Contacts of the helix formed by residues 386 - 403 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 5.2 8.3 - - + -
382B ILE* 3.7 12.3 - - + +
383B LYS* 2.6 26.5 + - - +
384B LEU 2.9 2.4 - - - -
385B PHE* 1.3 76.3 - - - +
387B GLU* 1.3 61.5 + - - +
388B LEU 3.1 2.2 - - - -
389B SER* 2.7 31.5 + - - +
390B PHE* 3.7 9.3 + - - -
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B HIS* 3.1 36.5 + - - -
384B LEU* 3.2 31.4 + - + +
386B THR* 1.3 77.5 + - - +
388B LEU* 1.3 64.9 - - + +
390B PHE* 3.4 4.3 + - - +
391B THR* 3.0 38.0 + - + +
2002B OLC 3.7 26.6 - - + +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 5.6 9.0 - - + +
147B ILE* 4.8 3.6 - - + -
148B TYR* 3.5 33.7 - - + +
384B LEU 5.6 0.2 - - - +
385B PHE* 3.7 27.1 - - + +
386B THR 3.1 0.6 - - - -
387B GLU* 1.3 84.8 - - + +
389B SER* 1.3 56.2 + - - +
391B THR* 3.1 8.5 + - - +
392B SER* 2.9 31.2 + - - -
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 6.1 0.2 - - - -
147B ILE* 3.6 26.4 - - - +
386B THR* 2.7 30.8 + - - +
388B LEU* 1.3 78.3 - - - +
390B PHE* 1.3 73.7 + - - +
392B SER* 2.5 23.6 + - - -
393B PHE* 3.0 23.1 + - - -
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 4.9 17.9 - - + -
386B THR* 3.7 7.6 + - - +
387B GLU 3.4 6.6 + - - +
388B LEU 3.4 0.4 - - - -
389B SER* 1.3 92.7 + - - +
391B THR* 1.3 64.3 + - - +
393B PHE* 3.2 5.2 + - - +
394B GLN* 3.0 27.7 + - - +
2002B OLC 4.7 40.2 - - + -
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Residues in contact with THR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 4.3 6.8 - - - -
152B TYR* 3.4 17.0 + - - -
190B ARG* 4.0 20.3 + - - +
387B GLU* 3.0 30.4 + - + +
388B LEU* 3.1 17.2 + - - +
390B PHE* 1.3 74.4 - - - +
392B SER* 1.3 61.2 + - - +
394B GLN* 3.5 30.5 - - - +
2002B OLC 4.1 20.4 - - + -
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE 4.0 3.3 + - - -
148B TYR* 3.5 27.7 - - - -
151B GLY* 3.5 10.1 - - - +
152B TYR* 3.5 24.0 + - - -
155B SER* 2.9 20.1 + - - -
388B LEU 2.9 14.9 + - - -
389B SER* 2.5 24.9 + - - -
391B THR* 1.3 79.7 + - - +
393B PHE* 1.3 67.6 + - - +
394B GLN 3.2 1.8 + - - -
395B GLY 4.2 1.4 + - - -
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.0 14.6 - - + -
150B VAL* 4.6 8.5 - - + -
151B GLY* 3.8 24.2 - - - -
154B LEU* 3.9 23.8 - - + -
155B SER* 3.9 3.6 - - - -
389B SER* 3.0 35.1 + - - +
390B PHE* 3.2 5.1 + - - +
392B SER* 1.3 81.1 + - - +
394B GLN* 1.3 64.4 + - - +
395B GLY 3.4 0.7 - - - -
396B LEU* 3.3 26.0 + - + +
397B MET* 3.1 23.1 + - + +
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Residues in contact with GLN 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PHE* 3.9 13.2 - - + -
190B ARG* 3.1 29.4 + - - +
241B TYR* 4.9 7.3 + - - -
356B LEU* 5.6 0.3 - - - +
359B LEU* 4.9 4.7 + - + +
360B LEU* 3.4 47.8 + - + +
390B PHE 3.0 14.2 + - - +
391B THR* 3.5 31.9 - - - +
392B SER 3.2 1.2 - - - -
393B PHE* 1.3 77.1 - - - +
395B GLY* 1.3 64.0 + - - +
397B MET* 3.2 7.0 + - - +
398B VAL* 3.0 26.4 + - - +
2002B OLC 5.3 6.1 - - - +
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B SER* 3.7 7.7 + - - -
159B LEU* 3.4 34.3 - - - +
187B PHE* 3.9 17.0 - - - -
391B THR 5.1 0.2 + - - -
392B SER 4.2 1.6 + - - -
