Contacts of the helix formed by residues 386 - 396 (chain A) in PDB entry 1K79
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 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 3.7 25.6 - - + -
368A PRO* 3.4 38.4 - - + +
369A ASP* 4.4 10.8 + - - +
372A ALA* 3.3 9.5 - - - +
385A ASN* 1.3 73.0 - - - +
387A GLU* 1.3 64.4 + - + +
389A LEU* 4.0 10.1 - - + -
390A SER* 2.9 40.6 + - - -
410A TYR* 3.9 21.2 - + - -
412A TYR* 2.7 29.1 + + - -
5B G 4.7 15.9 - - + -
6B C 2.5 30.4 + - - -
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Residues in contact with GLU 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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385A ASN* 2.8 20.2 + - - +
386A TYR* 1.3 80.8 - - + +
388A LYS* 1.3 62.9 + - + +
390A SER* 3.0 20.4 + - - -
391A ARG* 3.3 8.8 + - - +
394A ARG* 4.5 3.6 + - - -
5B G 5.5 7.0 - - - +
6B C 5.7 8.5 + - + +
9C C 5.9 3.6 + - - -
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Residues in contact with LYS 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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383A LYS* 2.5 40.7 + - - +
384A MET* 3.9 13.5 - - + -
385A ASN* 2.9 28.6 + - - +
387A GLU* 1.3 72.3 - - + +
389A LEU* 1.3 68.2 + - - +
391A ARG* 3.0 14.6 + - - +
392A GLY* 3.2 7.8 + - - -
6C T 4.4 9.8 + - + +
7C T 2.9 78.9 + - + +
8C C 4.6 8.9 + - + -
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Residues in contact with LEU 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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337A LEU* 3.6 17.3 - - + +
341A LEU* 5.6 1.8 - - + -
365A LEU* 4.3 17.0 - - + -
371A VAL* 4.1 10.1 - - + -
372A ALA* 3.7 19.3 - - + +
375A TRP* 3.4 42.2 - - + +
384A MET* 3.8 9.1 - - - -
385A ASN 3.0 18.6 + - - +
386A TYR* 3.8 10.3 - - + +
388A LYS* 1.3 77.3 - - - +
390A SER* 1.3 60.5 + - - +
392A GLY* 2.9 17.8 + - - -
393A LEU* 3.2 30.8 + - + -
6C T 4.8 3.8 - - - -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A TYR* 2.9 31.2 + - - -
387A GLU* 3.0 15.8 + - - -
389A LEU* 1.3 73.2 - - - +
391A ARG* 1.3 60.0 + - - +
392A GLY 3.1 1.3 - - - -
393A LEU* 3.2 12.6 + - - +
394A ARG* 2.8 55.8 + - - +
412A TYR* 3.6 20.2 - - - -
6B C 5.7 2.0 - - - -
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Residues in contact with ARG 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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387A GLU 3.3 4.8 + - - +
388A LYS 3.0 12.1 + - - +
390A SER* 1.3 79.4 + - - +
392A GLY* 1.3 63.9 + - - +
394A ARG* 3.2 28.7 + - - +
395A TYR* 3.2 50.9 + - + +
8B G 3.0 49.4 + - - +
9B G 2.6 44.9 + - - -
6C T 4.3 0.4 - - + -
7C T 3.4 31.2 - - + +
8C C 4.2 2.2 - - - +
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Residues in contact with GLY 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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337A LEU* 4.1 12.8 - - - -
388A LYS 3.2 4.4 + - - -
389A LEU 2.9 10.6 + - - -
391A ARG* 1.3 80.8 - - - +
393A LEU* 1.3 61.3 + - - +
395A TYR* 3.1 20.5 + - - +
396A TYR* 3.7 11.6 + - - -
5C T 4.2 13.4 - - - +
6C T 4.2 15.6 - - - +
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Residues in contact with LEU 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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337A LEU* 3.6 20.9 - - + -
341A LEU* 3.6 26.5 - - + -
363A PHE* 5.4 0.4 - - + -
365A LEU* 4.9 5.4 - - + -
386A TYR* 5.0 0.2 - - + -
389A LEU* 3.2 26.7 + - + +
390A SER* 3.2 8.9 + - - +
392A GLY* 1.3 75.7 - - - +
394A ARG* 1.3 56.3 + - - +
396A TYR* 2.8 41.4 + - + +
397A TYR* 3.7 9.6 - - - -
402A ILE* 4.5 9.4 - - + +
412A TYR* 3.4 52.3 - - + +
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Residues in contact with ARG 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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387A GLU 4.5 3.2 + - - -
390A SER* 2.8 40.4 + - - +
391A ARG* 3.2 36.3 + - - +
393A LEU* 1.3 76.5 - - + +
395A TYR* 1.3 60.9 + - - +
396A TYR 3.0 0.2 - - - -
397A TYR* 3.1 40.2 + - + +
398A ASP 4.6 0.2 + - - -
412A TYR* 5.1 0.6 + - + -
6B C 4.2 16.0 - - - +
7B C 3.4 66.9 + - - +
8B G 2.8 46.1 + - + +
8C C 5.4 0.2 - - - +
9C C 4.9 1.2 - - - +
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Residues in contact with TYR 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 ARG* 3.2 49.5 + - + -
392A GLY* 3.1 12.3 + - - +
394A ARG* 1.3 78.0 - - - +
396A TYR* 1.3 62.3 + - + +
397A TYR 3.2 1.0 + - - -
398A ASP* 4.2 5.5 + - - +
399A LYS* 3.6 24.4 + - - +
9B G 4.3 2.6 + + - -
10B A 3.1 28.8 + - - -
11B A 3.6 8.0 + - - -
5C T 3.4 31.6 - + + +
6C T 3.4 30.3 - - + -
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.1 25.8 + - + +
338A TRP* 2.9 50.5 + + + -
392A GLY 4.0 6.3 - - - -
393A LEU* 2.8 24.3 + - + +
395A TYR* 1.3 81.6 - - + +
397A TYR* 1.3 59.6 + - - +
398A ASP 3.4 0.4 - - - -
399A LYS* 3.6 24.0 - - + -
400A ASN* 2.8 25.5 + - - -
401A ILE* 3.1 15.3 + - + -
402A ILE* 3.3 37.0 - - + +
4C A 5.8 0.2 - - + -
5C T 2.5 35.0 + - - -
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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