Contacts of the helix formed by residues 385 - 395 (chain A) in PDB entry 4KKA
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 GLU 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A LEU* 3.7 22.7 - - - +
245A SER* 2.6 48.9 + - - +
324A THR 5.1 3.7 - - - +
325A ALA* 6.0 1.4 - - - -
376A VAL* 4.2 2.5 - - - -
383A HIS 4.0 0.4 + - - +
384A LEU* 1.3 74.4 - - - +
386A ALA* 1.3 67.4 + - - +
387A GLY* 3.0 10.1 + - - +
388A THR* 3.1 23.2 + - + +
389A PHE* 3.6 4.4 - - - -
54C VAL* 5.6 7.1 - - - +
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Residues in contact with ALA 386 (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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326A GLY* 5.6 5.6 - - - -
369A THR* 3.8 18.4 - - + +
372A GLY* 3.4 36.5 - - - +
373A MET* 3.4 16.8 - - + +
376A VAL* 3.8 7.8 - - + +
385A GLU* 1.3 73.2 - - - +
387A GLY* 1.3 57.5 + - - +
389A PHE* 3.0 22.1 + - - +
390A ALA 3.1 9.0 + - - -
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Residues in contact with GLY 387 (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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244A LEU* 3.3 22.1 - - - +
323A ALA 5.3 0.4 - - - -
324A THR* 3.2 37.4 + - - +
326A GLY* 6.0 0.2 - - - -
385A GLU* 3.0 5.5 - - - +
386A ALA* 1.3 77.3 - - - +
388A THR* 1.3 62.2 + - - +
390A ALA* 3.6 4.9 + - - -
391A ILE* 3.3 17.3 + - - +
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Residues in contact with THR 388 (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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244A LEU* 3.8 10.5 - - + +
245A SER* 3.6 33.9 - - - +
246A ASP 4.7 3.8 - - - +
255A TYR* 2.7 28.4 + - - +
384A LEU* 5.4 1.2 - - - +
385A GLU* 3.1 18.5 + - + +
387A GLY* 1.3 76.3 - - - +
389A PHE* 1.3 64.0 + - - +
391A ILE* 3.3 3.1 + - - +
392A ALA* 3.1 26.7 + - - +
421A LEU* 3.7 28.8 - - + +
424A PRO* 5.6 0.3 - - - +
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Residues in contact with PHE 389 (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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251A THR* 5.3 0.2 - - - -
254A LEU* 3.9 23.1 - - + -
255A TYR* 3.4 40.8 - + - -
258A LEU* 3.7 7.2 - - + +
368A GLY* 3.4 26.8 - - - +
371A PHE* 3.7 22.0 - + + -
372A GLY* 3.5 22.9 - - - +
375A ALA* 4.2 4.0 - - + -
384A LEU* 3.9 39.0 - - + -
385A GLU 3.6 11.9 - - - -
386A ALA 3.0 5.7 + - - +
388A THR* 1.3 89.8 - - - +
390A ALA* 1.3 63.7 + - - +
392A ALA* 4.4 0.9 - - - +
393A GLY 3.0 16.6 + - - -
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Residues in contact with ALA 390 (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 THR* 4.1 16.6 - - - +
365A THR* 3.7 21.3 + - + +
368A GLY* 3.9 0.4 - - - -
369A THR* 3.2 37.1 - - - +
386A ALA 3.1 8.2 + - - +
387A GLY* 3.7 9.4 - - - +
388A THR 3.3 0.2 - - - -
389A PHE* 1.3 76.6 - - - +
391A ILE* 1.3 56.1 + - - +
393A GLY 3.2 1.6 + - - -
394A MET* 2.9 29.5 + - - +
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Residues in contact with ILE 391 (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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241A VAL* 3.6 20.4 - - + -
244A LEU* 4.5 4.7 - - + -
324A THR* 4.3 10.1 - - + +
387A GLY 3.3 15.1 + - - +
388A THR 3.3 3.3 + - - +
389A PHE 3.2 0.6 - - - -
390A ALA* 1.3 76.1 - - - +
392A ALA* 1.3 64.1 + - - +
394A MET* 3.6 12.3 + - - +
395A GLY 4.5 1.2 + - - -
412A VAL* 3.7 15.1 - - + +
416A THR* 3.6 41.1 - - + +
418A ASN* 4.2 15.7 - - + -
421A LEU* 4.0 20.0 - - + -
425A MET* 4.0 24.6 - - + +
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Residues in contact with ALA 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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255A TYR* 3.7 22.0 - - + -
258A LEU* 4.4 2.0 - - + -
388A THR 3.1 13.4 + - - +
389A PHE 4.0 3.6 - - - +
390A ALA 3.4 0.2 - - - -
391A ILE* 1.3 77.9 - - - +
393A GLY* 1.3 61.9 + - - +
394A MET 3.6 0.3 + - - -
395A GLY 4.2 5.0 + - - -
396A ALA* 3.9 5.7 + - - +
421A LEU* 6.6 0.2 - - + -
424A PRO* 4.0 10.3 - - + +
425A MET* 4.1 16.6 - - + +
428A THR* 3.5 35.9 - - - +
429A GLY 5.3 0.5 + - - -
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Residues in contact with GLY 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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258A LEU* 4.2 3.1 - - - -
262A PHE* 3.3 17.7 - - - -
364A GLY* 3.1 26.9 - - - -
368A GLY* 4.6 0.4 - - - -
389A PHE 3.0 17.0 + - - -
390A ALA 3.6 2.5 - - - -
391A ILE 3.2 0.2 - - - -
392A ALA* 1.3 77.6 - - - +
394A MET* 1.3 63.0 + - - +
395A GLY 3.4 0.4 - - - -
396A ALA* 3.2 19.0 + - - -
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Residues in contact with MET 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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239A ILE* 3.9 7.2 - - + -
320A ILE* 4.1 16.6 - - - -
360A MET 3.8 6.4 - - - +
361A LEU* 3.7 32.4 - - + +
364A GLY* 4.4 0.3 - - - -
365A THR* 3.3 29.4 - - - +
390A ALA 2.9 12.5 + - - +
391A ILE* 3.8 13.2 - - - +
392A ALA 3.4 0.8 - - - -
393A GLY* 1.3 79.1 - - - +
395A GLY* 1.3 57.9 + - - +
396A ALA 3.4 1.6 + - - -
397A LEU 4.6 1.0 + - - -
398A LEU* 4.8 1.4 - - - +
412A VAL* 3.7 23.8 - - + -
415A MET* 3.5 31.6 - - + -
416A THR* 3.5 32.5 - - + -
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Residues in contact with GLY 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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391A ILE 4.5 0.8 + - - -
392A ALA 4.2 5.4 + - - -
393A GLY 3.4 0.2 - - - -
394A MET* 1.3 78.0 - - - +
396A ALA* 1.3 57.7 + - - +
397A LEU 3.6 1.1 - - - -
398A LEU* 3.6 18.2 - - - +
399A ALA* 3.2 23.0 + - - +
405A PRO* 5.4 0.3 - - - +
408A GLY* 4.4 14.8 - - - -
409A ILE* 5.2 2.1 + - - +
412A VAL* 3.5 19.1 - - - +
429A GLY* 5.4 1.7 - - - -
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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