Contacts of the helix formed by residues 295 - 306 (chain A) in PDB entry 1L2L
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 ASN 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLU* 4.9 0.2 + - - -
294A LEU* 1.3 74.5 - - - +
296A GLU* 1.3 69.8 + - - +
297A VAL* 3.1 12.1 + - - +
298A GLU* 2.9 56.8 + - - +
299A LEU* 3.0 27.9 + - - +
344A PHE* 3.5 6.2 - - - -
345A HIS* 3.0 31.9 - - + +
346A THR* 5.0 0.4 - - - -
442A GLY* 5.7 2.0 - - - -
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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
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295A ASN* 1.3 88.3 - - - +
297A VAL* 1.3 75.3 + - - +
299A LEU* 3.4 0.6 + - - +
300A ALA* 2.9 30.8 + - - +
315A ILE* 3.6 14.3 - - + +
316A ILE* 3.6 9.7 - - + +
321A ALA* 3.9 20.6 - - + -
344A PHE* 3.6 10.1 - - + -
346A THR* 3.0 44.6 - - + +
347A TYR* 3.8 20.1 + - - -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 5.4 14.6 - - + -
295A ASN* 3.1 9.8 + - - +
296A GLU* 1.3 91.3 - - - +
298A GLU* 1.3 61.4 + - + +
300A ALA* 3.4 2.8 + - - +
301A SER* 2.9 28.0 + - - -
316A ILE* 4.3 11.7 - - + -
347A TYR* 6.1 0.4 - - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.0 25.8 - - - +
270A PHE* 3.1 24.0 - - + +
271A ALA* 3.2 19.8 - - - +
272A PHE* 3.7 16.4 + - + +
294A LEU* 3.2 13.8 - - + -
295A ASN* 2.9 40.0 + - - +
297A VAL* 1.3 76.3 - - + +
299A LEU* 1.3 59.9 + - - +
301A SER* 3.4 6.4 + - - -
302A VAL* 3.0 35.4 + - - +
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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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294A LEU* 4.2 18.8 - - + +
295A ASN 3.0 18.8 + - - +
296A GLU 3.7 3.6 - - - +
298A GLU* 1.3 74.9 - - - +
300A ALA* 1.3 59.9 + - - +
302A VAL* 3.2 6.1 + - + +
303A VAL* 2.8 35.3 + - + +
315A ILE* 4.2 11.2 - - + -
326A VAL* 3.8 45.1 - - + +
329A GLY* 4.3 24.7 - - - +
330A LEU* 3.9 15.3 - - + -
333A LEU* 5.8 4.3 - - + -
344A PHE* 3.8 8.7 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU 2.9 18.1 + - - +
297A VAL* 3.7 3.8 - - - +
299A LEU* 1.3 76.8 - - - +
301A SER* 1.3 57.7 + - - +
303A VAL* 2.8 27.6 - - - +
304A SER* 2.9 17.5 + - - -
312A ALA* 3.5 19.3 - - + +
315A ILE* 4.2 4.4 - - + +
316A ILE* 3.4 27.8 - - + -
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Residues in contact with SER 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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272A PHE* 3.8 20.3 - - - -
273A THR 5.1 0.7 + - - -
279A ARG* 2.8 54.0 + - - +
297A VAL* 2.9 19.1 + - - -
298A GLU* 3.5 9.6 - - - -
300A ALA* 1.3 77.0 - - - +
302A VAL* 1.3 61.8 + - - +
304A SER* 3.5 3.7 + - - -
305A VAL 3.2 17.3 + - - -
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Residues in contact with VAL 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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270A PHE* 3.5 43.5 - - + -
279A ARG* 4.5 3.6 - - + +
283A VAL* 3.5 20.4 - - + -
294A LEU* 4.6 5.6 - - + -
298A GLU 3.0 21.7 + - - +
299A LEU* 3.2 9.2 + - + +
301A SER* 1.3 75.2 - - - +
303A VAL* 1.3 65.8 + - - +
305A VAL* 3.0 24.9 - - - +
306A MET* 3.1 12.0 + - - +
333A LEU* 3.7 26.2 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 2.8 29.8 + - + +
300A ALA* 2.8 27.1 - - - +
302A VAL* 1.3 75.0 - - - +
304A SER* 1.3 61.4 + - - +
306A MET* 3.1 14.8 + - - +
307A GLY 3.4 0.2 + - - -
308A GLU* 3.0 53.0 + - + +
311A LEU* 3.7 19.3 - - + -
312A ALA* 3.3 22.0 - - - -
315A ILE* 5.3 3.4 - - + -
329A GLY* 4.8 8.5 - - - +
332A LYS* 5.4 2.9 - - + -
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 5.2 3.7 + - - -
300A ALA 2.9 19.1 + - - -
301A SER* 3.6 6.7 - - - -
303A VAL* 1.3 77.9 - - - +
305A VAL* 1.3 57.3 + - - +
307A GLY* 3.0 20.4 + - - -
308A GLU 4.1 5.8 - - - -
309A LYS* 3.8 26.2 + - - +
312A ALA* 3.7 17.0 - - - -
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Residues in contact with VAL 305 (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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276A GLU* 3.6 40.2 - - + +
279A ARG* 3.9 18.6 - - - +
280A LEU* 3.9 38.4 - - + +
283A VAL* 4.3 7.4 - - + -
301A SER 3.2 11.4 + - - +
302A VAL* 3.0 24.5 - - - +
304A SER* 1.3 74.0 - - - +
306A MET* 1.3 58.0 + - - +
307A GLY 3.1 5.7 + - - -
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Residues in contact with MET 306 (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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280A LEU* 4.8 5.4 - - + -
283A VAL* 3.5 22.2 - - + -
302A VAL* 3.1 19.5 + - - +
303A VAL* 3.1 13.6 + - - +
304A SER 3.1 1.4 - - - -
305A VAL* 1.3 80.0 - - + +
307A GLY* 1.3 59.1 + - - +
308A GLU* 3.4 7.5 + - + +
329A GLY 5.8 0.7 - - - +
332A LYS* 3.9 35.6 + - - +
333A LEU* 4.0 25.1 - - + +
336A GLU* 3.0 55.3 - - + +
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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