Contacts of the helix formed by residues 303 - 314 (chain A) in PDB entry 1LT8
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 GLU 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.5 30.0 - - - +
35A LYS* 4.6 16.0 + - - +
36A ARG* 3.1 27.8 + - - -
63A PHE* 3.6 7.2 - - - -
301A GLY 4.0 9.8 - - - +
302A PHE* 1.3 76.3 - - - +
304A PRO* 1.3 76.2 - - + +
305A TYR* 3.3 28.5 - - + -
306A HIS* 2.9 23.1 + - + +
307A ILE* 3.3 5.0 + - - +
35B LYS* 5.7 3.2 - - + +
36B ARG* 5.5 1.0 - - - +
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Residues in contact with PRO 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 4.0 5.6 - - - +
59A LEU* 4.3 2.7 - - + -
62A GLU* 3.5 50.9 - - + +
63A PHE* 3.4 24.0 - - + -
66A ALA* 3.3 11.9 - - + +
303A GLU* 1.3 100.8 - - + +
305A TYR* 1.3 62.7 + - - +
307A ILE* 3.0 3.3 + - - +
308A ARG* 3.0 18.4 + - - -
35B LYS* 3.8 11.7 - - + +
36B ARG* 4.1 9.6 - - + +
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 4.1 2.6 - - - +
278A ARG* 3.6 41.9 - - + +
303A GLU* 3.3 18.8 - - + -
304A PRO* 1.3 75.9 - - - +
306A HIS* 1.3 102.1 + + - +
308A ARG* 3.7 26.6 + - - +
309A ALA* 3.0 21.1 + - - +
34B GLU 4.8 0.2 - - - +
35B LYS* 3.1 57.1 + - + +
272B GLU* 2.6 38.8 + - - +
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Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 4.2 4.9 - - + -
275A VAL* 3.8 10.3 - - + -
276A ALA* 2.6 31.1 + - + +
277A THR 4.2 3.4 - - - -
278A ARG* 4.6 0.4 - - - -
281A ILE* 3.3 33.1 - - + +
301A GLY 3.4 18.8 + - - -
302A PHE* 3.5 24.0 - + + -
303A GLU* 2.9 30.3 + - + +
305A TYR* 1.3 113.8 + + - +
307A ILE* 1.3 61.5 + - - +
309A ALA* 3.2 19.5 + - - +
310A ILE* 3.4 2.4 + - - +
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Residues in contact with ILE 307 (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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24A ILE* 3.6 14.5 - - + +
25A GLY 3.5 16.2 - - - +
26A ASP 3.9 13.2 - - - +
27A GLY* 4.0 2.0 - - - +
63A PHE* 3.8 28.5 - - + -
66A ALA* 3.9 13.8 - - + +
68A SER* 3.3 27.6 - - - +
298A GLY 4.6 3.4 - - - +
302A PHE* 3.9 19.3 - - + -
303A GLU 3.3 2.6 + - - +
304A PRO 3.0 7.9 + - - +
306A HIS* 1.3 76.5 - - - +
308A ARG* 1.3 65.9 + - - +
310A ILE* 3.0 27.7 + - + +
311A ALA* 3.2 9.2 + - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.3 20.8 + - + +
278A ARG* 3.8 12.1 - - - +
304A PRO 3.0 12.1 + - - +
305A TYR* 3.7 23.6 + - - +
306A HIS 3.3 0.2 - - - -
307A ILE* 1.3 76.7 - - - +
309A ALA* 1.3 58.5 + - - +
311A ALA* 3.0 1.7 + - - +
312A GLU* 2.8 60.5 + - + +
322A PRO* 4.2 8.1 - - + -
324A ALA* 3.0 34.7 + - + +
325A SER* 4.1 6.1 - - - +
327A LYS* 4.0 9.9 + - - +
328A HIS* 3.2 36.3 + - - +
34B GLU* 3.9 10.8 + - - -
35B LYS 5.9 0.2 - - - -
37B GLY* 3.9 21.3 - - - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.5 35.2 - - + +
