Contacts of the helix formed by residues 391 - 404 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361D ASN* 4.7 1.6 - - - -
389D PRO 4.0 0.4 + - - -
390D MET* 1.3 78.3 - - - +
392D GLU* 1.3 62.1 + - - -
393D ILE 3.4 2.5 - - - -
394D ASP* 3.8 17.2 + - - -
395D ALA* 2.8 28.6 + - - +
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Residues in contact with GLU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D SER* 3.1 26.5 + - - -
348D LYS* 5.3 5.8 - - - +
349D ILE* 3.5 13.5 - - + +
359D ASP* 3.4 26.3 - - - +
361D ASN* 3.4 24.9 + - - +
362D ARG* 5.4 2.4 - - - +
391D GLY* 1.3 73.4 - - - -
393D ILE* 1.3 64.5 + - + +
395D ALA* 3.4 5.2 + - - +
396D MET* 3.3 27.2 + - - +
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D LYS* 4.4 24.5 - - + +
349D ILE* 3.8 27.1 - - + -
352D LYS* 3.7 26.0 - - + +
354D VAL* 5.8 1.1 - - + -
391D GLY 3.4 0.2 - - - -
392D GLU* 1.3 77.3 - - + +
394D ASP* 1.3 68.1 + - - +
395D ALA 3.4 0.2 + - - -
396D MET* 3.4 5.2 + - - +
397D GLU* 3.2 42.0 + - + +
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Residues in contact with ASP 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D MET* 4.4 14.4 - - + +
391D GLY* 3.5 22.9 + - - +
392D GLU 3.3 0.2 - - - -
393D ILE* 1.3 83.7 - - - +
395D ALA* 1.3 57.5 + - - +
397D GLU* 3.6 14.5 + - - +
398D PHE* 3.0 30.0 + - - +
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D TYR* 5.4 5.4 - - + -
361D ASN* 5.1 4.0 - - - +
387D ILE* 3.6 34.3 - - + +
390D MET* 4.4 10.3 - - + +
391D GLY 2.8 20.0 + - - +
392D GLU* 3.6 8.1 - - - +
393D ILE 3.2 0.2 - - - -
394D ASP* 1.3 78.0 - - - +
396D MET* 1.3 61.5 + - + +
398D PHE* 3.3 4.0 + - - +
399D LEU* 2.8 30.0 + - - +
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Residues in contact with MET 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D VAL* 4.7 16.4 - - + -
349D ILE* 3.7 24.0 - - + -
354D VAL* 4.5 15.7 - - + -
356D PRO* 3.3 26.5 - - + +
358D ILE* 3.2 29.4 - - + +
360D TYR* 4.8 12.8 - - - -
392D GLU 3.3 14.4 + - - +
393D ILE 3.4 5.6 + - - +
395D ALA* 1.3 74.5 - - - +
397D GLU* 1.3 61.9 + - - +
399D LEU* 3.8 12.1 - - + +
400D ILE* 2.8 47.1 + - + +
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Residues in contact with GLU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D LYS* 2.7 35.2 + - - +
354D VAL* 5.5 10.1 - - + -
393D ILE* 3.2 24.6 + - + +
394D ASP* 4.0 13.5 - - - +
396D MET* 1.3 75.9 - - + +
398D PHE* 1.3 61.0 + - - +
400D ILE* 4.7 4.3 - - - -
401D ASN* 3.0 38.7 + - - +
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Residues in contact with PHE 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D LEU* 4.5 21.1 - - + -
386D ILE* 5.1 13.0 - - + -
387D ILE* 4.3 13.0 - - + -
390D MET* 3.9 30.1 - - + -
394D ASP 3.0 18.8 + - - +
395D ALA 3.6 2.5 - - - +
397D GLU* 1.3 77.5 - - - +
399D LEU* 1.3 65.6 + - + +
401D ASN* 4.0 3.2 - - - +
402D LYS* 3.2 66.4 + - + +
412D PHE* 5.3 4.0 - + - -
416D MET* 5.4 10.1 - - + -
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D VAL* 3.7 37.2 - - + -
164D LEU* 4.5 12.8 - - + -
360D TYR* 4.6 17.0 - - + -
383D LEU* 4.6 15.7 - - + -
387D ILE* 4.9 10.8 - - + -
395D ALA 2.8 21.1 + - - +
396D MET* 3.2 15.0 + - + +
398D PHE* 1.3 76.3 - - + +
400D ILE* 1.3 60.9 + - + +
402D LYS* 3.3 5.1 + - + -
403D LEU* 2.9 60.1 + - + +
412D PHE* 5.7 2.2 - - + -
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Residues in contact with ILE 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 5.4 14.6 - - + +
354D VAL* 3.8 28.0 - - + -
355D PHE 4.6 13.7 - - - +
356D PRO* 5.3 4.5 - - + -
396D MET* 2.8 37.1 + - + +
397D GLU* 4.3 2.9 - - - +
399D LEU* 1.3 72.6 - - + +
401D ASN* 1.3 66.8 + - - +
403D LEU* 3.4 5.4 + - - +
404D ALA* 3.0 34.6 + - + +
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Residues in contact with ASN 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D GLU* 3.0 24.5 + - - +
398D PHE* 4.1 4.3 - - - +
400D ILE* 1.3 84.8 - - - +
402D LYS* 1.3 69.7 + - - +
404D ALA* 3.8 4.9 + - - +
405D MET* 3.3 26.9 + - - +
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Residues in contact with LYS 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D PHE* 3.2 56.1 + - + +
399D LEU* 3.8 5.2 - - + +
400D ILE 3.2 0.2 - - - -
401D ASN* 1.3 82.0 - - - +
403D LEU* 1.3 66.2 + - + +
404D ALA 3.2 0.6 + - - -
405D MET* 3.4 21.7 + - + +
406D THR* 4.4 5.5 + - - +
412D PHE* 3.5 41.9 - - + -
416D MET* 5.5 4.9 - - - -
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 4.5 13.0 - - + +
160D ARG* 3.1 53.2 + - + +
161D VAL* 3.9 20.4 - - + +
164D LEU* 4.5 13.7 - - + -
399D LEU* 2.9 47.5 + - + +
400D ILE* 4.2 4.3 - - + +
402D LYS* 1.3 77.8 - - + +
404D ALA* 1.3 57.8 + - - +
405D MET 3.3 0.2 - - - -
406D THR* 2.9 21.3 + - - +
409D ASN* 4.3 7.0 - - - +
412D PHE* 4.6 18.6 - - + -
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Residues in contact with ALA 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 5.2 9.2 - - + +
400D ILE* 3.0 22.3 + - + +
401D ASN* 4.2 7.0 - - - +
402D LYS 3.2 0.4 - - - -
403D LEU* 1.3 76.3 - - - +
405D MET* 1.3 66.2 + - - +
406D THR 3.2 5.6 + - - +
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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