Contacts of the helix formed by residues 386 - 403 (chain A) in PDB entry 6KJV
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 THR 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 5.3 8.1 - - + -
382A ILE* 3.8 10.3 - - + +
383A LYS* 2.6 26.3 + - - +
384A LEU* 2.9 2.9 - - - -
385A PHE* 1.3 74.6 - - - +
387A GLU* 1.3 61.3 + - - +
388A LEU 3.2 1.3 - - - -
389A SER* 2.7 31.1 + - - +
390A PHE* 3.7 10.8 + - - -
2002A OLC 5.9 0.2 - - - +
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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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363A HIS* 3.4 35.3 + - + -
384A LEU* 3.2 31.5 + - + +
386A THR* 1.3 79.2 + - - +
388A LEU* 1.3 62.4 - - + +
390A PHE* 3.4 2.7 + - - +
391A THR* 3.0 38.3 + - + +
2002A OLC 3.7 29.2 - - + +
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Residues in contact with LEU 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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144A LEU* 5.4 9.9 - - + +
147A ILE* 4.8 3.6 - - + -
148A TYR* 3.5 33.1 - - + -
385A PHE* 3.7 29.8 - - + +
386A THR 3.2 0.6 - - - -
387A GLU* 1.3 81.9 - - + +
389A SER* 1.3 58.8 + - - +
391A THR* 3.0 8.2 + - - +
392A SER* 2.9 31.2 + - - -
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 6.0 0.2 - - - -
147A ILE* 3.6 25.8 - - - +
385A PHE 4.5 0.4 + - - -
386A THR* 2.7 30.8 + - - -
388A LEU* 1.3 79.3 - - - +
390A PHE* 1.3 71.1 + - - +
392A SER* 2.5 24.0 + - - -
393A PHE* 3.0 26.6 + - - -
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Residues in contact with PHE 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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359A LEU* 4.6 24.7 - - + -
386A THR* 3.7 6.9 + - - +
387A GLU 3.4 6.1 + - - +
388A LEU 3.4 0.4 - - - -
389A SER* 1.3 88.9 + - - +
391A THR* 1.3 66.2 + - - +
393A PHE* 3.2 5.0 + - + +
394A GLN* 3.0 30.4 + - + +
397A MET* 6.5 0.7 - - - -
2002A OLC 4.4 37.2 - - + -
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Residues in contact with THR 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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148A TYR* 4.3 7.3 - - - -
152A TYR* 3.3 16.1 + - - -
190A ARG* 4.0 20.3 + - - +
387A GLU* 3.0 31.7 + - + +
388A LEU* 3.0 16.1 + - - +
390A PHE* 1.3 75.3 - - - +
392A SER* 1.3 60.3 + - - +
394A GLN* 3.5 34.4 - - - +
395A GLY 5.2 0.2 + - - -
2002A OLC 4.0 14.6 - - + -
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Residues in contact with SER 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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147A ILE 4.0 3.5 + - - -
148A TYR* 3.5 27.3 - - - -
151A GLY* 3.5 11.0 - - - +
152A TYR* 3.5 23.6 + - - -
155A SER* 2.9 19.8 + - - -
388A LEU 2.9 15.1 + - - -
389A SER* 2.5 26.3 + - - -
391A THR* 1.3 80.5 + - - +
393A PHE* 1.3 67.1 + - - +
394A GLN 3.2 1.9 + - - -
395A GLY 4.2 1.2 + - - -
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Residues in contact with PHE 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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147A ILE* 3.9 14.6 - - + -
150A VAL* 4.5 8.5 - - + -
151A GLY* 3.7 27.4 - - - -
154A LEU* 4.0 22.9 - - + -
155A SER* 3.8 3.8 - - - -
389A SER* 3.0 35.4 + - - +
390A PHE* 3.2 4.9 + - - +
392A SER* 1.3 82.1 + - - +
394A GLN* 1.3 64.9 + - - +
395A GLY 3.3 1.1 - - - -
396A LEU* 3.3 26.0 + - + +
397A MET* 3.1 22.2 + - - +
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Residues in contact with GLN 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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187A PHE* 3.9 14.7 - - + -
190A ARG* 3.1 29.3 + - - +
241A TYR* 5.0 7.9 + - - -
356A LEU* 5.5 0.2 - - - +
359A LEU* 5.0 9.6 + - + +
360A LEU* 4.3 34.6 + - + +
390A PHE* 3.0 21.9 + - + +
391A THR* 3.5 34.8 - - - +
392A SER 3.2 1.4 - - - -
393A PHE* 1.3 76.5 - - - +
395A GLY* 1.3 58.1 + - - +
397A MET* 3.1 8.8 + - - +
398A VAL* 2.9 32.0 + - - +
2002A OLC 5.0 5.9 - - - +
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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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155A SER* 3.7 7.7 + - - -
