Contacts of the strand formed by residues 246 - 256 (chain C) in PDB entry 4LL4
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 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C GLU* 3.8 0.2 - - - -
203C ASN* 2.9 30.3 + - - +
242C ILE* 3.2 18.0 - - - +
243C ILE* 2.9 35.9 + - + +
245C GLY* 1.3 83.8 - - - +
247C CYS* 1.3 69.1 + - - +
34D PRO* 3.6 4.6 - - - +
73D CYS* 4.0 15.6 - - - +
74D MET 3.0 15.5 - - - +
91D GLY* 3.6 24.0 - - - +
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Residues in contact with CYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C PHE 3.1 11.4 - - - +
202C GLU* 3.8 18.6 - - - -
242C ILE* 4.8 1.6 - - - -
246C THR* 1.3 75.6 - - - +
248C ALA* 1.3 61.3 + - - +
31D TRP* 3.7 17.0 - - + -
32D CYS* 2.2 53.8 - - + -
34D PRO* 3.5 11.9 - - - -
73D CYS* 3.0 9.8 - - - +
74D MET* 2.6 34.3 + - + +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP* 3.6 0.5 - - - -
201C PHE* 2.9 34.2 + - + +
240C ASN* 6.6 0.4 - - + -
242C ILE* 4.0 26.9 - - + -
247C CYS* 1.3 76.6 - - - +
249C SER* 1.3 67.6 + - - +
250C TRP* 6.4 0.9 - - + -
31D TRP* 3.8 1.5 - - - -
72D LYS 3.6 19.7 - - - +
73D CYS* 4.1 5.8 - - + +
74D MET* 4.5 4.3 - - - -
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Residues in contact with SER 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ALA 3.0 5.4 - - - -
200C ASP* 2.8 23.9 + - - -
201C PHE* 4.6 0.7 - - - -
248C ALA* 1.3 78.3 - - - +
250C TRP* 1.3 72.3 + - - +
251C ARG* 3.7 29.9 + - - +
31D TRP* 3.1 18.0 - - - -
60D ASP* 5.1 0.2 + - - -
72D LYS 4.7 2.7 + - - +
74D MET* 4.1 6.8 - - - +
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Residues in contact with TRP 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 3.6 24.0 - - + +
198C HIS* 3.3 6.9 - - - +
199C ALA* 2.6 42.3 + - + +
200C ASP* 5.0 0.7 - - - +
201C PHE* 3.8 28.3 - + - -
211C PRO* 3.9 14.4 - - + +
212C LYS* 3.9 26.2 - - - -
213C ALA* 4.0 20.9 - - + -
237C VAL* 4.5 7.4 - - + -
239C GLY* 3.8 30.4 - - - -
240C ASN 5.2 0.6 - - - +
248C ALA* 6.4 0.4 - - + -
249C SER* 1.3 79.9 - - - +
251C ARG* 1.3 61.0 + - - +
252C GLY 3.4 0.7 - - - -
253C LYS* 3.7 49.2 - - + +
278C ILE* 4.4 6.5 - - + -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C HIS* 3.9 16.6 + - + +
249C SER* 3.7 27.1 + - - +
250C TRP* 1.3 73.6 - - - +
252C GLY* 1.3 62.5 + - - +
253C LYS 4.2 1.0 - - - +
59D VAL* 3.3 29.9 + - - +
60D ASP* 2.3 32.1 + - - +
63D GLN* 3.9 37.9 + - - +
66D ALA* 5.7 1.2 - - - +
74D MET* 4.8 2.6 - - - +
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Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C SER* 3.7 22.7 + - - -
197C ILE 3.0 14.8 + - - -
198C HIS* 3.6 17.9 + - - -
250C TRP 3.4 1.2 + - - -
251C ARG* 1.3 77.1 - - - +
253C LYS* 1.3 67.4 + - - +
254C SER* 3.2 7.8 + - - -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ILE 3.4 1.7 - - - +
197C ILE* 2.5 40.3 + - + +
237C VAL* 4.4 19.7 - - + -
238C ARG 4.6 7.2 - - - -
239C GLY* 4.4 11.0 - - - -
250C TRP* 3.7 69.3 - - + +
251C ARG 3.5 3.0 - - - +
252C GLY* 1.3 73.0 - - - +
254C SER* 1.3 66.1 + - - +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLU* 3.2 37.6 + - - +
195C ILE 3.2 6.7 - - - -
196C SER* 4.2 4.0 - - - +
237C VAL* 4.0 16.1 - - - +
252C GLY 3.2 8.2 + - - -
253C LYS* 1.3 79.5 - - - +
255C LEU* 1.3 63.6 + - - +
256C ARG 5.0 0.5 + - - -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLU* 4.0 1.1 - - - -
195C ILE* 2.6 47.3 + - + +
197C ILE* 4.3 12.3 - - + -
213C ALA 4.3 4.0 - - - -
214C ALA* 4.0 17.5 - - - +
215C ILE* 4.2 13.0 - - + -
235C SER* 3.2 35.9 - - - +
236C SER* 4.1 11.0 - - - +
237C VAL* 4.4 11.7 - - + -
254C SER* 1.3 76.3 + - - +
256C ARG* 1.3 64.3 + - - +
257C VAL* 3.7 0.3 + - - +
276C LEU* 3.9 28.5 - - + -
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLY* 2.2 39.7 + - - +
193C ASP* 3.8 6.9 - - - +
194C GLU* 2.5 38.9 + - + +
215C ILE* 3.8 5.4 - - - +
235C SER* 3.0 24.7 + - - +
254C SER* 5.0 0.8 + - - -
255C LEU* 1.3 80.0 - - - +
257C VAL* 1.3 70.8 + - - +
258C GLN* 4.2 10.3 + - + +
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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