Contacts of the helix formed by residues 303 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 5.0 5.3 - - + +
36A ARG* 5.2 2.4 + - - +
31B PHE 5.1 0.3 - - - -
32B ALA* 3.5 29.6 + - - +
35B LYS* 4.9 11.3 + - - +
36B ARG* 3.1 29.5 + - - -
63B PHE* 3.6 6.8 - - - -
301B GLY 4.0 10.2 - - - +
302B PHE* 1.3 77.1 - - - +
304B PRO* 1.3 75.1 - - + +
305B TYR* 3.3 18.4 - - + -
306B HIS* 2.9 32.1 + - + +
307B ILE* 3.4 3.8 + - - +
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Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS 3.5 12.1 - - - +
36A ARG* 3.9 17.3 - - + +
36B ARG* 4.0 6.5 - - - +
59B LEU* 4.5 0.7 - - + -
62B GLU* 3.5 43.5 - - + +
63B PHE* 3.6 25.3 - - + -
66B ALA* 3.2 12.7 - - + +
303B GLU* 1.3 97.5 - - + +
305B TYR* 1.3 62.4 + - - +
307B ILE 3.1 2.6 + - - -
308B ARG* 2.9 18.2 + - - +
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.0 60.9 + - + +
36A ARG 5.4 0.2 - - - -
37A GLY* 6.0 0.4 - - - +
272A GLU* 2.8 37.6 + - - +
275B VAL* 4.1 2.9 - - - +
278B ARG* 3.7 41.5 - - + +
303B GLU* 3.2 15.7 + - + -
304B PRO* 1.3 74.9 - - - +
306B HIS* 1.3 97.0 + + - +
308B ARG* 3.4 31.6 + - - +
309B ALA* 3.0 26.2 + - - +
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Residues in contact with HIS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ALA* 4.5 5.8 - - + -
275B VAL* 3.9 9.1 - - + +
276B ALA 2.8 30.3 + - - -
277B THR 4.3 1.4 + - - -
278B ARG* 5.4 0.2 - - - +
281B ILE* 3.2 29.8 - - + +
301B GLY 3.5 15.6 + - - -
302B PHE* 3.5 25.6 - + + -
303B GLU* 2.9 41.9 + - + +
305B TYR* 1.3 107.2 + + - +
307B ILE* 1.3 65.9 + - - +
309B ALA* 3.0 22.4 + - - +
310B ILE* 3.3 1.0 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.7 12.7 - - + +
25B GLY 3.3 20.4 - - - +
26B ASP 3.7 14.8 - - - +
27B GLY* 3.9 1.3 - - - +
63B PHE* 3.6 29.4 - - + -
66B ALA* 4.0 11.4 - - + +
68B SER* 3.3 27.1 - - - +
298B GLY 4.3 2.5 - - - +
302B PHE* 3.8 19.5 - - + -
303B GLU 3.4 1.8 + - - +
304B PRO 3.1 7.7 + - - +
306B HIS* 1.3 74.9 - - - +
308B ARG* 1.3 64.3 + - - +
310B ILE* 2.9 29.1 + - + +
311B ALA* 3.2 10.0 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.6 14.8 + - - -
37A GLY* 3.9 21.2 - - - -
66B ALA* 3.3 24.9 + - + +
278B ARG* 3.5 25.3 - - - +
304B PRO 2.9 12.6 + - - +
305B TYR* 3.5 25.6 - - - +
306B HIS 3.2 0.2 - - - -
307B ILE* 1.3 78.9 - - - +
309B ALA* 1.3 56.6 + - - +
311B ALA* 3.2 2.1 + - - +
312B GLU* 2.8 53.6 + - + +
322B PRO* 4.5 7.6 - - + -
324B ALA* 3.0 32.8 + - + +
325B SER* 4.5 0.4 - - - +
327B LYS* 3.3 17.4 + - - +
328B HIS* 3.7 16.7 - - - -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.4 33.9 - - + +
281B ILE* 3.7 10.5 - - + -
282B GLN* 3.2 23.0 - - + +
305B TYR 3.0 11.9 + - - +
306B HIS 3.0 15.3 + - - +
308B ARG* 1.3 77.6 - - - +
310B ILE* 1.3 56.7 + - - +
312B GLU* 4.6 3.6 - - - -
313B GLU* 2.9 25.8 + - - +
328B HIS* 6.4 0.2 - - - -
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.2 19.1 - - + -
281B ILE* 3.7 11.2 - - + -
284B TYR* 4.2 5.8 - - + -
285B ALA* 3.9 17.0 - - + -
296B ILE* 3.7 47.1 - - + +
297B GLY 4.0 16.2 - - - +
302B PHE* 4.2 11.0 - - + -
306B HIS 3.6 8.3 - - - +
307B ILE* 2.9 20.1 + - + +
309B ALA* 1.3 77.9 - - - +
311B ALA* 1.3 63.9 + - - +
313B GLU* 3.8 0.5 - - - +
314B LEU* 3.1 32.6 + - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.5 24.8 - - + +
66B ALA 3.7 21.5 - - - +
67B GLY* 4.5 0.7 - - - -
307B ILE 3.2 2.9 + - - +
308B ARG 3.5 6.7 - - - +
310B ILE* 1.3 81.2 - - - +
312B GLU* 1.3 56.8 + - - +
314B LEU* 3.8 1.3 - - - -
315B ALA* 3.0 27.2 + - - +
318B ARG* 4.4 9.4 + - - +
320B PHE 4.4 4.2 - - - +
322B PRO* 3.7 19.6 - - + +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN* 4.0 16.5 + - - +
308B ARG* 2.8 34.4 + - + +
309B ALA* 4.0 3.6 - - - +
311B ALA* 1.3 71.2 - - - +
313B GLU* 1.3 68.1 + - - +
314B LEU 3.2 0.2 - - - -
315B ALA* 3.2 20.5 + - - +
316B PRO* 4.0 2.8 - - - +
321B LEU* 4.2 8.8 - - + +
322B PRO* 4.7 1.1 - - + -
325B SER* 2.9 29.9 + - - +
328B HIS* 2.9 44.9 + - - +
329B GLY 4.5 5.2 + - - +
330B SER* 5.4 3.6 - - - -
331B TRP 5.7 0.3 + - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN* 2.7 63.2 + - + +
285B ALA* 4.1 4.0 - - + -
286B ARG* 2.8 63.5 + - + +
309B ALA 2.9 19.0 + - - +
310B ILE 3.8 3.4 - - - +
312B GLU* 1.3 77.6 - - - +
314B LEU* 1.3 62.6 + - + +
315B ALA 3.4 0.6 + - - -
316B PRO* 3.7 6.1 - - - +
331B TRP* 3.9 12.1 + - - -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.0 21.5 - - + -
24B ILE* 6.0 0.4 - - + -
285B ALA* 4.1 17.3 - - + +
286B ARG* 3.6 28.7 - - - +
289B TYR* 4.0 21.8 - - + -
296B ILE* 3.6 30.7 - - + -
310B ILE* 3.1 22.4 + - + +
311B ALA* 3.8 2.5 - - - +
313B GLU* 1.3 78.4 - - + +
315B ALA* 1.3 65.7 + - - +
316B PRO* 3.2 3.8 - - - -
317B GLU* 3.0 9.9 + - - +
318B ARG* 2.9 33.7 + - + +
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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