Contacts of the strand formed by residues 396 - 405 (chain A) in PDB entry 4DGX
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 TYR 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A SER 5.3 0.4 - - - -
393A ALA* 3.0 49.5 + - + +
395A ASP* 1.3 89.9 - - + +
397A THR* 1.3 70.4 + - - +
398A LEU* 4.2 11.0 - - + -
418A TYR* 3.8 28.7 - + - -
419A HIS 2.9 23.1 - - - +
420A PHE* 3.8 4.5 - - - -
421A ARG* 3.9 8.0 - - - +
437A ASP* 5.4 3.1 - - + -
438A PHE* 3.6 33.9 - + + -
441A GLU* 3.9 21.0 - - + +
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Residues in contact with THR 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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390A GLU* 4.1 20.2 - - + +
391A SER 3.5 15.4 + - - +
392A ALA* 4.8 6.9 - - + +
396A TYR* 1.3 77.2 + - - +
398A LEU* 1.3 70.3 + - - +
399A ARG* 4.0 15.2 + - + +
417A GLN 3.4 1.7 - - - +
419A HIS* 2.8 42.9 + - - +
421A ARG* 3.5 32.6 + - - +
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Residues in contact with LEU 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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389A LYS 3.8 0.5 - - - +
390A GLU* 3.3 4.9 - - - -
391A SER* 2.9 52.9 + - - +
396A TYR* 4.0 17.8 - - + -
397A THR* 1.3 73.4 - - - +
399A ARG* 1.3 76.8 + - - +
400A GLU* 4.7 0.9 - - + +
416A TRP* 4.1 26.9 - - + -
417A GLN 3.3 18.2 - - - +
418A TYR* 3.8 34.8 - - + +
445A LYS* 5.3 1.6 - - - +
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Residues in contact with ARG 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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371A TRP* 3.2 41.6 - - - +
387A ASN* 3.8 4.9 - - - +
389A LYS 3.5 4.5 - - - +
390A GLU* 2.8 44.9 + - - -
397A THR* 4.1 11.7 - - + +
398A LEU* 1.3 79.3 - - - +
400A GLU* 1.3 62.2 + - - +
401A LEU* 3.6 13.7 + - + -
415A VAL 3.6 0.5 - - - +
416A TRP* 3.6 1.4 - - - -
417A GLN* 2.7 69.2 + - - +
419A HIS* 3.2 28.7 + - - +
421A ARG* 3.5 20.4 - - - +
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Residues in contact with GLU 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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387A ASN* 3.8 0.3 - - - +
388A VAL* 2.8 57.6 + - + +
389A LYS* 2.9 26.2 + - + +
398A LEU* 4.1 2.1 + - + +
399A ARG* 1.3 71.2 - - - +
401A LEU* 1.3 60.6 + - - +
402A LYS* 4.2 11.3 - - - -
414A THR* 3.6 25.5 + - + +
415A VAL 4.1 2.0 - - - -
416A TRP* 3.6 36.3 - - + -
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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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342A TRP* 3.8 28.9 - - + -
353A ILE* 5.1 3.4 - - + -
370A TYR* 5.6 0.7 - - + -
371A TRP* 4.4 15.3 - - + -
372A PRO* 4.8 0.2 - - + -
385A VAL* 3.9 12.6 - - + -
386A ARG 3.2 4.5 - - - +
387A ASN* 3.9 24.7 - - + +
399A ARG* 3.9 19.7 - - + +
400A GLU* 1.3 83.0 - - - +
402A LYS* 1.3 62.4 + - - +
403A LEU* 4.0 0.8 + - + -
414A THR* 3.3 5.1 - - - +
415A VAL* 2.6 51.5 + - + +
417A GLN* 4.0 25.6 - - + +
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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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377A LEU* 5.4 0.5 - - - +
384A ARG 3.4 6.8 - - - +
385A VAL* 3.4 2.0 - - - -
386A ARG* 2.9 42.7 + - + +
388A VAL* 3.4 29.1 - - + +
400A GLU* 4.2 9.6 + - - -
401A LEU* 1.3 72.8 - - - +
403A LEU* 1.3 60.5 + - - +
404A SER* 4.0 1.0 + - - -
412A GLU* 3.4 33.9 + - + +
413A ARG 3.5 5.8 - - - +
414A THR* 3.8 22.0 - - + +
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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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342A TRP* 3.8 13.0 - - + +
345A VAL* 3.8 30.1 - - + +
346A PHE* 4.0 27.1 - - + +
383A MET* 4.2 18.2 - - + -
384A ARG 3.4 3.4 - - - +
385A VAL* 3.4 26.5 - - + -
401A LEU* 4.0 1.6 + - + -
402A LYS* 1.3 71.9 - - - +
404A SER* 1.3 70.3 + - - +
411A THR 3.3 2.8 - - - +
412A GLU* 3.2 2.8 - - - -
413A ARG* 2.8 56.2 + - - +
415A VAL* 4.1 10.3 - - + -
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Residues in contact with SER 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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346A PHE* 4.7 2.9 - - - -
383A MET* 3.7 9.6 - - - +
384A ARG* 2.9 57.7 + - - +
402A LYS 5.0 1.0 + - - -
403A LEU* 1.3 76.6 - - - +
405A LYS* 1.3 65.5 + - - +
408A GLN 5.1 0.9 - - - -
409A GLY* 6.2 1.6 - - - -
410A ASN 6.1 0.2 - - - -
411A THR* 3.4 16.4 - - - -
412A GLU* 4.0 22.6 + - - -
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Residues in contact with LYS 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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294A ASP 5.5 6.9 + - - -
346A PHE* 4.3 19.3 - - + -
382A VAL* 3.5 33.5 - - + +
383A MET* 3.9 20.2 - - + +
384A ARG* 4.7 2.6 + - - -
404A SER* 1.3 78.8 + - - +
406A VAL* 1.3 70.1 + - - +
407A GLY 3.5 0.7 + - - -
408A GLN* 3.0 47.2 + - + +
411A THR* 2.6 26.9 + - + +
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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