393B PHE 3.4 0.6 - - - -
394B GLN* 1.3 79.2 - - - +
396B LEU* 1.3 62.7 + - - +
398B VAL* 3.2 5.0 + - - +
399B ALA 2.9 18.2 + - - -
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 4.2 19.1 - - + +
155B SER* 2.9 28.8 + - - +
158B ALA* 3.7 22.7 - - + -
393B PHE* 3.3 34.9 + - + +
395B GLY* 1.3 74.9 - - - +
397B MET* 1.3 64.7 + - + +
399B ALA* 3.1 7.9 + - - +
400B ILE* 3.0 42.9 + - + +
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Residues in contact with MET 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 5.0 1.8 - - + -
359B LEU* 4.6 22.4 - - + -
393B PHE 3.1 13.0 + - - +
394B GLN* 3.2 7.6 + - - +
396B LEU* 1.3 79.3 - - + +
398B VAL* 1.3 63.0 + - - +
400B ILE* 3.6 20.8 - - + +
401B LEU* 2.9 48.2 + - + +
2001B 97Y 4.3 27.4 - - + -
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 4.6 2.0 - - + -
183B LEU* 3.8 24.0 - - + -
184B PHE* 3.7 24.2 - - + -
187B PHE* 3.9 28.3 - - + -
356B LEU* 4.2 23.8 - - + -
360B LEU* 5.3 4.3 - - + -
394B GLN* 3.0 21.4 + - + +
395B GLY* 3.2 9.2 + - - +
397B MET* 1.3 76.8 - - - +
399B ALA* 1.3 57.0 + - - +
401B LEU* 5.1 0.7 - - - -
402B TYR* 2.9 36.9 + - + +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ALA* 3.9 17.0 - - + +
159B LEU* 3.7 22.8 - - + +
162B ALA* 4.3 4.3 - - + -
184B PHE* 4.4 7.6 - - - -
395B GLY 2.9 8.2 + - - +
396B LEU 3.5 7.2 - - - +
398B VAL* 1.3 76.9 - - - +
400B ILE* 1.3 58.5 + - - +
403B CYS* 2.8 31.9 + - - +
404B PHE* 3.2 23.2 + - + -
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B LEU* 3.0 35.5 + - + +
397B MET* 3.6 25.1 - - + +
399B ALA* 1.3 74.8 - - - +
401B LEU* 1.3 69.7 + - + +
404B PHE* 3.1 45.1 + - + -
405B VAL* 3.2 32.0 + - + +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B SER* 3.0 31.2 + - - +
355B THR* 4.0 26.0 - - + -
356B LEU* 4.0 27.1 - - + -
397B MET* 2.9 47.6 + - + +
398B VAL 4.3 0.9 - - - +
400B ILE* 1.3 82.5 - - + +
402B TYR* 1.3 59.7 + - + +
405B VAL* 3.9 13.8 - - + +
406B ASN 5.2 0.5 + - - -
2001B 97Y 3.4 44.9 - - + +
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Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 5.0 5.2 - - - +
177B ASN* 5.1 0.7 - - - +
180B HIS* 3.5 44.7 - + + -
183B LEU* 3.6 29.2 - - + -
184B PHE* 4.0 11.2 - + + -
244B LEU* 5.1 0.9 - - + +
247B GLU* 3.1 23.9 - - + +
349B LEU* 4.0 8.5 - - + -
352B SER* 3.6 21.5 - - - -
353B THR* 2.5 34.8 + - - +
356B LEU* 3.4 23.7 - - + +
398B VAL* 2.9 23.8 + - + +
401B LEU* 1.3 84.7 - - - +
403B CYS* 1.3 60.8 + - - +
406B ASN* 4.6 9.2 - - - +
409B VAL* 5.9 0.2 - - - +
2001B 97Y 4.7 4.0 - - - -
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Residues in contact with CYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ALA* 3.6 42.6 - - + -
165B ILE* 4.4 14.8 - - - -
166B LEU* 4.3 15.3 - - + -
184B PHE* 4.6 5.6 - - + -
399B ALA 2.8 15.4 + - - +
400B ILE 3.4 0.2 + - - -
402B TYR* 1.3 81.2 - - - +
404B PHE* 1.3 72.1 + - + +
405B VAL 3.3 2.0 - - - -
406B ASN* 3.0 26.5 + - - +
409B VAL* 3.2 17.4 - - - +
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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
------------------------------------------------------------
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