Contacts of the helix formed by residues 285 - 295 (chain A) in PDB entry 1LI5
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 ASP 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LEU* 4.2 0.2 - - - -
284A TYR* 1.3 76.7 - - - +
286A ALA* 1.3 63.0 + - - +
287A GLU* 3.2 6.4 + - - +
288A THR* 2.6 57.5 + - - +
289A VAL* 3.2 10.2 + - - +
313A ARG* 2.8 29.7 + - - +
396A GLN* 5.4 0.2 - - - +
401A PHE* 3.3 14.3 - - + -
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Residues in contact with ALA 286 (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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102A ALA* 3.1 31.9 - - + +
103A LEU* 3.9 6.1 - - - +
281A LEU* 3.5 24.8 - - + +
284A TYR 3.7 1.6 + - - -
285A ASP* 1.3 73.6 - - - +
287A GLU* 1.3 60.0 + - - +
289A VAL* 3.6 3.4 + - - +
290A ARG* 3.2 20.3 + - - +
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Residues in contact with GLU 287 (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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285A ASP* 3.2 10.0 + - - +
286A ALA* 1.3 75.3 - - - +
288A THR* 1.3 61.2 + - - +
289A VAL 3.2 0.7 - - - -
290A ARG* 3.2 6.3 + - + +
291A TYR* 2.8 27.9 + - - +
316A LEU* 3.4 15.1 - - + +
320A TYR* 2.9 24.6 + - - -
392A GLY 4.9 3.4 - - - +
393A LEU* 3.4 18.9 - - + +
394A LEU* 2.6 30.3 + - - -
395A GLU 4.7 1.2 + - - -
396A GLN* 2.7 35.3 - - - +
401A PHE* 4.6 1.3 - - + -
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Residues in contact with THR 288 (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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284A TYR* 4.6 7.6 - - + -
285A ASP* 2.6 39.7 + - - -
287A GLU* 1.3 76.4 - - - +
289A VAL* 1.3 57.9 + - - +
291A TYR* 3.3 3.5 + - - +
292A PHE* 2.9 27.2 + - - +
309A LEU* 3.5 22.0 - - + +
312A ALA* 3.7 3.7 - - + +
313A ARG* 3.5 43.0 - - + +
316A LEU* 3.7 13.4 - - - +
401A PHE* 4.1 0.3 - - - -
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Residues in contact with VAL 289 (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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38A ILE* 5.2 5.8 - - + -
103A LEU* 4.0 18.8 - - + -
277A VAL* 5.9 2.5 - - + -
280A VAL* 3.8 32.8 - - + -
281A LEU* 4.2 10.8 - - + -
284A TYR* 3.9 19.5 - - + +
285A ASP 3.2 14.5 + - - +
286A ALA 3.9 5.6 - - - +
287A GLU 3.2 0.4 - - - -
288A THR* 1.3 77.8 - - - +
290A ARG* 1.3 56.7 + - - +
292A PHE* 3.1 8.9 + - + +
293A LEU* 2.8 48.6 + - + +
309A LEU* 4.5 5.8 - - + -
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Residues in contact with ARG 290 (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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45A VAL* 4.0 19.9 - - + +
48A ASP* 2.8 25.8 + - - +
49A VAL* 3.9 14.1 - - - +
52A ARG* 3.5 10.7 - - - +
103A LEU* 2.8 40.9 + - + +
104A ASN* 3.1 22.0 + - - -
105A ILE* 3.9 7.1 - - - +
286A ALA 3.2 12.4 + - - +
287A GLU* 3.2 10.8 + - - +
289A VAL* 1.3 79.0 - - - +
291A TYR* 1.3 62.5 + - - +
293A LEU* 3.2 19.4 + - - +
294A MET* 3.2 20.7 + - + +
391A LEU 2.8 30.4 + - - -
392A GLY* 3.4 21.0 + - - -
393A LEU* 4.5 3.1 - - + -
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Residues in contact with TYR 291 (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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287A GLU 2.8 17.2 + - - +
288A THR* 3.5 5.2 - - - +
290A ARG* 1.3 77.8 - - - +
292A PHE* 1.3 62.8 + - - +
294A MET* 3.2 3.4 + - - -
295A SER* 3.1 15.5 + - - -
312A ALA* 3.7 25.4 - - + -
315A ALA* 3.5 23.7 - - + +
316A LEU* 3.8 24.5 - - + -
319A LEU* 4.3 19.7 - - + -
356A TYR* 2.7 64.3 + + - +
360A PHE* 3.1 25.7 - + - -
393A LEU* 3.8 11.4 - - + +
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Residues in contact with PHE 292 (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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38A ILE* 5.8 0.7 - - + -
260A VAL* 5.2 2.9 - - + -
288A THR 2.9 13.6 + - - +
289A VAL* 3.5 10.1 - - + +
291A TYR* 1.3 78.5 - - - +
293A LEU* 1.3 76.0 + - + +
294A MET 3.0 0.2 + - - -
295A SER* 2.6 31.4 + - - -
302A LEU* 3.4 38.8 - - + +
303A ASN 3.5 13.9 - - - -
304A TYR* 3.5 43.5 - + + -
308A ASN* 4.0 16.8 - - + -
309A LEU* 3.4 32.5 - - + -
312A ALA* 3.8 14.1 - - + -
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Residues in contact with LEU 293 (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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38A ILE* 4.0 14.8 - - + +
41A GLY* 3.8 13.7 - - - -
42A ARG* 3.3 58.0 + - + +
45A VAL* 3.7 30.6 - - + +
46A ALA* 5.9 1.0 + - - +
103A LEU* 4.1 11.7 - - + -
260A VAL* 5.3 1.3 - - + -
289A VAL* 2.8 42.1 + - + +
290A ARG* 3.2 7.6 + - - +
292A PHE* 1.3 92.3 - - + +
294A MET* 1.3 58.8 + - - +
302A LEU* 4.0 5.3 - - + +
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Residues in contact with MET 294 (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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42A ARG* 5.0 0.2 - - - +
45A VAL* 3.5 26.5 - - + -
46A ALA* 5.5 2.5 - - - +
49A VAL* 3.4 31.0 - - + -
290A ARG* 3.2 18.4 + - + +
291A TYR 3.2 2.0 + - - -
292A PHE 3.0 0.6 - - - -
293A LEU* 1.3 74.7 - - - +
295A SER* 1.3 59.4 + - - +
296A GLY 3.0 12.9 + - - +
352A THR* 2.9 37.3 + - + -
353A PRO* 4.2 0.9 - - - +
356A TYR* 3.0 41.1 + - + +
391A LEU* 3.6 29.2 - - + +
393A LEU* 3.7 21.3 - - + -
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Residues in contact with SER 295 (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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291A TYR* 3.1 15.6 + - - -
292A PHE* 2.6 35.1 + - - -
294A MET* 1.3 77.0 - - - +
296A GLY* 1.3 57.2 + - - +
302A LEU* 3.9 6.1 - - - +
312A ALA* 6.2 0.4 - - - -
353A PRO* 3.4 17.3 - - - +
356A TYR* 3.7 19.1 - - - -
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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