73.7 - - + +
401A ASN* 1.3 66.6 + - - +
403A LEU* 3.8 5.0 - - + +
404A ALA* 2.9 34.1 + - + +
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Residues in contact with ASN 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 GLU* 3.0 25.6 + - - +
398A PHE* 4.1 5.1 - - - +
400A ILE* 1.3 85.2 - - - +
402A LYS* 1.3 69.4 + - - +
404A ALA* 3.8 5.5 + - - +
405A MET* 3.3 26.9 + - - +
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Residues in contact with LYS 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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398A PHE* 3.2 58.7 + - + +
399A LEU* 3.9 2.9 - - - +
400A ILE 3.2 0.2 - - - -
401A ASN* 1.3 85.2 - - - +
403A LEU* 1.3 62.6 + - - +
404A ALA 3.6 0.2 + - - -
405A MET* 3.6 20.3 + - + +
406A THR* 4.4 6.8 + - - +
412A PHE* 3.6 34.6 - - + -
415A MET* 6.6 0.2 - - + -
416A MET* 5.3 6.1 - - - -
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Residues in contact with LEU 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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157A LEU* 4.4 15.2 - - + +
160A ARG* 3.4 49.7 + - + +
161A VAL* 4.0 19.1 - - + -
164A LEU* 4.6 10.5 - - + -
399A LEU* 3.0 44.9 + - + +
400A ILE* 4.2 4.0 - - - +
402A LYS* 1.3 75.4 - - - +
404A ALA* 1.3 60.2 + - - +
405A MET 3.2 0.2 - - - -
406A THR* 2.8 23.3 + - - +
409A ASN* 4.8 1.8 - - - +
412A PHE* 3.9 31.4 - - + -
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Residues in contact with ALA 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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157A LEU* 5.4 8.0 - - + +
400A ILE* 2.9 22.8 + - + +
401A ASN* 4.2 7.2 - - - +
402A LYS 3.3 0.6 - - - -
403A LEU* 1.3 76.7 - - - +
405A MET* 1.3 65.1 + - - +
406A THR 3.2 5.3 + - - +
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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