Contacts of the helix formed by residues 304 - 310 (chain J) in PDB entry 6LTJ
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 ILE 304 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201J PHE* 5.8 2.1 - - - -
202J ILE* 4.7 9.8 - - + +
205J GLN* 3.9 34.6 + - + +
206J CYS* 4.5 18.2 - - + -
209J LEU* 3.7 27.1 - - + -
267J LEU* 3.7 33.4 - - + -
300J GLU* 3.3 25.8 - - + +
302J LEU 3.2 0.8 - - - -
303J LYS* 1.3 80.1 - - - +
305J PRO* 1.3 68.6 - - + +
306J GLU 3.1 6.2 + - - -
307J GLY* 3.5 9.4 + - - -
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Residues in contact with PRO 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J PHE* 5.9 0.4 - - + -
202J ILE* 4.3 13.0 - - + -
267J LEU* 3.9 17.3 - - + -
268J GLN 4.1 7.0 - - - +
269J VAL* 3.6 28.9 - - + +
302J LEU 3.6 13.5 - - - +
304J ILE* 1.3 90.9 - - + +
306J GLU* 1.3 61.3 + - - +
307J GLY 3.2 1.1 - - - -
308J LEU* 2.6 54.0 - - + +
309J PHE* 4.8 2.4 - - - -
357J ILE* 4.8 4.9 - - + -
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Residues in contact with GLU 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J VAL* 3.4 25.3 - - - +
270J SER 2.9 31.5 + - - +
271J ASP 3.7 5.5 - - - +
272J SER* 5.2 9.3 + - - +
302J LEU* 4.2 17.2 - - + +
303J LYS* 4.5 15.0 - - + +
304J ILE 3.1 2.0 + - - -
305J PRO* 1.3 76.2 - - - +
307J GLY* 1.3 56.2 + - - +
308J LEU 3.0 4.9 - - - -
309J PHE* 3.0 30.7 + - - +
310J ASP* 3.6 6.9 + - - +
363J ARG* 3.5 21.0 + - - -
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Residues in contact with GLY 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J LEU* 4.2 8.8 - - - +
201J PHE* 4.7 12.5 - - - -
303J LYS 5.1 0.6 + - - -
304J ILE 3.5 7.5 + - - -
305J PRO 3.2 1.2 - - - -
306J GLU* 1.3 73.3 - - - +
308J LEU* 1.3 52.0 + - - +
309J PHE 3.0 5.2 - - - -
310J ASP* 2.7 46.7 + - - +
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Residues in contact with LEU 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J LEU* 3.4 41.4 - - + +
198J ALA* 5.4 0.4 - - - -
201J PHE* 4.3 7.0 - - + -
202J ILE* 4.0 21.5 - - + -
269J VAL* 5.5 0.7 - - + -
305J PRO* 2.6 37.3 + - + +
307J GLY* 1.3 74.5 - - - +
309J PHE* 1.3 73.5 + - + +
310J ASP 3.6 0.2 - - - -
323J LEU 4.1 3.2 - - - +
324J GLY* 3.8 2.8 - - - -
325J VAL* 3.4 29.5 + - + +
354J ASN* 6.1 5.2 - - + +
357J ILE* 6.0 5.4 - - + -
360J PHE* 4.7 20.9 - - + -
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Residues in contact with PHE 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J VAL* 5.0 9.0 - - + -
305J PRO 4.8 2.2 - - - -
306J GLU* 3.0 23.6 + - - +
308J LEU* 1.3 85.4 - - + +
310J ASP* 1.3 58.4 + - - +
311J PRO* 4.0 7.7 - - - +
324J GLY* 3.8 13.2 - - - -
325J VAL* 3.3 44.2 - - + -
326J SER* 3.8 10.1 - - - -
327J HIS* 5.5 6.7 + - + -
360J PHE* 4.9 15.7 - + - -
363J ARG* 4.2 18.4 - - + -
364J LEU* 5.1 13.7 - - + -
367J GLU* 3.8 33.2 - - - +
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Residues in contact with ASP 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J LEU* 5.2 1.8 - - - +
306J GLU 4.2 2.7 - - - +
307J GLY* 2.7 38.7 + - - +
309J PHE* 1.3 74.5 - - - +
311J PRO* 1.3 78.0 - - - +
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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