Contacts of the helix formed by residues 288 - 303 (chain A) in PDB entry 3LEZ
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 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ALA* 3.6 34.1 - - + +
233A LEU* 4.0 8.7 - - + +
256A ARG* 3.0 41.4 + - - +
286A TYR* 3.3 10.9 - - - -
287A ASP* 1.3 73.8 + - - +
289A LYS* 1.3 64.2 + - + +
290A LEU 3.1 0.2 - - - -
291A ILE* 3.0 23.4 + - - +
292A GLU 3.3 8.3 + - - -
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.0 15.7 - - + -
232A ALA* 5.7 5.8 + - - +
287A ASP* 2.9 20.5 + - - +
288A ASP* 1.3 80.2 - - + +
290A LEU* 1.3 62.5 + - - +
292A GLU* 3.4 27.0 + - - +
293A LYS* 2.9 39.2 + - + +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 23.6 - - + +
56A PHE* 3.8 40.4 - - + -
58A VAL* 3.8 26.9 - - + -
60A LEU* 4.3 12.3 - - + -
256A ARG* 5.9 1.3 - - + -
277A SER* 3.5 35.2 - - - +
287A ASP 3.0 16.9 + - - +
289A LYS* 1.3 77.5 - - - +
291A ILE* 1.3 65.8 + - + +
293A LYS* 3.5 0.8 + - - -
294A ALA* 2.9 27.7 + - - +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.7 38.8 - - + -
234A ILE* 3.9 7.2 - - + +
256A ARG* 3.8 31.2 - - + +
257A ASN* 5.0 0.7 - - - +
258A ASP* 3.9 14.4 - - + -
275A ILE* 3.7 34.8 - - + +
277A SER* 4.4 1.1 - - - +
287A ASP 4.8 0.2 - - - +
288A ASP* 3.0 12.2 + - - +
290A LEU* 1.3 90.8 - - + +
292A GLU* 1.3 65.1 + - - +
294A ALA* 3.4 5.0 + - - +
295A THR* 2.9 29.7 + - - -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 4.0 8.8 - - - +
233A LEU 3.6 17.3 + - - +
236A ALA* 3.4 35.7 - - - +
237A GLY* 3.8 0.5 - - - -
288A ASP 3.3 5.2 + - - +
289A LYS* 3.4 38.3 + - - +
291A ILE* 1.3 79.6 - - - +
293A LYS* 1.3 60.1 + - + +
295A THR* 3.2 6.4 + - - -
296A GLU* 3.0 48.1 + - - +
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.8 22.2 - - + -
55A GLU* 3.0 24.5 + - - +
56A PHE* 4.1 20.2 - - + -
289A LYS* 2.9 28.8 + - + +
290A LEU 3.9 0.7 - - - +
292A GLU* 1.3 79.1 - - + +
294A ALA* 1.3 66.3 + - - +
296A GLU* 3.3 18.1 + - - +
297A ILE* 3.0 28.6 + - + +
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Residues in contact with ALA 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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49A LEU* 4.0 13.7 - - + +
52A LEU* 3.5 17.2 - - + +
60A LEU* 4.7 3.8 - - + -
62A VAL* 4.6 6.1 - - + -
275A ILE* 4.0 24.9 - - + -
290A LEU 2.9 18.5 + - - +
291A ILE 3.8 4.3 - - - +
292A GLU 3.3 0.2 - - - -
293A LYS* 1.3 75.3 - - - +
295A THR* 1.3 58.0 + - - +
297A ILE* 3.3 2.9 + - - +
298A VAL* 2.9 34.1 + - - +
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Residues in contact with THR 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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234A ILE* 3.5 41.8 - - + +
237A GLY* 3.8 14.1 - - - +
238A VAL* 3.9 10.5 - - + -
262A ILE* 4.7 1.1 - - + -
273A ILE* 4.3 6.9 - - + +
275A ILE* 3.4 17.0 - - - +
291A ILE 2.9 14.1 + - - -
292A GLU 3.4 9.0 - - - -
294A ALA* 1.3 77.4 - - - +
296A GLU* 1.3 63.2 + - - +
298A VAL* 3.2 7.4 + - - +
299A LEU* 3.0 28.4 + - + +
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA 4.1 4.7 - - - +
237A GLY* 3.7 20.1 - - - +
292A GLU* 3.0 42.5 + - - +
293A LYS* 3.3 20.6 + - - +
295A THR* 1.3 75.4 - - - +
297A ILE* 1.3 59.5 + - + +
299A LEU* 3.4 3.0 + - - +
300A GLN* 3.0 39.7 + - + +
