Contacts of the helix formed by residues 385 - 397 (chain B) in PDB entry 1TUB
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 GLN 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B HIS* 5.8 5.4 - - + -
382B THR* 3.1 19.7 + - - +
383B ALA 3.0 1.4 - - - +
384B ILE* 1.3 76.5 - - - +
386B GLU* 1.3 57.8 - - + +
388B PHE* 4.1 3.6 - - - -
389B LYS* 1.4 99.7 - - + +
429B VAL* 3.2 9.6 - - + +
432B TYR* 3.9 13.5 - - + -
433B GLN* 2.1 61.8 + - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B CYS* 4.2 7.2 - - - +
306B ASP* 4.1 22.0 + - - +
309B HIS* 2.7 50.5 + - + +
383B ALA* 2.4 28.6 + - - +
384B ILE 1.9 19.8 + - - -
385B GLN* 1.3 67.0 - - + +
387B LEU* 1.3 54.2 - - - +
388B PHE 2.0 25.5 + - - -
389B LYS* 2.8 12.4 + - - -
390B ARG* 3.3 14.9 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 5.9 0.9 - - + -
172B VAL* 3.3 27.6 - - + -
173B PRO 4.2 0.4 - - - +
203B CYS* 3.8 28.5 - - + -
205B ASP* 3.1 27.4 - - - +
269B MET* 5.2 0.4 - - - -
304B ALA* 3.5 1.1 - - + -
305B CYS* 3.2 18.9 - - - -
384B ILE* 2.8 17.7 + - + -
386B GLU* 1.3 73.0 - - - +
388B PHE* 1.6 70.3 + - + +
390B ARG* 3.5 28.0 - - - +
391B ILE* 3.4 23.5 - - + +
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Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B SER* 6.0 1.3 - - - -
267B PHE* 4.2 33.9 - + + -
384B ILE* 2.7 42.4 + - + +
385B GLN* 4.9 1.8 - - - -
386B GLU 2.0 22.0 + - - -
387B LEU* 1.6 69.9 - - + +
389B LYS* 1.3 51.7 + - - +
390B ARG 2.4 17.5 + - - -
391B ILE* 2.5 26.0 + - + +
392B SER* 2.8 16.5 + - - -
425B MET* 4.7 21.5 - - + +
428B LEU* 4.3 25.4 - - + -
429B VAL* 4.2 16.4 - - + -
432B TYR* 5.5 2.2 - + - -
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN* 1.4 81.9 - - + +
386B GLU* 2.8 3.5 + - - +
388B PHE* 1.3 73.1 - - - +
390B ARG* 1.3 52.6 + - - +
392B SER* 3.4 11.9 - - - +
393B GLU* 2.8 32.1 - - - +
429B VAL* 1.2 77.5 + - + +
430B SER* 4.3 1.0 - - - +
433B GLN* 3.0 3.6 + - - -
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO* 3.8 13.4 + - - -
174B SER* 3.4 8.7 - - - +
175B PRO* 2.5 47.0 - - - +
207B GLU* 5.2 0.2 - - - +
304B ALA* 3.2 27.7 + - - +
305B CYS* 5.1 0.2 - - - +
386B GLU* 3.6 11.4 - - - +
387B LEU* 3.5 36.6 - - - +
388B PHE 2.4 10.1 + - - -
389B LYS* 1.3 75.7 - - - +
391B ILE* 1.3 56.8 + - + +
392B SER 3.2 1.6 - - - -
393B GLU* 3.8 4.0 + - - +
394B GLN* 2.3 46.2 + - + +
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Residues in contact with ILE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 4.5 7.2 - - + -
172B VAL* 4.7 1.1 - - + -
173B PRO* 2.7 46.0 - - + -
183B GLU* 3.4 37.1 - - - +
186B ASN* 5.1 4.5 - - + -
187B ALA* 4.4 15.0 - - + +
387B LEU* 3.4 19.3 - - + +
388B PHE* 2.5 23.5 + - + +
390B ARG* 1.3 78.2 - - - +
392B SER* 1.3 50.5 + - - +
394B GLN* 2.9 4.6 - - - +
395B PHE* 2.7 30.2 + - - +
425B MET* 5.5 5.6 - - - -
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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
----------------------------------------------------------
388B PHE* 2.8 16.5 + - - -
389B LYS* 3.4 14.9 + - - +
391B ILE* 1.3 76.1 - - - +
393B GLU* 1.3 68.3 + - - +
394B GLN 2.8 5.2 - - - -
395B PHE* 3.5 7.8 - - - +
396B THR* 3.0 28.9 + - - -
422B GLU* 4.2 11.4 - - - +
425B MET* 6.1 3.1 - - - -
426B ASN* 5.7 9.3 + - - -
429B VAL* 4.7 7.7 - - - +
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Residues in contact with GLU 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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389B LYS* 2.8 32.9 - - - +
390B ARG* 3.8 6.5 + - - +
392B SER* 1.3 89.1 + - - +
394B GLN* 1.3 64.6 + - + +
396B THR* 4.2 3.7 - - - -
397B ALA* 3.2 25.3 + - - +
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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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183B GLU* 2.2 57.0 + - - +
390B ARG* 2.3 36.0 + - + +
391B ILE* 2.9 8.3 - - - +
393B GLU* 1.3 81.5 - - - +
395B PHE* 1.3 47.0 + - - -
397B ALA* 3.6 2.2 - - - +
398B MET* 2.5 44.1 + - - +
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.2 1.8 - - - +
184B PRO* 3.0 51.8 - - + -
187B ALA* 3.7 15.5 - - + -
188B THR* 4.8 2.0 - - + -
391B ILE 2.7 18.3 + - - +
392B SER* 3.3 8.9 + - - +
394B GLN* 1.3 75.6 - - - +
396B THR* 1.3 62.4 + - - +
398B MET* 3.0 12.9 + - - -
399B PHE* 3.5 2.6 + - + -
400B ARG* 3.1 38.3 + - + -
418B PHE* 3.1 55.9 - + + -
421B ALA* 5.1 0.7 - - + -
422B GLU* 3.5 29.6 - - + -
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Residues in contact with THR 396 (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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392B SER 3.0 15.4 + - - -
393B GLU* 4.2 4.5 - - - -
395B PHE* 1.3 76.6 - - - +
397B ALA* 1.3 59.3 + - + +
400B ARG* 3.7 7.9 - - + +
401B ARG* 3.0 31.6 + - - +
422B GLU* 1.8 44.8 + - - +
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Residues in contact with ALA 397 (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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393B GLU 3.2 17.0 + - - +
394B GLN* 3.6 2.7 - - - +
395B PHE 3.1 0.4 - - - -
396B THR* 1.3 76.0 - - + +
398B MET* 1.3 53.0 + - - +
401B ARG* 2.5 50.2 + - - +
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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