Contacts of the helix formed by residues 297 - 305 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLY 3.3 0.8 - - - -
296B SER* 1.3 76.0 - - - +
298B TRP* 1.3 56.8 + - - +
300B GLU* 3.1 34.1 - - - +
301B LEU* 4.4 0.7 - - - +
351B TRP* 3.9 7.5 - - + -
355B GLN 5.5 1.8 - - - -
358B ALA* 3.0 43.0 + - - +
359B LEU* 3.8 20.5 - - + +
360B ASN* 3.1 28.9 + - - +
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Residues in contact with TRP 298 (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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294B TRP* 3.5 41.4 - + + -
295B GLY 3.3 10.9 + - - +
296B SER 3.0 1.2 + - - -
297B ARG* 1.3 74.8 - - - +
299B ASP* 1.3 66.7 + - - +
300B GLU 3.3 0.4 - - - -
301B LEU* 3.1 16.3 + - + +
302B LEU* 2.9 31.9 + - + +
310B LEU* 4.3 7.6 - - + -
314B MET* 3.3 31.4 - - + -
337B PHE* 3.8 19.3 - + - -
338B PHE* 3.8 34.3 - + - -
359B LEU* 3.5 35.2 - - + +
360B ASN* 2.9 32.5 + - - -
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Residues in contact with ASP 299 (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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61B ASN* 4.8 4.2 + - - -
65B VAL* 3.8 29.7 + - + +
295B GLY 4.4 2.1 - - - +
296B SER* 3.0 25.4 + - - +
298B TRP* 1.3 78.0 - - - +
300B GLU* 1.3 57.5 + - - +
302B LEU* 3.3 10.3 + - - +
303B ARG* 2.9 31.6 + - - +
368B LYS* 2.8 32.8 + - - -
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Residues in contact with GLU 300 (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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296B SER 4.9 1.6 - - - +
297B ARG* 3.1 30.6 - - - +
299B ASP* 1.3 74.1 - - + +
301B LEU* 1.3 57.6 + - + +
303B ARG* 3.1 9.8 + - - +
304B LYS* 2.7 43.0 + - + +
351B TRP* 3.6 27.9 + - + -
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Residues in contact with LEU 301 (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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297B ARG 4.4 2.0 - - - +
298B TRP* 3.1 15.6 + - + +
300B GLU* 1.3 77.9 - - - +
302B LEU* 1.3 62.0 + - - +
304B LYS* 3.4 30.0 + - - +
305B ASP* 3.2 26.2 + - - +
310B LEU* 4.0 14.6 - - + -
338B PHE* 4.3 5.6 - - + -
347B LEU* 3.5 23.7 - - + +
348B VAL* 4.1 10.3 - - + -
351B TRP* 3.5 40.2 - - + -
359B LEU* 3.9 27.4 - - + -
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Residues in contact with LEU 302 (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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60B ILE* 4.1 20.0 - - + -
61B ASN* 6.0 0.7 - - - +
294B TRP* 4.6 6.5 - - + -
298B TRP* 2.9 33.8 + - + +
299B ASP* 3.9 10.3 - - - +
301B LEU* 1.3 73.9 - - - +
303B ARG* 1.3 66.0 + - - +
305B ASP* 3.6 15.4 + - + +
310B LEU* 3.8 25.6 - - + -
311B ILE* 4.0 30.3 - - + +
314B MET* 4.1 14.6 - - + -
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Residues in contact with ARG 303 (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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299B ASP 2.9 18.7 + - - +
300B GLU* 3.1 8.3 + - - +
302B LEU* 1.3 80.5 - - - +
304B LYS* 1.3 62.1 + - + +
305B ASP 3.4 2.9 + - - +
306B THR* 4.8 4.5 + - - +
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Residues in contact with LYS 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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300B GLU* 2.7 31.3 + - + +
301B LEU* 3.4 19.9 - - - +
303B ARG* 1.3 74.0 - - + +
305B ASP* 1.3 58.6 + - - +
306B THR* 2.8 20.3 + - - +
346B ALA 5.8 0.2 - - - -
347B LEU* 2.9 57.1 + - + +
350B ASP* 4.6 7.5 + - - -
351B TRP* 4.1 7.3 - - - +
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Residues in contact with ASP 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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301B LEU 3.2 19.1 + - - +
302B LEU* 3.6 11.4 + - + +
303B ARG 3.3 4.3 - - - +
304B LYS* 1.3 73.6 - - - +
306B THR* 1.3 59.2 + - - +
307B SER* 2.6 26.9 + - - -
308B GLY* 3.4 10.5 + - - -
309B LYS* 3.1 6.5 + - - +
310B LEU* 2.8 37.3 + - + +
311B ILE* 4.3 1.0 + - - +
343B GLU* 4.8 3.1 - - - +
347B LEU* 3.8 25.4 - - + +
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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