Contacts of the helix formed by residues 391 - 403 (chain B) in PDB entry 6QVC
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 LEU 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 5.6 16.6 - - + +
176B ALA* 6.5 1.6 - - - -
177B LEU* 5.7 11.7 - - + -
180B HIS* 6.0 6.3 - - + -
389B HIS* 3.4 24.4 - - + +
390B ARG* 1.3 80.3 - - + +
392B LEU* 1.3 61.6 + - - +
393B TYR 3.4 0.4 + - - -
394B PRO* 3.7 10.2 - - - +
395B GLY* 4.7 3.5 + - - -
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Residues in contact with LEU 392 (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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385B PHE* 4.0 27.4 - - + -
389B HIS* 3.8 33.5 + - + +
390B ARG 3.2 2.2 - - - -
391B LEU* 1.3 81.3 - - - +
393B TYR* 1.3 66.3 + - - +
394B PRO 3.6 0.2 - - - -
395B GLY* 4.0 0.7 + - - -
396B ILE* 3.2 55.3 + - + +
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Residues in contact with TYR 393 (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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372B VAL* 5.5 1.6 - - - +
376B VAL* 5.3 3.8 - - + +
382B LEU* 5.9 9.0 - - + -
386B LEU* 4.0 24.0 - - + -
389B HIS 5.0 0.8 + - - -
390B ARG 3.7 2.0 + - - +
391B LEU 3.4 0.2 - - - -
392B LEU* 1.3 83.7 - - - +
394B PRO* 1.4 72.0 - - + +
396B ILE* 3.6 15.2 - - + +
397B VAL* 4.0 22.1 - - + +
473B VAL* 5.1 4.7 + - - +
476B THR* 3.3 28.9 - - + +
477B MET* 3.8 26.1 + - + +
478B PRO* 3.8 17.9 - - + -
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Residues in contact with PRO 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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172B ILE* 4.6 9.4 - - + -
176B ALA* 4.7 17.7 - - + -
390B ARG 4.0 7.2 - - - +
391B LEU* 3.7 12.6 - - - +
393B TYR* 1.4 94.3 - - + +
395B GLY* 1.3 66.6 - - - +
397B VAL* 3.0 19.5 + - + +
398B THR* 3.1 14.9 + - - -
477B MET* 4.0 25.4 - - + +
478B PRO* 4.0 28.5 - - + +
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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
----------------------------------------------------------
169B LEU* 4.5 20.7 - - - +
172B ILE* 4.9 6.7 - - - -
173B LEU* 5.9 3.6 - - - -
391B LEU 4.7 3.1 + - - -
392B LEU 4.0 2.2 + - - -
393B TYR 3.6 0.4 - - - -
394B PRO* 1.3 81.9 - - - +
396B ILE* 1.3 51.3 + - - +
398B THR* 2.9 14.2 - - - -
399B PHE* 2.7 33.2 + - - +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 6.0 1.8 - - + -
392B LEU* 3.2 52.0 + - + +
393B TYR* 3.6 9.6 - - + +
395B GLY* 1.3 73.9 - - - +
397B VAL* 1.3 87.0 + - + +
399B PHE* 2.8 35.4 - - + +
400B VAL* 2.9 8.8 + - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B TYR* 4.0 24.7 - - + +
394B PRO* 3.0 18.2 + - + +
396B ILE* 1.3 92.2 - - + +
398B THR* 1.3 66.4 + - - +
400B VAL* 3.1 16.3 + - + +
401B ILE* 2.9 27.5 + - - +
473B VAL* 4.0 26.9 - - + -
477B MET* 4.2 12.6 - - + -
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Residues in contact with THR 398 (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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168B PRO* 4.4 7.2 - - + +
169B LEU* 4.4 15.9 - - + +
172B ILE* 3.9 23.6 - - + +
227B ILE* 3.9 28.4 - - + +
394B PRO 3.1 16.1 + - - -
395B GLY* 2.9 15.9 - - - +
397B VAL* 1.3 75.3 - - - +
399B PHE* 1.3 54.3 + - - +
401B ILE* 3.1 13.4 + - - +
402B ALA* 2.9 30.3 + - + +
477B MET* 4.2 12.1 - - - +
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Residues in contact with PHE 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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161B PHE* 5.3 11.0 - + - -
165B VAL* 4.1 31.2 - - + +
169B LEU* 5.0 18.6 - - + +
395B GLY 2.7 12.6 + - - +
396B ILE* 2.8 25.4 - - + +
398B THR* 1.3 71.4 - - - +
400B VAL* 1.3 67.1 + - + +
402B ALA* 3.1 10.0 + - - +
403B SER* 2.9 29.8 + - - -
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Residues in contact with VAL 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 ILE 2.9 12.3 + - - +
397B VAL* 3.1 29.3 + - + +
399B PHE* 1.3 84.8 - - + +
401B ILE* 1.3 66.0 + - + +
403B SER* 3.0 33.5 + - - +
404B PHE* 3.4 22.3 + - + -
469B TRP* 6.4 2.2 - - + -
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Residues in contact with ILE 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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227B ILE* 3.6 33.9 - - + -
228B PRO* 5.0 5.6 - - + -
397B VAL 2.9 15.3 + - - +
398B THR* 3.3 16.2 - - - +
400B VAL* 1.3 82.6 - - + +
402B ALA* 1.3 54.5 - - - +
404B PHE* 3.0 20.0 + - + +
405B THR* 2.2 26.9 + - - +
466B MET* 5.6 0.2 - - + -
469B TRP* 5.1 11.7 - - + -
470B MET* 3.7 49.9 - - + +
473B VAL* 5.3 13.0 - - + -
474B ALA* 5.4 3.8 - - + -
477B MET* 6.1 3.6 - - + -
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Residues in contact with ALA 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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161B PHE* 5.4 0.7 - - - -
164B TRP* 3.3 38.7 + - + +
165B VAL* 4.8 10.5 - - + +
168B PRO* 5.6 7.2 - - + -
227B ILE* 5.9 3.1 - - + -
398B THR* 2.9 15.2 + - + +
399B PHE* 3.3 12.1 - - - +
401B ILE* 1.3 78.3 - - - +
403B SER* 1.3 55.4 + - - +
404B PHE 3.1 0.2 - - - -
405B THR* 3.0 25.0 + - - -
406B PHE* 3.4 4.0 + - - +
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Residues in contact with SER 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 4.9 20.3 - - - -
165B VAL* 5.6 0.9 - - - +
399B PHE* 2.9 16.6 + - - -
400B VAL* 3.0 27.2 + - - +
402B ALA* 1.3 76.5 - - - +
404B PHE* 1.3 72.1 + - - +
405B THR 3.5 0.2 - - - -
406B PHE* 4.9 4.4 + - - +
410B MET* 4.7 4.9 - - - +
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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