Contacts of the helix formed by residues 341 - 355 (chain A) in PDB entry 1T5A
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 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A SER* 3.4 17.9 - - - +
340A PRO* 1.3 77.0 - - - +
342A ARG* 1.3 62.6 + - - +
343A ALA* 3.3 8.3 + - - +
344A GLU* 2.7 57.0 + - - +
345A GLY* 3.0 11.3 + - - -
329C GLN* 3.0 26.7 - - - +
332C GLU* 4.7 14.6 - - + -
344C GLU* 5.3 4.4 + - - +
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 6.2 0.6 - - - +
340A PRO 3.7 13.7 + - - -
341A THR* 1.3 71.6 - - - +
343A ALA* 1.3 58.0 + - - +
345A GLY* 3.4 1.8 + - - +
346A SER* 2.9 29.4 + - - -
178C ASP* 3.6 13.5 + - - -
294C ARG* 2.8 62.6 + - + +
295C GLY 2.9 19.5 + - - +
298C GLY* 3.3 18.1 + - - -
299C ILE* 3.3 25.3 - - - +
303C ALA* 5.9 6.0 - - - +
306C VAL* 4.7 11.7 - - + +
328C THR 4.1 4.5 - - - +
329C GLN* 3.0 33.0 + - + +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 3.1 6.6 + - - +
342A ARG* 1.3 80.4 - - - +
344A GLU* 1.3 57.7 + - + +
346A SER* 3.4 2.1 + - - -
347A ASP* 2.8 28.6 + - - +
294C ARG* 4.5 0.2 - - - +
329C GLN 3.5 23.3 + - - +
330C MET 4.1 5.4 - - - +
343C ALA* 3.8 5.5 - - - +
344C GLU* 4.1 15.3 - - + -
347C ASP* 3.6 32.3 + - + +
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Residues in contact with GLU 344 (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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329A GLN 4.5 1.0 - - - +
330A MET 3.2 19.5 - - - +
331A LEU* 3.6 13.4 - - + -
332A GLU* 3.0 17.7 + - - +
333A SER* 2.6 52.8 + - - -
340A PRO* 3.5 3.6 - - - +
341A THR* 2.7 32.3 + - - +
343A ALA* 1.3 75.7 - - + +
345A GLY* 1.3 65.5 + - - +
347A ASP* 3.0 14.6 + - - +
348A VAL* 3.1 18.7 + - - +
341C THR* 5.4 5.6 + - - +
343C ALA* 4.2 10.5 - - + -
344C GLU* 5.8 1.8 - - + -
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 4.5 2.1 - - - +
340A PRO* 4.9 5.3 - - - +
341A THR 3.0 12.1 + - - -
342A ARG* 3.9 3.1 - - - -
344A GLU* 1.3 77.6 - - - +
346A SER* 1.3 60.7 + - - +
348A VAL* 3.4 0.5 + - - +
349A ALA* 3.2 22.4 + - - +
381A ILE* 3.7 26.9 - - - +
303C ALA* 5.4 9.6 - - - -
307C PHE* 5.4 2.8 - - - -
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Residues in contact with SER 346 (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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342A ARG 2.9 17.2 + - - -
343A ALA 3.5 2.2 - - - -
345A GLY* 1.3 76.2 - - - +
347A ASP* 1.3 61.8 + - - +
349A ALA* 4.0 4.9 - - - +
350A ASN* 3.0 39.2 + - - +
294C ARG* 3.8 6.4 + - - -
307C PHE* 4.8 12.0 - - - +
310C GLN* 5.2 5.7 + - - -
347C ASP* 2.8 31.5 + - - -
350C ASN* 5.1 0.2 - - - +
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 2.4 48.0 + - - -
310A GLN* 5.2 1.2 + - - -
330A MET* 3.6 15.8 - - - +
343A ALA 2.8 14.3 + - - +
344A GLU 3.0 8.7 + - - +
346A SER* 1.3 77.6 - - - +
348A VAL* 1.3 62.9 + - - +
350A ASN* 3.4 3.3 + - - +
351A ALA* 3.1 20.4 + - - +
343C ALA* 3.5 25.5 - - + +
346C SER* 2.8 23.9 + - - -
347C ASP* 5.5 0.4 - - - +
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A MET* 3.5 28.7 - - + -
331A LEU* 4.2 18.4 - - + -
344A GLU 3.1 13.1 + - - +