159A LEU* 3.3 35.3 - - - +
187A PHE* 3.9 18.7 - - - -
391A THR 5.2 0.2 + - - -
392A SER 4.2 1.4 + - - -
393A PHE 3.3 0.6 - - - -
394A GLN* 1.3 75.9 - - - +
396A LEU* 1.3 65.1 + - - +
398A VAL* 3.1 3.5 + - - +
399A ALA 2.9 18.7 + - - -
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Residues in contact with LEU 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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154A LEU* 4.3 18.4 - - + +
155A SER* 2.9 28.8 + - - +
158A ALA* 3.7 22.0 - - + -
393A PHE* 3.3 35.8 + - + +
395A GLY* 1.3 76.0 - - - +
397A MET* 1.3 63.4 + - - +
399A ALA* 3.2 5.7 + - - +
400A ILE* 2.9 44.9 + - + +
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Residues in contact with MET 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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355A THR* 5.5 0.9 - - - -
356A LEU* 4.5 2.2 - - + -
359A LEU* 3.8 32.5 - - + -
390A PHE* 6.5 0.7 - - - -
393A PHE 3.1 13.2 + - - +
394A GLN* 3.1 9.8 + - - +
396A LEU* 1.3 78.4 - - + +
398A VAL* 1.3 57.8 + - - +
400A ILE* 3.3 12.7 + - + +
401A LEU* 2.9 54.2 + - + +
2001A 97Y 3.9 27.6 - - + -
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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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159A LEU* 4.5 2.0 - - + -
183A LEU* 3.7 23.6 - - + -
184A PHE* 3.5 27.1 - - + -
187A PHE* 3.9 27.6 - - + -
356A LEU* 4.2 24.0 - - + -
360A LEU* 5.4 3.4 - - + -
394A GLN* 2.9 21.6 + - + +
395A GLY* 3.1 8.5 + - - +
397A MET* 1.3 76.6 - - - +
399A ALA* 1.3 57.7 + - - +
402A TYR* 2.9 37.5 + - + +
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Residues in contact with ALA 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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158A ALA* 3.8 21.5 - - + +
159A LEU* 3.9 13.7 - - + +
162A ALA* 4.1 5.6 - - + -
184A PHE* 4.4 6.5 - - - -
395A GLY 2.9 12.6 + - - +
396A LEU 3.2 7.8 + - - +
398A VAL* 1.3 76.2 - - - +
400A ILE* 1.3 57.8 + - - +
403A CYS* 2.8 32.6 + - - +
404A PHE* 3.2 24.6 + - + -
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Residues in contact with ILE 400 (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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396A LEU* 2.9 33.9 + - + +
397A MET* 3.7 15.0 - - + +
399A ALA* 1.3 75.1 - - - +
401A LEU* 1.3 75.4 + - + +
404A PHE* 3.1 47.2 + - + -
405A VAL* 3.1 32.4 + - + +
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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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352A SER* 2.9 33.2 + - - +
355A THR* 3.9 29.4 - - + -
356A LEU* 4.0 21.1 - - + -
397A MET* 2.9 46.0 + - + +
398A VAL 4.5 0.9 - - - +
400A ILE* 1.3 84.2 - - + +
402A TYR* 1.3 60.4 + - + +
405A VAL* 3.9 7.1 - - + +
2001A 97Y 3.1 54.4 + - + +
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Residues in contact with TYR 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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166A LEU* 5.0 6.9 - - - +
177A ASN* 5.1 0.9 - - - +
180A HIS* 3.5 44.4 - + + -
183A LEU* 3.7 28.3 - - + -
184A PHE* 3.9 11.0 - + + -
244A LEU* 5.1 0.9 - - + +
247A GLU* 3.1 25.3 - - + +
349A LEU* 4.0 9.6 - - + -
352A SER* 3.6 21.5 - - - -
353A THR* 2.6 32.0 + - - +
356A LEU* 3.4 24.0 - - + +
398A VAL* 2.9 23.4 + - + +
401A LEU* 1.3 83.3 - - - +
403A CYS* 1.3 60.1 + - - +
406A ASN* 4.5 10.0 - - - +
2001A 97Y 4.5 4.6 - - - +
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Residues in contact with CYS 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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162A ALA* 3.6 41.7 - - + -
165A ILE* 4.1 26.5 - - - -
166A LEU* 4.4 11.7 - - + -
184A PHE* 4.9 4.0 - - + -
399A ALA* 2.8 16.3 + - - +
400A ILE 3.4 0.2 + - - -
402A TYR* 1.3 81.4 - - - +
404A PHE* 1.3 64.0 + - + +
405A VAL 3.3 2.2 - - - -
406A ASN* 3.0 26.9 + - - +
409A VAL* 3.2 18.1 - - - +
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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
------------------------------------------------------------
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