Contacts of the strand formed by residues 210 - 215 (chain J) in PDB entry 5LN3
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 THR 210 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J VAL* 3.4 24.9 - - - +
141J GLU 4.6 0.7 + - - -
142J LYS* 3.4 21.9 - - - +
204J ALA* 4.8 0.4 - - - -
209J CYS* 1.4 75.9 - - - +
211J PHE* 1.4 60.7 + - - +
212J ILE* 3.6 13.0 + - + +
241J HIS* 4.4 11.9 - - + +
243J PRO 3.6 8.0 + - - +
244J SER* 3.3 28.5 - - - +
245J ILE* 3.0 28.9 + - - +
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Residues in contact with PHE 211 (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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139J MET 6.1 0.4 - - - -
140J VAL* 3.5 8.5 - - - +
141J GLU* 3.2 61.8 + - + +
197J THR* 5.4 1.1 - - + -
200J ALA* 4.3 12.1 - - + -
201J ARG* 3.6 49.6 - - + -
204J ALA* 4.0 20.8 - - + +
209J CYS 3.9 1.8 + - - -
210J THR* 1.4 70.4 - - - +
212J ILE* 1.3 61.1 + - - +
213J ARG* 4.0 17.9 + - + -
245J ILE* 3.6 19.7 - - + -
247J PHE* 3.8 40.2 - + + -
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Residues in contact with ILE 212 (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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140J VAL* 4.1 19.5 - - + -
210J THR* 3.8 17.9 - - + +
211J PHE* 1.3 75.2 - - - +
213J ARG* 1.4 63.8 + - - +
214J VAL* 3.8 20.6 + - + +
234J LEU* 5.3 13.2 - - + -
238J ALA* 4.9 6.7 - - + -
241J HIS* 4.5 16.6 - - + -
244J SER* 3.7 31.0 - - - +
245J ILE 3.0 14.3 + - - +
246J ILE* 3.7 6.5 - - + -
247J PHE* 3.0 28.1 + - - +
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Residues in contact with ARG 213 (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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137J LEU* 4.3 16.3 - - + +
139J MET* 3.7 48.7 + - - +
140J VAL* 5.7 0.2 - - - +
141J GLU* 4.8 4.5 - - - +
201J ARG* 3.5 27.5 - - - +
211J PHE* 4.0 20.5 + - + -
212J ILE* 1.4 75.0 - - - +
214J VAL* 1.4 61.3 + - - +
215J SER* 4.1 1.9 + - - +
247J PHE* 3.6 11.9 - - + -
249J ASP* 3.5 29.1 + - + +
256J SER* 5.1 2.8 - - - -
257J SER* 3.0 28.8 + - - -
319K PRO* 5.8 1.2 - - - +
320K ALA* 4.2 16.4 - - - +
323K ARG* 4.0 21.7 - - - +
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Residues in contact with VAL 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J VAL* 6.1 3.1 - - + -
212J ILE* 3.8 20.9 - - + +
213J ARG* 1.4 77.0 - - - +
215J SER* 1.3 66.5 + - - +
216J GLY 3.5 0.9 + - - -
219J LEU* 4.0 34.5 - - + -
234J LEU* 4.5 22.0 - - + -
246J ILE* 4.1 23.3 - - + -
247J PHE 3.1 7.7 + - - +
248J MET* 3.7 12.2 - - + +
249J ASP* 3.1 22.3 + - - +
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Residues in contact with SER 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 4.4 19.8 - - - +
213J ARG* 4.1 2.7 + - - +
214J VAL* 1.3 75.8 - - - +
216J GLY* 1.4 63.8 + - - +
217J SER 3.5 1.1 - - - -
218J GLU* 3.3 28.0 + - - +
219J LEU* 3.7 8.1 + - - +
249J ASP* 3.4 24.8 + - - -
250J GLU* 3.4 25.2 + - - -
257J SER* 5.9 0.2 - - - -
319K PRO* 5.7 2.4 - - - +
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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