Contacts of the helix formed by residues 361 - 370 (chain A) in PDB entry 1T9G
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 PRO 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ARG* 4.1 23.4 - - - +
273A GLU* 3.4 34.3 - - + +
351A LEU* 4.9 3.4 - - + -
360A TYR* 1.3 98.4 - - + +
362A VAL* 1.3 64.9 + - + +
363A GLU 3.8 0.2 - - - -
364A LYS* 3.9 15.2 - - + +
365A LEU* 3.5 17.3 - - - +
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Residues in contact with VAL 362 (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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273A GLU* 3.6 31.9 - - + -
344A ALA 4.9 0.7 - - - +
347A ALA* 3.9 22.9 - - + +
348A VAL* 3.7 23.1 - - + +
351A LEU* 4.1 17.3 - - + -
355A GLY* 3.6 28.7 - - - +
360A TYR* 3.2 3.0 + - + -
361A PRO* 1.3 79.9 - - + +
363A GLU* 1.3 70.8 + - - +
364A LYS 3.1 1.6 - - - -
365A LEU* 2.9 24.3 + - + +
366A MET 3.3 8.0 + - - -
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Residues in contact with GLU 363 (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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218A ARG* 5.7 0.2 + - - -
348A VAL* 4.0 7.2 - - - -
355A GLY 3.3 18.3 + - - +
356A PHE* 4.3 5.6 - - - +
357A ASN 4.1 3.4 - - - +
358A THR* 3.4 40.1 - - - +
360A TYR 4.2 4.5 + - - +
362A VAL* 1.3 83.1 - - - +
364A LYS* 1.3 71.9 + - - +
366A MET* 3.2 12.0 + - - +
367A ARG* 2.7 40.7 + - - -
215B MET* 3.0 43.3 - - + +
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Residues in contact with LYS 364 (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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39A ALA* 4.4 12.0 - - + +
40A ALA* 5.2 6.3 - - - -
43A ASP* 3.8 36.1 - - + +
90A GLY 4.7 3.0 + - - -
91A CYS* 3.1 39.1 - - - +
269A ARG* 6.0 0.2 - - - +
360A TYR 5.4 0.9 - - - +
361A PRO* 3.9 14.2 + - + +
362A VAL 3.1 0.8 - - - -
363A GLU* 1.3 84.4 + - - +
365A LEU* 1.3 64.9 + - + +
367A ARG* 3.0 23.9 + - - +
368A ASP* 2.9 51.5 + - - +
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Residues in contact with LEU 365 (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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89A TYR 5.6 1.1 - - - +
266A LEU* 3.7 31.4 - - + +
269A ARG* 4.0 26.2 - - + +
270A ALA* 3.8 33.2 - - + +
273A GLU* 4.6 1.3 - - + -
344A ALA* 3.8 11.0 - - + -
361A PRO 3.5 19.7 - - - +
362A VAL* 2.9 21.7 + - + +
364A LYS* 1.3 80.0 - - + +
366A MET* 1.3 65.1 + - - +
368A ASP* 3.2 11.0 + - - +
369A ALA* 2.9 27.2 + - - +
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Residues in contact with MET 366 (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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215A MET* 4.2 6.7 - - - +
341A ASN* 4.6 2.9 + - - +
344A ALA* 3.7 9.6 - - + +
345A THR* 3.5 42.8 - - - +
348A VAL* 3.9 10.5 - - + -
362A VAL 3.3 4.1 + - - +
363A GLU 3.2 9.4 + - - +
365A LEU* 1.3 78.7 - - - +
367A ARG* 1.3 62.6 + - - +
369A ALA* 3.4 7.3 + - - +
370A LYS 3.8 7.6 + - - -
215B MET* 3.6 30.1 - - + -
341B ASN* 5.5 1.8 - - - +
366B MET* 3.8 41.9 - - + +
370B LYS* 3.8 21.8 - - + -
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Residues in contact with ARG 367 (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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43A ASP* 2.7 41.4 + - - -
215A MET* 3.2 45.1 + - + +
216A GLY* 3.3 16.6 - - - -
218A ARG* 3.2 22.4 - - - +
363A GLU* 2.7 41.4 + - - +
364A LYS* 3.0 31.1 + - - +
366A MET* 1.3 75.3 - - - +
368A ASP* 1.3 65.6 + - - +
369A ALA 3.5 0.2 + - - -
370A LYS 4.1 0.3 + - - -
215B MET* 3.9 21.5 - - - -
356B PHE* 3.5 17.0 - - - -
367B ARG* 4.1 11.6 - - + +
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Residues in contact with ASP 368 (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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43A ASP* 4.7 1.7 - - - +
92A THR* 3.4 25.3 + - - +
93A GLY 5.2 0.2 - - - -
216A GLY* 3.6 2.4 - - - -
217A GLN* 2.6 37.4 + - + +
218A ARG 4.5 0.5 + - - -
266A LEU* 3.7 12.1 - - + -
364A LYS* 2.9 57.6 + - - +
365A LEU* 3.2 5.2 + - - +
367A ARG* 1.3 79.9 + - - +
369A ALA* 1.3 64.2 + - - +
370A LYS 3.3 0.7 + - - -
371A ILE* 3.1 26.3 + - - +
372A TYR* 4.0 0.7 - - - -
356B PHE* 4.6 0.3 - - - -
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Residues in contact with ALA 369 (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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266A LEU* 3.7 17.7 - - + -
340A ALA* 4.0 12.3 - - + +
341A ASN* 3.1 38.3 - - - +
344A ALA* 4.5 3.6 - - + -
365A LEU 2.9 17.2 + - - +
366A MET 3.4 1.5 + - - +
367A ARG 3.3 1.2 - - - -
368A ASP* 1.3 77.4 - - - +
370A LYS* 1.3 54.1 + - - +
372A TYR* 2.7 35.4 + - - +
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Residues in contact with LYS 370 (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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215A MET* 3.7 27.1 - - + -
341A ASN* 3.2 18.2 - - - +
366A MET 3.8 1.8 + - - -
368A ASP 3.3 0.8 + - - -
369A ALA* 1.3 73.9 - - - +
371A ILE* 1.3 57.0 + - - +
373A GLN* 2.8 49.2 + - - +
374A ILE* 3.6 8.4 + - + +
345B THR* 3.2 44.9 + - + +
348B VAL* 4.0 21.3 - - + -
349B GLN* 2.9 34.5 - - - +
356B PHE* 3.9 9.2 - - + -
366B MET* 4.3 2.7 - - + -
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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