Contacts of the helix formed by residues 297 - 305 (chain A) in PDB entry 1L8A
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 ARG 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A GLY* 3.1 1.6 + - - -
296A SER* 1.3 77.8 - - - +
298A TRP* 1.3 61.1 + - + +
300A GLU* 4.1 11.1 + - - +
351A TRP* 3.9 17.9 - - + -
355A GLN 4.6 2.2 - - - -
358A ALA* 2.9 50.0 + - - +
359A LEU* 3.5 26.3 - - + +
360A ASN* 4.8 8.7 - - - +
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Residues in contact with TRP 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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294A TRP* 3.5 40.5 - + + -
295A GLY 3.2 15.7 + - - +
296A SER 3.1 0.6 - - - -
297A ARG* 1.3 77.3 - - + +
299A ASP* 1.3 66.0 + - - +
300A GLU 3.2 2.9 - - - -
301A LEU* 2.9 24.8 + - + +
302A LEU* 3.0 24.0 + - + +
310A LEU* 4.6 5.2 - - + -
314A MET* 3.4 28.9 - - + -
333A VAL* 6.3 1.1 - - + -
337A PHE* 4.1 20.4 - + - -
338A PHE* 4.0 15.7 - + - -
359A LEU* 3.4 53.3 - - + +
360A ASN 2.9 31.1 + - - -
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Residues in contact with ASP 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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61A ASN* 5.0 2.8 - - - +
65A VAL* 3.0 36.8 + - + +
295A GLY 4.5 1.0 - - - +
296A SER* 3.2 23.0 + - - +
298A TRP* 1.3 77.6 - - - +
300A GLU* 1.3 60.9 + - - +
302A LEU* 3.7 11.5 + - - +
303A ARG* 3.2 32.0 + - - +
368A LYS* 2.6 34.0 + - - -
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Residues in contact with GLU 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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296A SER 4.5 0.6 + - - -
297A ARG 4.1 8.5 + - - +
298A TRP 3.2 1.0 - - - -
299A ASP* 1.3 76.7 - - - +
301A LEU* 1.3 70.4 + - - +
303A ARG* 3.4 10.2 + - - +
304A LYS* 3.0 40.7 + - - +
350A ASP* 5.4 1.0 - - - +
351A TRP* 3.5 34.8 + - + -
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Residues in contact with LEU 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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297A ARG 4.7 0.9 - - - +
298A TRP* 2.9 18.7 + - + +
300A GLU* 1.3 80.8 - - - +
302A LEU* 1.3 57.8 + - - +
304A LYS* 2.9 37.2 - - - +
305A ASP* 2.9 28.1 + - - +
310A LEU* 4.0 10.8 - - + -
338A PHE* 3.8 29.4 - - + -
347A LEU* 3.8 25.3 - - + +
348A VAL* 4.2 2.7 - - + -
351A TRP* 3.6 33.7 - - + -
359A LEU* 3.9 13.5 - - + -
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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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60A ILE* 4.2 17.5 - - + -
294A TRP* 4.9 6.5 - - + -
298A TRP* 3.0 32.1 + - + +
299A ASP* 4.1 11.2 - - - +
301A LEU* 1.3 77.0 - - - +
303A ARG* 1.3 63.6 + - - +
305A ASP* 3.2 23.5 + - - +
310A LEU* 3.6 23.6 - - + -
311A ILE* 4.0 30.4 - - + +
314A MET* 4.0 16.2 - - + -
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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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65A VAL* 4.8 18.8 - - - +
66A GLU* 5.1 7.9 + - - -
299A ASP* 3.2 25.8 + - - +
300A GLU* 3.8 9.2 - - - +
301A LEU 3.3 0.2 - - - -
302A LEU* 1.3 78.1 - - - +
304A LYS* 1.3 61.4 + - - +
305A ASP 4.5 2.6 - - - -
306A THR* 4.8 3.5 + - - -
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Residues in contact with LYS 304 (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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300A GLU* 3.0 29.6 + - - +
301A LEU* 2.9 37.5 - - - +
303A ARG* 1.3 76.0 - - - +
305A ASP* 1.3 54.4 + - - +
306A THR* 2.6 24.1 + - - -
347A LEU* 2.6 56.7 + - + +
350A ASP* 4.0 8.2 + - - -
351A TRP* 3.4 14.1 - - - +
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Residues in contact with ASP 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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301A LEU 2.9 14.5 + - - +
302A LEU* 3.2 22.3 + - - +
303A ARG 4.5 2.4 - - - +
304A LYS* 1.3 71.7 - - - +
306A THR* 1.3 60.1 + - - +
307A SER* 3.6 7.9 + - - -
308A GLY* 3.1 26.3 + - - -
309A LYS* 3.2 8.5 + - - +
310A LEU* 3.2 35.1 + - + +
311A ILE* 3.8 13.7 + - - +
343A GLU 5.5 0.3 - - - +
344A THR* 5.3 0.3 - - - +
347A LEU* 3.8 19.4 - - + +
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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