Contacts of the strand formed by residues 400 - 405 (chain A) in PDB entry 3K72
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 SER 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.5 3.9 - - - +
393A ALA* 2.9 50.7 + - - +
395A TRP* 5.8 3.6 - - - -
398A VAL* 4.2 4.7 + - - +
399A GLN* 1.3 83.9 + - - +
401A LEU* 1.3 63.5 + - - +
416A ILE* 4.6 5.2 - - - -
417A PHE 3.6 12.5 + - - -
418A THR* 4.7 1.6 - - - +
419A GLN* 5.8 1.3 - - - +
427A LYS* 3.6 29.4 + - - +
478A LEU* 5.6 3.5 - - - +
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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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340A VAL* 4.7 9.0 - - + -
342A THR* 5.1 3.8 - - + -
347A VAL* 3.9 43.5 - - + -
360A ALA* 5.1 2.5 - - + +
362A LEU* 5.2 2.9 - - + -
372A ILE* 3.9 28.7 - - + -
390A THR* 6.3 1.1 - - - -
391A GLU 3.8 11.0 - - - +
392A LEU* 4.5 13.5 - - + -
399A GLN* 6.4 0.7 - - + -
400A SER* 1.3 74.7 - - - +
402A VAL* 1.3 73.1 + - - +
403A LEU* 5.1 5.8 - - + -
416A ILE* 3.4 1.6 - - - +
417A PHE* 2.9 36.9 + - + +
419A GLN* 4.0 21.4 - - + +
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Residues in contact with VAL 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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389A SER 3.6 0.5 - - - +
390A THR* 3.3 4.3 - - - -
391A GLU* 3.2 36.5 + - + +
392A LEU 5.2 1.6 - - - +
393A ALA* 4.8 12.8 - - + -
401A LEU* 1.3 85.3 - - - +
403A LEU* 1.3 75.7 + - - +
414A ALA* 5.2 1.1 - - + -
415A VAL 3.7 12.6 - - - +
416A ILE* 3.7 30.5 - - + -
417A PHE* 5.2 0.2 - - - -
443A LEU* 3.1 35.3 - - + +
457A VAL* 5.3 11.4 - - + -
478A LEU* 5.7 0.4 - - + -
485A TRP* 6.5 0.4 - - + -
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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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347A VAL* 5.9 0.7 - - + -
359A GLY* 4.1 21.1 - - - +
360A ALA* 4.1 15.7 - - + +
372A ILE* 4.7 6.1 - - + +
386A LEU* 3.5 30.7 - - + +
387A GLY* 3.7 8.7 - - - +
389A SER 3.4 3.1 - - - -
390A THR* 3.5 23.3 - - + -
401A LEU* 5.1 7.4 - - + -
402A VAL* 1.3 96.0 - - - +
404A GLY* 1.3 60.4 + - - +
405A ALA 4.0 0.3 + - - -
414A ALA* 3.8 3.1 - - - +
415A VAL 3.1 30.5 + - - +
417A PHE* 3.5 30.3 - - + -
443A LEU* 4.8 1.3 - - - -
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A TYR 3.1 15.2 - - - +
387A GLY 3.4 2.9 + - - +
388A TYR* 3.3 8.5 + - - +
389A SER* 3.0 17.9 + - - -
403A LEU* 1.3 73.1 - - - +
405A ALA* 1.3 59.3 + - - -
406A PRO* 3.0 16.6 - - - +
413A LYS 4.4 0.9 - - - -
414A ALA* 4.9 0.7 - - - -
440A GLY* 3.4 22.4 - - - -
443A LEU* 3.9 5.8 - - - +
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Residues in contact with ALA 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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381A MET* 5.5 4.9 - - + -
384A SER* 3.1 29.8 - - - +
386A LEU* 4.1 18.2 - - + +
403A LEU 4.0 0.4 + - - -
404A GLY* 1.3 73.6 - - - -
406A PRO* 1.3 64.0 - - - +
407A ARG 2.9 4.8 + - - -
408A TYR* 3.4 6.8 + - + -
412A GLY* 3.2 0.3 - - - -
413A LYS* 2.9 42.1 + - + +
414A ALA* 5.4 0.2 - - - -
415A VAL* 5.6 1.3 - - + -
439A PHE 4.2 1.3 - - - -
440A GLY* 4.3 1.0 - - - -
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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