Contacts of the helix formed by residues 418 - 433 (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 PHE 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B PRO* 4.9 0.4 - - + -
188B THR* 4.7 5.6 - - + -
395B PHE* 3.1 40.7 - + + -
399B PHE* 3.7 20.0 - + + -
400B ARG* 5.3 6.3 - - + -
405B LEU* 1.9 61.0 - - + -
408B TYR* 3.4 12.8 - + + -
413B MET* 4.0 16.4 - - + -
415B GLU* 3.6 14.4 - - - +
416B MET 3.3 17.0 - - - -
417B GLU* 1.0 86.0 - - + +
419B THR* 1.3 65.2 + - - +
420B GLU 3.3 0.7 - - - -
421B ALA* 3.2 1.5 + - - +
422B GLU 3.1 18.4 + - - -
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Residues in contact with THR 419 (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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400B ARG* 3.6 41.2 + - - +
415B GLU* 3.4 21.5 + - - +
416B MET* 5.4 3.8 - - - -
418B PHE* 1.3 77.7 - - - +
420B GLU* 1.3 64.5 + - + +
422B GLU* 3.5 2.1 + - - +
423B SER* 3.0 27.2 + - - +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 3.6 7.5 - - + +
416B MET* 3.6 31.4 - - + +
417B GLU* 4.4 21.7 + - - +
418B PHE 3.3 0.8 - - - +
419B THR* 1.3 80.5 - - + +
421B ALA* 1.3 59.5 + - - +
423B SER* 3.4 6.6 + - - -
424B ASN* 3.1 31.9 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA* 3.8 19.0 - - + +
188B THR* 4.0 8.5 - - + -
191B VAL* 2.6 26.9 - - + +
395B PHE* 5.1 1.3 - - + -
417B GLU* 3.9 19.7 - - - +
418B PHE* 3.2 9.8 + - - +
420B GLU* 1.3 78.8 - - - +
422B GLU* 1.3 58.8 + - - +
425B MET* 2.9 30.2 - - - +
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA* 6.0 0.7 - - - -
392B SER* 4.2 10.8 - - - +
395B PHE* 3.5 26.6 - - + -
396B THR* 1.8 35.7 + - - +
400B ARG* 2.4 56.9 + - - +
418B PHE 3.1 8.0 + - - +
419B THR 4.0 0.2 - - - +
421B ALA* 1.3 77.1 - - - +
423B SER* 1.3 53.8 + - - +
424B ASN 3.3 0.4 - - - -
425B MET* 4.7 1.1 - - - -
426B ASN* 2.4 46.2 + - + +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 5.3 3.8 - - - -
419B THR* 3.0 19.9 + - - +
420B GLU* 3.4 8.7 + - - -
422B GLU* 1.3 81.5 - - - +
424B ASN* 1.3 63.5 + - - +
426B ASN* 3.8 6.1 - - - -
427B ASP* 2.9 35.9 + - - +
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Residues in contact with ASN 424 (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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191B VAL* 3.2 27.8 - - + +
194B LEU* 4.4 6.7 - - - +
195B VAL* 3.9 25.3 - - - +
264B ARG* 4.8 18.1 + - - +
420B GLU 3.1 18.4 + - - +
423B SER* 1.3 84.8 + - - +
425B MET* 1.3 57.2 + - - +
426B ASN 3.2 0.2 - - - -
427B ASP* 4.4 4.2 + - - +
428B LEU* 3.9 12.6 + - - +
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Residues in contact with MET 425 (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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186B ASN 4.7 0.4 - - - +
187B ALA* 2.4 24.0 - - - +
190B SER* 1.1 70.9 - - - +
191B VAL* 3.2 5.8 - - + +
194B LEU* 4.2 7.9 - - + -
388B PHE* 4.7 18.6 - - + +
391B ILE* 5.5 6.3 - - - -
392B SER* 6.1 4.0 - - - -
421B ALA 2.9 18.3 + - - +
422B GLU* 4.6 1.1 - - - +
424B ASN* 1.3 74.3 - - - +
426B ASN* 1.3 58.3 + - - +
428B LEU* 2.6 40.6 - - + +