281A ILE* 3.9 10.1 - - + -
282A GLN* 3.4 14.9 - - + +
305A TYR 3.0 13.4 + - - +
306A HIS 3.2 12.8 - - - +
307A ILE 3.1 0.2 - - - -
308A ARG* 1.3 78.6 - - - +
310A ILE* 1.3 62.4 + - - +
312A GLU* 4.6 4.7 - - - +
313A GLU* 3.1 26.3 + - - +
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Residues in contact with ILE 310 (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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24A ILE* 3.5 28.0 - - + -
281A ILE* 3.6 12.3 - - + -
284A TYR* 4.2 2.2 - - + -
285A ALA* 4.0 17.5 - - + -
296A ILE* 3.7 37.0 - - + +
297A GLY 3.9 17.7 - - - +
302A PHE* 4.1 8.3 - - + -
306A HIS 3.4 10.3 + - - +
307A ILE* 3.0 28.4 + - + +
309A ALA* 1.3 77.3 - - - +
311A ALA* 1.3 62.4 + - - +
313A GLU* 3.9 0.9 - - - +
314A LEU* 3.2 29.3 + - + +
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Residues in contact with ALA 311 (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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24A ILE* 4.8 6.7 - - + +
66A ALA 3.6 11.4 - - - +
67A GLY* 4.6 3.4 - - - -
307A ILE 3.2 2.6 + - - +
308A ARG 3.0 8.9 + - - +
310A ILE* 1.3 78.7 - - - +
312A GLU* 1.3 65.2 + - - +
314A LEU 3.5 2.3 + - - -
315A ALA* 3.0 22.5 + - - +
318A ARG* 4.5 19.3 + - - +
320A PHE 4.5 4.2 - - - +
322A PRO* 3.4 32.1 - - + -
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 4.2 10.3 - - - +
308A ARG* 2.8 38.4 + - + +
309A ALA* 4.3 3.8 - - - +
311A ALA* 1.3 71.8 - - - +
313A GLU* 1.3 63.4 + - - +
315A ALA* 3.1 17.5 + - - +
316A PRO* 4.0 3.1 - - - +
321A LEU* 4.0 12.3 - - + -
322A PRO* 4.7 0.4 - - + -
325A SER* 2.9 36.1 + - - +
328A HIS* 2.8 38.1 + - - -
329A GLY* 3.7 12.0 + - - +
331A TRP* 3.7 27.3 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 2.7 65.6 + - + +
283A LYS* 5.7 0.2 - - - -
285A ALA* 4.2 3.8 - - + -
286A ARG* 2.8 68.1 + - + +
309A ALA 3.1 19.8 + - - +
310A ILE 3.9 3.8 - - - +
311A ALA 3.4 0.2 - - - -
312A GLU* 1.3 77.6 - - - +
314A LEU* 1.3 59.1 + - + +
315A ALA 3.4 0.6 + - - -
316A PRO* 3.8 5.0 - - - +
331A TRP* 5.1 0.9 - - - +
349A LYS* 3.9 12.1 + - - -
353A GLU* 4.3 1.8 - - - +
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Residues in contact with LEU 314 (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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22A ILE* 3.9 23.3 - - + -
24A ILE* 5.2 0.4 - - + -
285A ALA* 3.9 22.9 - - + +
286A ARG* 3.6 28.5 - - - +
289A TYR* 3.9 22.7 - - + -
296A ILE* 3.7 30.3 - - + -
310A ILE* 3.2 18.8 + - + +
311A ALA 3.6 2.9 - - - -
312A GLU 3.2 0.6 - - - -
313A GLU* 1.3 78.2 - - + +
315A ALA* 1.3 64.9 + - - +
316A PRO 3.2 2.5 - - - -
317A GLU* 3.1 10.9 + - + +
318A ARG* 2.8 35.0 + - + +
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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