345A GLY 3.8 2.0 - - - +
347A ASP* 1.3 75.7 - - - +
349A ALA* 1.3 65.2 + - - +
351A ALA* 3.0 14.2 + - - +
352A VAL* 3.2 12.7 + - + +
359A ILE* 3.9 28.5 - - + -
378A GLN* 4.3 10.8 - - + +
381A ILE* 3.6 31.2 - - + -
382A ALA 4.6 3.8 - - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLY 3.2 12.6 + - - +
346A SER 4.0 3.8 - - - +
348A VAL* 1.3 78.1 - - - +
350A ASN* 1.3 57.4 + - - +
352A VAL* 3.3 5.1 + - - +
353A LEU* 2.9 32.8 + - - +
381A ILE* 3.5 10.8 - - + +
385A ALA* 3.6 7.6 - - + +
307C PHE* 3.5 50.9 - - + -
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLN* 5.1 0.9 - - - +
346A SER* 3.0 36.8 + - - +
347A ASP* 3.9 4.0 - - - +
348A VAL 3.2 0.2 - - - -
349A ALA* 1.3 77.5 - - - +
351A ALA* 1.3 56.6 + - - +
353A LEU* 3.9 7.9 - - - +
354A ASP* 2.7 44.5 + - - +
307C PHE* 5.7 1.8 - - - +
310C GLN* 6.1 0.8 - - - +
311C LYS* 3.1 35.1 + - - +
346C SER* 4.9 1.1 - - - +
350C ASN* 3.4 45.7 - - - +
354C ASP* 5.6 0.8 + - - -
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLN* 4.2 8.0 - - - +
326A CYS* 3.8 34.5 - - + -
330A MET* 3.9 9.0 - - + -
347A ASP 3.1 11.4 + - - +
348A VAL 3.0 10.6 + - - +
350A ASN* 1.3 74.4 - - - +
352A VAL* 1.3 66.3 + - - +
354A ASP* 3.2 9.0 + - - +
355A GLY 3.1 5.4 + - - -
356A ALA* 3.1 24.7 + - + +
359A ILE* 4.3 6.7 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.8 22.2 - - + +
348A VAL* 3.2 12.7 + - + +
349A ALA 3.5 7.2 - - - +
351A ALA* 1.3 77.3 - - - +
353A LEU* 1.3 54.2 + - - +
355A GLY* 2.6 21.5 + - - -
356A ALA 4.5 4.0 - - - +
359A ILE* 4.4 8.3 - - + -
382A ALA* 3.9 22.2 - - + +
385A ALA* 3.6 20.4 - - + +
386A GLU* 3.7 22.9 - - + +
389A ILE* 4.4 1.0 - - + +
467A ARG* 2.9 35.7 + - - +
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Residues in contact with LEU 353 (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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349A ALA 2.9 20.6 + - - +
350A ASN* 3.9 11.2 - - - +
352A VAL* 1.3 73.2 - - - +
354A ASP* 1.3 67.0 + - - +
355A GLY* 3.1 1.2 + - - -
385A ALA* 3.7 25.1 - - + +
388A ALA* 3.8 25.1 - - + +
389A ILE* 3.9 14.7 - - + +
30C MET* 6.0 0.5 - - - +
307C PHE* 4.1 15.3 - - + -
311C LYS* 3.6 35.2 - - + +
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Residues in contact with ASP 354 (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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310A GLN* 2.9 27.0 + - - -
311A LYS* 2.8 46.3 + - - +
314A ILE* 3.4 27.1 - - + +
318A ASN* 4.3 3.3 + - - -
350A ASN* 2.7 29.9 + - - +
351A ALA 3.3 7.6 - - - +
353A LEU* 1.3 75.1 - - - +
355A GLY* 1.3 59.5 + - - +
30C MET* 4.2 25.0 - - - +
350C ASN* 5.6 0.5 + - - -
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 3.4 5.3 - - - +
318A ASN* 3.0 32.9 - - - +
324A VAL* 4.1 0.9 - - - +
352A VAL 2.6 15.4 + - - -
353A LEU 3.0 1.8 - - - -
354A ASP* 1.3 81.1 - - - +
356A ALA* 1.3 59.8 + - - +
357A ASP 3.9 0.2 + - - -
389A ILE* 5.9 0.7 - - - -
394A LEU* 6.4 2.0 - - - -
445A ARG* 3.2 11.7 + - - -
467A ARG* 3.3 11.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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