Contacts of the helix formed by residues 394 - 408 (chain A) in PDB entry 4X61
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ASN* 3.4 16.9 - - - +
319A LEU 3.1 32.9 + - - +
324A TYR* 2.9 28.7 + - - +
392A GLU* 2.7 23.2 + - + +
393A LYS* 1.3 71.0 - - - +
395A PRO* 1.4 66.3 - - - +
396A ASN* 3.0 28.9 + - - +
397A ALA* 2.9 18.4 + - + +
398A VAL* 3.0 14.0 + - - +
701A SAM 3.7 4.5 + - - +
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Residues in contact with PRO 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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318A ASN* 3.7 14.6 - - - +
393A LYS 3.0 13.1 - - - +
394A ASN* 1.4 85.8 - - - +
396A ASN* 1.3 70.6 + - - +
398A VAL* 3.4 15.1 - - + +
399A VAL* 3.2 25.0 + - - +
417A SER* 4.6 8.1 - - - +
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Residues in contact with ASN 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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318A ASN* 3.7 20.6 - - - +
319A LEU 5.3 3.6 + - - +
394A ASN* 3.0 23.2 + - - +
395A PRO* 1.3 85.3 - - - +
397A ALA* 1.3 58.1 + - - +
399A VAL* 3.2 26.3 - - - +
400A THR* 3.9 4.7 + - - -
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Residues in contact with ALA 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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324A TYR* 3.9 28.9 - - + +
367A GLY 3.4 28.0 - - - +
368A ARG* 4.5 4.3 - - + +
392A GLU* 4.4 2.9 - - + -
394A ASN* 2.9 11.2 + - + +
396A ASN* 1.3 73.6 - - - +
398A VAL* 1.3 54.4 + - - +
399A VAL 2.9 4.7 - - - -
400A THR* 2.7 31.7 + - - -
401A LEU* 3.0 13.2 + - - +
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Residues in contact with VAL 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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392A GLU* 3.5 37.0 - - + +
394A ASN 3.0 19.8 + - - +
395A PRO* 3.4 12.8 - - + +
396A ASN 3.3 0.2 - - - -
397A ALA* 1.3 75.0 - - - +
399A VAL* 1.3 60.4 + - + +
401A LEU* 3.8 10.5 - - + -
402A GLU* 3.1 42.6 + - + +
415A VAL* 4.6 5.8 - - + -
416A VAL 4.9 0.7 - - - +
417A SER* 3.5 32.3 - - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PRO 3.2 14.7 + - - +
396A ASN* 3.2 15.3 - - - +
397A ALA 2.9 0.2 - - - -
398A VAL* 1.3 78.5 - - - +
400A THR* 1.3 65.2 + - - +
402A GLU* 3.4 5.4 + - - +
403A ASN* 3.0 36.7 + - - +
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Residues in contact with THR 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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368A ARG* 4.1 39.7 + - + +
396A ASN 4.1 3.1 + - - -
397A ALA* 2.7 22.2 + - - -
399A VAL* 1.3 76.9 - - - +
401A LEU* 1.3 56.6 + - - -
403A ASN* 3.3 7.0 + - + +
404A TRP* 2.8 47.3 + - + +
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Residues in contact with LEU 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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366A ALA* 3.9 15.9 - - + -
367A GLY 3.3 27.4 - - - +
368A ARG 3.6 3.6 - - - +
369A GLY* 3.5 27.6 - - - +
372A VAL* 5.0 1.1 - - + -
390A ALA* 4.3 5.4 - - + +
392A GLU* 3.7 26.5 - - + -
397A ALA 3.0 7.7 + - - +
398A VAL* 3.8 11.0 - - + +
399A VAL 3.2 0.2 - - - -
400A THR* 1.3 77.4 - - - +
402A GLU* 1.3 51.4 + - - +
404A TRP* 3.2 7.1 + - - +
405A GLN* 2.8 35.5 + - - +
409A TRP* 3.8 12.7 - - + -
415A VAL* 3.7 28.0 - - + -
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Residues in contact with GLU 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 VAL* 3.1 31.8 + - - +
399A VAL* 3.4 5.0 + - - +
401A LEU* 1.3 78.4 - - - +
403A ASN* 1.3 59.2 + - - +
405A GLN* 3.7 11.0 - - + +
406A PHE* 3.1 28.9 + - - +
415A VAL* 3.9 27.2 - - + +
417A SER* 5.3 4.0 - - - -
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Residues in contact with ASN 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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399A VAL* 3.0 34.9 + - - +
400A THR* 3.7 7.0 - - + +
402A GLU* 1.3 77.8 - - - +
404A TRP* 1.3 63.3 + - - +
406A PHE* 4.9 2.2 - - - -
407A GLU* 3.2 48.5 + - - +
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Residues in contact with TRP 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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368A ARG 3.7 22.4 + - - -
373A ASN* 3.8 23.8 - - - -
400A THR* 2.8 33.3 + - + +
401A LEU 3.4 8.3 - - - +
403A ASN* 1.3 72.5 - - - +
405A GLN* 1.3 57.8 + - - +
407A GLU* 5.0 1.1 - - - -
408A GLU* 2.8 64.3 + - + +
409A TRP* 3.3 50.9 + + + -
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Residues in contact with GLN 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 LEU 2.8 17.9 + - - +
402A GLU* 3.7 12.6 - - + +
403A ASN 3.3 0.2 - - - -
404A TRP* 1.3 74.5 - - - +
406A PHE* 1.3 73.3 + - - +
409A TRP* 3.5 25.0 + - + -
410A GLY* 2.8 47.8 + - - +
411A SER* 4.7 1.6 - - - +
413A VAL 2.7 28.8 + - - +
414A THR* 5.0 0.6 - - - +
415A VAL* 3.7 18.7 - - + +
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Residues in contact with PHE 406 (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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402A GLU 3.1 18.3 + - - +
403A ASN* 4.3 3.8 - - - +
405A GLN* 1.3 88.9 - - + +
407A GLU* 1.3 73.6 + - + +
408A GLU 5.3 0.2 - - - -
410A GLY* 5.3 1.7 + - - -
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Residues in contact with GLU 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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403A ASN* 3.2 38.4 + - - +
404A TRP* 4.8 0.7 - - - -
406A PHE* 1.3 89.5 - - + +
408A GLU* 1.3 82.6 + - + +
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Residues in contact with GLU 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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404A TRP* 2.8 45.7 + - + +
406A PHE 3.4 1.0 - - - -
407A GLU* 1.3 100.0 - - + +
409A TRP* 1.3 67.7 + - + +
410A GLY* 3.4 2.5 + - - -
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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