Contacts of the helix formed by residues 343 - 357 (chain A) in PDB entry 1LWT
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 HIS 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A VAL* 3.9 24.6 - - + +
301A LYS* 5.9 7.6 - - + +
341A THR* 3.1 10.1 + - - +
342A ILE* 1.3 100.2 + - + +
344A THR* 1.3 69.2 + - - +
345A SER* 4.1 8.5 - - - +
346A VAL* 3.0 24.2 + - + +
347A ARG* 3.0 17.2 + - - +
381A TYR* 4.2 2.0 - - - -
14B G 6.3 0.2 - - - -
15B C 6.1 0.2 - - - -
29C C 4.8 12.1 + - - -
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Residues in contact with THR 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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342A ILE 3.8 3.4 + - - -
343A HIS* 1.3 68.2 - - - +
345A SER* 1.3 68.4 + - - +
347A ARG* 2.6 50.6 + - - +
348A ASP* 2.8 22.1 + - - +
381A TYR* 4.1 15.4 + - - +
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 3.5 36.3 + - - -
300A VAL* 4.2 4.7 - - - +
301A LYS 3.2 16.1 + - - -
302A ASN* 3.8 15.2 - - - +
303A ILE 4.2 1.3 + - - -
343A HIS* 4.1 10.4 - - - +
344A THR* 1.3 76.2 - - - +
346A VAL* 1.3 68.3 + - - +
348A ASP* 4.3 7.4 + - - -
349A GLY* 3.0 23.6 + - - -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 4.9 17.9 - - + +
301A LYS* 4.7 10.1 - - + -
302A ASN* 4.6 14.6 - - - +
303A ILE* 3.2 18.5 - - + +
322A LEU* 5.5 2.5 - - + -
339A ILE* 5.4 3.8 - - + -
341A THR* 3.4 26.0 - - + +
343A HIS* 3.0 28.5 + - + +
345A SER* 1.3 84.2 + - - +
347A ARG* 1.3 70.1 + - - +
350A LEU* 3.0 30.6 + - + +
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Residues in contact with ARG 347 (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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66A GLU* 3.5 30.5 + - - -
69A GLU* 6.0 5.8 - - - +
341A THR* 4.0 9.6 - - + +
343A HIS 3.0 11.0 + - - +
344A THR* 2.6 45.8 + - - +
346A VAL* 1.3 74.7 - - - +
348A ASP* 1.3 97.1 + - - +
350A LEU* 3.0 10.1 + - - +
351A VAL* 2.9 28.0 + - + +
363A VAL* 4.0 33.2 - - + +
381A TYR* 4.1 22.8 + - + -
383A ILE* 5.2 3.6 - - + -
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Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A THR* 2.8 22.5 + - - +
345A SER* 3.9 6.5 + - - +
347A ARG* 1.3 106.2 + - - +
349A GLY* 1.3 56.5 + - - +
350A LEU 2.5 15.4 + - - -
351A VAL* 2.5 24.4 + - - +
352A SER* 3.2 11.3 + - - -
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 3.5 31.9 - - - +
304A PRO 6.0 0.2 - - - -
305A SER* 5.9 2.1 - - - -
308A SER* 4.9 0.9 + - - -
345A SER 3.0 16.8 + - - -
348A ASP* 1.3 77.4 - - - +
350A LEU* 1.3 56.1 + - - +
352A SER* 2.7 21.1 + - - -
353A LEU* 3.3 13.5 + - - +
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Residues in contact with LEU 350 (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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303A ILE* 3.4 16.5 - - + +
319A LEU* 4.3 23.6 - - + -
322A LEU* 3.9 10.3 - - + -
339A ILE* 3.8 19.5 - - + -
346A VAL* 3.0 21.2 + - + +
347A ARG* 3.0 4.0 + - - +
348A ASP 2.5 5.5 + - - -
349A GLY* 1.3 72.4 - - - +
351A VAL* 1.3 54.9 + - - +
353A LEU* 3.1 7.8 + - + +
354A ALA* 2.6 41.9 + - + +
383A ILE* 3.6 40.2 - - + -
385A MSE 4.4 15.0 - - - -
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Residues in contact with VAL 351 (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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69A GLU* 4.5 11.9 - - + +