429B VAL* 3.8 6.6 + - - +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 5.7 8.9 + - - -
422B GLU* 2.4 35.6 + - + +
423B SER* 3.4 10.1 - - - +
424B ASN 3.2 0.2 - - - -
425B MET* 1.3 72.2 - - - +
427B ASP* 1.3 61.8 + - - +
428B LEU 2.5 3.1 - - - -
429B VAL* 2.0 57.6 + - - +
430B SER* 4.8 3.6 + - - +
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 4.3 2.5 - - - +
423B SER* 2.9 21.5 + - - +
424B ASN* 4.6 3.6 - - - +
426B ASN* 1.3 82.4 + - - +
428B LEU* 1.4 53.9 - - - +
429B VAL 3.0 0.2 - - - -
430B SER* 2.8 16.1 + - - +
431B GLU* 2.2 63.2 + - + +
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Residues in contact with LEU 428 (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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194B LEU* 3.7 40.4 - - + -
264B ARG* 4.6 22.0 - - + +
265B LEU 5.1 1.1 - - - +
267B PHE* 4.4 4.3 - - + -
388B PHE* 4.3 33.0 - - + -
424B ASN 3.9 5.0 + - - +
425B MET* 2.6 36.4 + - + +
426B ASN 2.3 10.1 + - - -
427B ASP* 1.4 71.9 - - - +
429B VAL* 1.3 49.0 + - - +
431B GLU* 4.6 5.6 - - + +
432B TYR* 2.7 58.7 + - + +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN* 3.3 7.2 - - - +
388B PHE* 4.2 18.6 - - + -
389B LYS* 1.2 100.7 + - + +
392B SER* 4.7 5.6 - - - +
425B MET 4.0 8.5 - - - +
426B ASN* 2.0 43.2 + - - +
428B LEU* 1.3 69.4 - - + +
430B SER* 1.3 59.1 + - - +
432B TYR* 4.4 1.3 - - - -
433B GLN* 3.1 16.1 + - - +
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Residues in contact with SER 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LYS* 4.6 1.8 - - - +
426B ASN* 3.4 4.1 + - - +
427B ASP* 2.8 34.5 + - - +
429B VAL* 1.3 78.9 - - - +
431B GLU* 1.3 57.3 + - - +
433B GLN* 3.2 7.8 + - - +
434B GLN* 2.6 41.3 + - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 1.5 61.8 + - - -
427B ASP* 2.2 44.5 + - + +
428B LEU* 4.2 2.4 - - + +
430B SER* 1.3 70.8 + - - +
432B TYR* 1.3 66.4 + - - +
434B GLN* 2.9 43.9 - - - +
435B TYR* 3.8 8.8 - - - -
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Residues in contact with TYR 432 (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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265B LEU 5.3 0.7 - - - -
266B HIS* 4.0 23.9 - + - -
267B PHE* 3.6 24.8 + + - +
313B LEU* 4.8 10.1 - - + +
380B ASN* 3.6 25.5 - - + +
381B SER 3.3 22.8 + - - -
382B THR* 4.6 4.9 - - - -
384B ILE* 3.6 22.8 - - + +
385B GLN* 3.9 20.0 - - + -
388B PHE* 5.7 1.6 - + - -
428B LEU* 2.7 40.1 + - + +
429B VAL* 3.9 4.3 - - - +
431B GLU* 1.3 78.5 - - - +
433B GLN* 1.3 62.9 + - - +
434B GLN 3.0 0.9 + - - -
435B TYR* 3.0 24.7 + + - +
436B GLN* 4.2 5.0 + - - -
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B THR* 4.8 1.6 - - + -
385B GLN* 2.1 52.7 + - - +
389B LYS* 3.0 2.6 + - - -
429B VAL 3.1 6.4 + - - +
430B SER* 3.5 7.1 - - - +
432B TYR* 1.3 72.3 - - - +
434B GLN* 1.3 73.9 - - - +
435B TYR 2.5 19.2 + - - +
436B GLN* 4.5 4.0 - - - +
437B ASP* 2.4 61.4 + - - +
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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
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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