Contacts of the helix formed by residues 379 - 390 (chain B) in PDB entry 3TQI
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 PHE 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLN* 4.1 26.0 - - + -
24B ALA* 3.6 31.6 - - + -
25B ARG* 3.8 35.7 - - + -
28B ARG* 4.0 24.0 - - + -
336B ILE* 5.0 0.9 - - - -
337B TYR* 3.7 30.7 - + - -
338B PRO* 3.9 22.4 - - + -
341B ILE* 4.6 3.6 - - + -
378B LEU* 1.3 76.3 - - - +
380B LYS* 1.3 68.0 + - - +
381B ASP* 3.3 5.4 - - + +
382B GLU* 2.9 33.7 + - + +
383B VAL* 3.0 14.2 + - - +
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Residues in contact with LYS 380 (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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25B ARG* 5.9 1.5 - - - +
238B VAL* 4.8 16.7 - - - +
239B ASP* 3.6 26.2 + - - +
336B ILE* 3.9 23.3 - - + +
338B PRO* 5.2 1.6 - - + +
379B PHE* 1.3 70.6 - - - +
381B ASP* 1.3 69.7 + - - +
382B GLU 3.1 0.2 + - - -
383B VAL* 3.1 7.0 + - + +
384B ARG* 3.0 59.6 + - - +
399B ARG 5.7 1.8 + - - -
401B PRO* 4.2 29.3 - - - +
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Residues in contact with ASP 381 (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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25B ARG* 3.3 44.1 + - - +
29B GLU* 6.2 0.3 - - - -
379B PHE* 4.8 3.4 - - + -
380B LYS* 1.3 77.2 - - - +
382B GLU* 1.3 68.5 + - + +
384B ARG* 3.4 24.1 + - - +
385B LYS* 3.1 30.2 + - + +
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Residues in contact with GLU 382 (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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28B ARG* 2.8 41.2 + - + +
208B TRP* 2.6 34.9 + - - -
210B THR* 6.3 0.7 - - + -
213B ILE* 4.5 5.8 - - + +
378B LEU* 3.4 17.9 - - + -
379B PHE* 2.9 26.1 + - + +
381B ASP* 1.3 83.1 - - + +
383B VAL* 1.3 67.6 + - - +
385B LYS* 3.2 13.7 + - + +
386B LEU* 2.9 28.6 + - + +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.1 11.9 - - + +
239B ASP* 4.1 13.9 - - - +
242B VAL* 3.7 21.9 - - + +
336B ILE* 3.9 26.0 - - + -
375B LEU* 4.0 21.8 - - + -
378B LEU* 4.0 18.6 - - + -
379B PHE 3.0 17.6 + - - +
380B LYS* 3.7 10.8 - - + +
382B GLU* 1.3 75.0 - - - +
384B ARG* 1.3 62.4 + - - +
386B LEU* 3.2 7.5 + - - +
387B GLY 3.0 19.6 + - - -
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Residues in contact with ARG 384 (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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25B ARG* 5.7 0.2 - - - +
238B VAL* 4.5 8.7 - - + -
380B LYS* 3.0 49.3 + - - +
381B ASP* 3.5 35.2 + - - +
383B VAL* 1.3 78.1 - - - +
385B LYS* 1.3 60.5 + - - +
387B GLY 3.3 0.9 + - - -
388B LEU* 3.1 22.0 + - - +
397B ILE* 3.4 46.8 - - + +
398B TYR* 3.8 29.0 - - + +
399B ARG 5.8 1.8 + - - -
401B PRO* 6.1 1.2 - - - +
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Residues in contact with LYS 385 (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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29B GLU* 4.4 25.5 + - - +
210B THR* 4.0 29.9 + - + -
381B ASP* 3.1 22.0 + - + +
382B GLU* 3.5 16.2 - - + +
384B ARG* 1.3 74.3 - - - +
386B LEU* 1.3 62.8 + - - +
388B LEU* 3.6 8.6 + - - +
389B GLU* 3.3 22.3 + - - +
398B TYR* 6.0 1.3 - - - +
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Residues in contact with LEU 386 (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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210B THR* 3.8 33.2 - - - +
213B ILE* 4.0 24.2 - - + -
214B ILE* 3.8 14.4 - - + -
217B SER* 5.9 0.7 - - - -
242B VAL* 4.2 19.3 - - + -
246B LEU* 4.5 17.0 - - + -
375B LEU* 4.3 4.3 - - + -
378B LEU* 3.9 24.0 - - + -
382B GLU* 2.9 15.4 + - + +
383B VAL* 3.4 9.2 - - - +
385B LYS* 1.3 73.6 - - - +
387B GLY* 1.3 56.3 + - - +
389B GLU* 2.9 8.2 + - - +
390B LEU* 2.7 39.7 + - + +
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Residues in contact with GLY 387 (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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242B VAL* 3.4 24.6 - - - +
383B VAL 3.0 7.9 + - - -
384B ARG 3.3 0.4 + - - -
386B LEU* 1.3 78.4 - - - +
388B LEU* 1.3 62.2 + - - +
390B LEU* 3.2 6.2 + - - +
391B GLY 3.2 5.7 + - - -
392B LEU* 3.0 27.0 + - - +
397B ILE* 3.5 17.0 - - - -
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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
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384B ARG 3.1 14.9 + - - +
385B LYS* 3.8 8.7 - - - +
386B LEU 3.1 0.2 - - - -
387B GLY* 1.3 76.3 - - - +
389B GLU* 1.3 62.3 + - - +
391B GLY* 3.2 13.7 + - - -
392B LEU 3.9 14.2 + - - +
394B ALA* 3.9 21.3 - - + +
397B ILE* 3.7 23.1 - - + +
398B TYR* 3.5 28.3 - - + +
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Residues in contact with GLU 389 (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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210B THR* 4.3 13.6 + - - +
211B LYS* 3.7 29.5 - - + -
214B ILE* 3.9 22.0 - - + -
249B LYS* 5.4 2.3 + - - -
385B LYS 3.3 10.2 + - - +
386B LEU 2.9 8.1 + - - +
388B LEU* 1.3 79.9 - - - +
390B LEU* 1.3 61.0 + - - +
391B GLY* 3.1 2.0 + - - -
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Residues in contact with LEU 390 (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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214B ILE* 3.8 34.1 - - + -
242B VAL* 4.2 27.8 - - + +
245B THR* 3.8 24.3 - - + +
246B LEU* 3.5 31.9 - - + +
249B LYS* 3.9 41.8 + - + +
386B LEU* 2.7 25.8 + - + +
387B GLY* 3.2 7.8 + - - +
389B GLU* 1.3 71.9 - - - +
391B GLY* 1.3 57.2 + - - +
392B LEU* 3.6 1.1 - - + +
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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
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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