Contacts of the helix formed by residues 325 - 340 (chain A) in PDB entry 1TAG
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLN* 2.7 32.5 + - - +
51A ILE* 4.0 15.6 - - + +
52A ILE* 3.7 21.7 - - + +
168A GLN* 5.6 0.3 + - - -
171A LEU* 4.0 9.5 - - - +
323A THR 3.5 2.1 + - - -
324A ASP* 1.3 72.2 + - - +
326A GLN* 1.3 57.9 + - - +
328A VAL* 3.4 0.5 + - - -
329A LYS* 2.9 30.2 + - + +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASP* 3.0 11.7 + - - +
325A THR* 1.3 77.6 - - - +
327A ASN* 1.3 62.6 + - - +
329A LYS* 3.4 21.8 + - - +
330A PHE* 3.1 47.9 + - + -
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Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LYS* 4.0 20.7 - - - +
319A MET 4.1 7.9 + - - -
320A THR* 3.2 12.6 - - - +
321A CYS* 2.8 31.4 + - + +
324A ASP* 3.2 31.8 + - + +
326A GLN* 1.3 78.1 - - - +
328A VAL* 1.3 56.8 + - - +
330A PHE* 3.3 8.1 + - - +
331A VAL* 2.9 40.0 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.9 18.8 - - + -
48A GLN* 3.7 28.5 - - + -
49A MET* 3.8 17.3 - - + -
52A ILE* 4.2 1.6 - - + -
263A PHE* 5.7 3.4 - - + -
320A THR* 5.7 2.7 - - - -
321A CYS 3.5 17.0 - - - +
322A ALA* 3.7 23.1 - - - +
324A ASP 3.0 15.3 + - - +
325A THR 3.9 2.9 - - - +
327A ASN* 1.3 75.1 - - - +
329A LYS* 1.3 60.6 + - - +
331A VAL* 3.9 4.9 - - + +
332A PHE* 2.8 32.1 + - + +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.8 33.3 - - + +
53A HIS* 5.8 2.5 + - + +
187A PHE* 5.9 0.2 - - - -
325A THR* 2.9 20.2 + - + +
326A GLN* 3.4 34.8 + - - +
328A VAL* 1.3 76.4 - - - +
330A PHE* 1.3 87.5 + - - +
332A PHE* 4.0 2.8 - - - +
333A ASP* 3.1 25.5 + - + +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLN* 3.1 53.3 + - + +
327A ASN* 3.7 7.9 - - - +
328A VAL 3.3 0.2 - - - -
329A LYS* 1.3 94.0 - - + +
331A VAL* 1.3 66.2 + - + +
333A ASP* 3.4 9.3 + - + +
334A ALA* 3.1 20.6 + - - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.4 37.0 - - + -
318A HIS* 3.9 26.7 - - + +
319A MET 4.5 1.8 - - - +
320A THR* 3.9 25.1 - - + -
327A ASN* 2.9 33.9 + - - +
328A VAL* 3.9 5.2 - - - +
330A PHE* 1.3 77.5 - - + +
332A PHE* 1.3 55.8 + - - +
334A ALA* 3.1 8.9 + - - +
335A VAL* 3.0 24.9 + - - +
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Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.9 12.8 - - + -
45A ILE* 5.7 2.5 - - + -
49A MET* 3.9 20.2 - - + -
53A HIS* 3.7 17.9 - - - +
185A PHE* 3.7 30.5 - + - -
187A PHE* 4.0 9.4 - + - -
192A PHE* 3.5 26.2 - + - -
194A MET* 3.7 20.2 - - + -
218A ILE* 4.3 15.7 - - + -
263A PHE* 5.0 4.0 - + + -
328A VAL* 2.8 23.0 + - + +
329A LYS* 4.2 3.1 - - - +
331A VAL* 1.3 71.3 - - - +
333A ASP* 1.3 62.3 + - - +
335A VAL* 3.3 9.6 + - + +
336A THR* 2.9 48.0 + - - -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.2 20.2 - - + -
188A LYS* 3.1 28.4 + - - -
329A LYS* 3.1 20.2 + - + +
330A PHE* 3.5 11.2 - - + +
332A PHE* 1.3 77.3 - - - +
334A ALA* 1.3 62.1 + - - +
336A THR* 3.1 3.8 + - - -
337A ASP* 3.0 37.2 + - - +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A HIS* 3.7 27.6 - - + +
330A PHE 3.1 12.4 + - - +
331A VAL 3.1 8.7 + - - +
333A ASP* 1.3 76.8 + - - +
335A VAL* 1.3 62.3 - - - +
337A ASP* 3.2 10.5 + - - +
338A ILE* 3.0 27.5 + - + +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.6 3.8 - - + -
216A CYS* 4.2 13.0 - - - -
218A ILE* 4.2 18.2 - - + -
261A VAL* 4.0 17.5 - - + -
263A PHE* 3.7 32.5 - - + -
318A HIS* 5.1 2.4 + - + -
331A VAL* 3.0 19.1 + - + +
332A PHE* 3.5 13.7 - - + +
333A ASP 3.3 0.2 - - - -
334A ALA* 1.3 75.0 - - - +
336A THR* 1.3 59.4 + - - +
338A ILE* 3.1 13.0 + - - +
339A ILE* 2.9 42.8 + - + +
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Residues in contact with THR 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.5 15.2 - - + -
188A LYS* 3.5 26.5 - - + -
190A LEU* 4.0 7.6 - - + -
192A PHE* 3.6 15.6 - - + -
332A PHE* 2.9 37.2 + - - -
333A ASP 3.1 8.5 + - - -
335A VAL* 1.3 75.9 - - - +
337A ASP* 1.3 56.3 + - - +
339A ILE* 3.2 10.3 + - - +
340A ILE* 2.9 36.2 + - + +
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LYS* 3.6 27.0 + - - +
333A ASP* 3.0 27.1 + - - +
334A ALA* 3.7 10.0 - - - +
336A THR* 1.3 76.1 - - - +
338A ILE* 1.3 62.4 + - - +
340A ILE* 3.4 24.7 + - - +
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 4.5 18.0 + - - +
261A VAL* 3.9 27.4 - - + -
316A TYR* 3.4 49.1 - - + -
318A HIS* 5.3 5.2 - - - +
334A ALA* 3.0 18.0 + - + +
335A VAL* 3.2 10.5 - - - +
337A ASP* 1.3 74.2 - - - +
339A ILE* 1.3 72.6 + - + +
340A ILE 3.4 3.5 + - - -
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.9 28.9 + - - +
30A VAL* 4.0 13.0 - - + -
32A LEU* 4.1 8.7 - - + -
190A LEU* 4.1 18.4 - - + -
192A PHE* 3.9 25.6 - - + -
215A THR* 4.4 4.7 - - + -
216A CYS* 3.8 35.4 - - + -
259A SER* 4.8 7.8 + - - -
335A VAL* 2.9 21.7 + - + +
336A THR* 3.4 9.6 - - - +
338A ILE* 1.3 82.1 - - + +
340A ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.5 9.6 + - - +
188A LYS* 4.2 24.5 - - + +
190A LEU* 3.7 24.2 - - + -
336A THR* 2.9 35.0 + - + +
337A ASP* 3.7 19.7 - - - +
338A ILE 3.2 4.2 - - - -
339A ILE* 1.3 81.8 - - - +
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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