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Residues in contact with ILE 297 (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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46A SER* 4.1 7.2 - - - +
48A ASP* 3.7 47.6 - - + +
49A LEU* 3.8 20.9 - - + -
52A LEU* 3.9 22.0 - - + -
73A ILE* 4.7 3.8 - - + -
293A LYS* 3.0 20.6 + - + +
294A ALA 3.6 6.1 - - - +
295A THR 3.3 0.2 - - - -
296A GLU* 1.3 73.5 - - + +
298A VAL* 1.3 65.4 + - - +
300A GLN* 3.3 17.9 + - + +
301A GLU* 3.0 27.0 + - + +
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Residues in contact with VAL 298 (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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49A LEU* 4.9 2.2 - - + -
62A VAL* 3.8 29.6 - - + -
64A ALA* 3.5 25.1 - - + -
73A ILE* 3.8 19.1 - - + -
271A ILE* 5.2 0.9 - - + -
273A ILE* 4.2 15.9 - - + -
275A ILE* 5.4 0.2 - - + -
294A ALA 2.9 20.9 + - - +
295A THR* 3.2 9.8 + - - +
297A ILE* 1.3 75.1 - - - +
299A LEU* 1.3 63.9 + - + +
301A GLU* 3.1 3.6 + - - +
302A LEU* 2.9 42.6 + - + +
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Residues in contact with LEU 299 (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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237A GLY 3.6 22.2 - - - +
238A VAL* 4.0 15.5 - - + -
239A PRO* 3.8 22.7 - - + -
242A TRP* 4.0 13.9 - - + -
262A ILE* 4.4 10.3 - - + -
271A ILE* 3.6 30.7 - - + -
295A THR* 3.0 19.4 + - + +
296A GLU* 3.9 3.8 - - - +
298A VAL* 1.3 83.2 - - + +
300A GLN* 1.3 60.6 + - + +
302A LEU* 4.5 2.5 - - + +
303A ARG* 2.9 42.2 + - + +
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Residues in contact with GLN 300 (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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48A ASP* 5.1 5.7 - - - +
296A GLU* 3.0 23.3 + - + +
297A ILE* 3.5 24.9 - - + +
299A LEU* 1.3 76.8 - - - +
301A GLU* 1.3 58.8 - - + +
304A ASN* 3.0 43.0 + - - +
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Residues in contact with GLU 301 (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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46A SER* 4.6 9.1 + - - +
47A GLU 5.7 0.7 + - - -
48A ASP* 5.0 6.9 - - - +
71A LYS* 2.8 34.2 + - - -
73A ILE* 3.5 34.3 - - + -
297A ILE* 3.0 17.9 + - + +
298A VAL 3.5 7.4 - - - +
300A GLN* 1.3 81.0 - - + +
302A LEU* 1.3 60.5 + - + +
303A ARG 3.5 0.2 + - - -
304A ASN 3.5 5.4 + - - -
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Residues in contact with LEU 302 (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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64A ALA* 4.2 7.2 - - + +
66A ASP* 4.1 26.4 - - + +
69A ALA* 4.5 8.0 - - - +
71A LYS* 3.5 54.4 - - + +
72A GLU* 4.0 12.3 - - - -
73A ILE* 4.2 6.1 - - + +
271A ILE* 3.8 30.1 - - + -
298A VAL* 2.9 41.8 + - + +
299A LEU* 4.3 2.9 - - + +
301A GLU* 1.3 74.4 - - - +
303A ARG* 1.3 64.2 + - + +
304A ASN 3.3 4.0 + - - +
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Residues in contact with ARG 303 (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 ASP* 3.0 32.5 + - - -
68A GLY* 6.0 0.4 - - - -
69A ALA* 5.3 4.0 - - - +
242A TRP* 3.9 25.7 - - + -
264A PRO* 3.9 25.6 - - - +
268A GLU* 3.0 38.6 + - - +
269A GLU 4.7 3.6 + - - -
271A ILE* 4.6 2.8 - - - +
299A LEU* 2.9 27.9 + - + +
302A LEU* 1.3 79.6 + - + +
304A ASN* 1.3 71.0 + - - +
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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