347A ARG* 2.9 39.0 - - + +
348A ASP* 2.5 12.9 + - - +
350A LEU* 1.3 70.2 - - + +
352A SER* 1.3 64.6 + - - +
354A ALA* 3.5 6.2 - - - +
355A ARG* 3.0 50.4 + - - +
361A VAL* 3.7 26.5 - - + -
363A VAL* 4.2 11.4 - - + -
383A ILE* 4.9 3.8 - - + -
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Residues in contact with SER 352 (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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305A SER* 5.6 3.3 - - - -
308A SER* 3.7 19.6 + - - -
348A ASP 3.2 4.1 + - - -
349A GLY* 2.7 30.3 + - - -
351A VAL* 1.3 78.0 - - - +
353A LEU* 1.3 57.8 + - - +
355A ARG* 5.1 4.9 - - - +
356A SER* 3.4 19.6 + - - -
449A GLN* 3.7 8.7 + - - +
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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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303A ILE* 4.7 5.8 - - + -
307A LEU* 3.8 45.5 - - + +
308A SER* 4.1 9.2 - - - +
315A ARG* 4.0 25.1 - - + +
318A PHE* 4.1 18.6 - - + -
319A LEU* 5.3 10.3 - - + -
349A GLY 3.4 14.6 - - - +
350A LEU* 3.1 8.7 + - + +
351A VAL 3.0 0.2 - - - -
352A SER* 1.3 79.9 + - - +
354A ALA* 1.3 70.1 + - - +
355A ARG 3.1 1.3 - - - -
356A SER* 2.5 36.8 + - - +
357A LEU* 3.5 7.3 + - + +
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Residues in contact with ALA 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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319A LEU* 5.7 1.8 - - - -
350A LEU* 2.6 24.9 + - + +
351A VAL* 3.5 4.5 - - - +
353A LEU* 1.3 76.2 - - - +
355A ARG* 1.3 61.1 + - - +
357A LEU* 3.3 9.1 + - - +
359A LEU* 3.4 24.3 - - - +
361A VAL* 3.3 28.7 - - + -
385A MSE 3.3 27.6 - - + -
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Residues in contact with ARG 355 (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 GLN* 5.1 2.8 + - - +
69A GLU* 3.4 41.8 + - - +
71A LEU* 3.4 31.5 - - - +
179A TYR* 4.5 21.9 + - + +
181A PRO* 4.1 0.5 - - - +
351A VAL* 3.0 30.2 + - - +
352A SER* 4.3 2.7 - - - +
354A ALA* 1.3 74.3 - - - +
356A SER* 1.3 54.9 + - - +
357A LEU 2.6 7.2 + - - -
358A GLY* 2.5 27.5 + - - -
359A LEU 3.9 12.8 - - - +
361A VAL* 4.0 24.9 + - + +
448A ASN* 4.4 11.2 + - - +
449A GLN* 3.0 30.3 - - - +
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Residues in contact with SER 356 (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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181A PRO* 3.4 1.7 - - - +
182A ILE* 2.7 42.6 + - - +
308A SER* 3.3 15.3 - - - -
315A ARG* 3.0 31.9 + - - -
352A SER 3.4 11.7 + - - -
353A LEU* 2.5 32.6 + - - +
355A ARG* 1.3 74.6 - - - +
357A LEU* 1.3 59.4 + - - +
449A GLN* 3.0 7.1 - - - +
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Residues in contact with LEU 357 (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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181A PRO* 3.4 10.2 - - - +
312A ILE* 3.4 33.7 - - + -
315A ARG* 4.5 23.8 - - + +
316A GLU* 4.1 11.2 - - + +
319A LEU* 5.5 5.8 - - + -
353A LEU* 4.6 7.4 - - + +
354A ALA* 3.3 12.1 + - - +
355A ARG 2.6 4.9 + - - -
356A SER* 1.3 85.6 + - - +
358A GLY* 1.3 56.5 + - - +
359A LEU* 3.6 22.7 - - + -
390A VAL* 3.9 2.3 - - + +
394A VAL* 4.2 18.6 - - + -
414A ARG* 2.7 44.6 + - - +
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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