Contacts of the strand formed by residues 288 - 297 (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 VAL 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C LYS* 4.2 25.4 - - + +
165C GLU 5.0 0.4 - - - +
166C LYS* 4.3 23.8 - - + -
178C VAL* 4.0 28.5 - - + +
179C SER* 5.0 0.9 - - - -
180C VAL* 3.3 29.9 - - + +
278C ILE 4.2 0.2 - - - +
279C TYR* 3.0 4.9 - - - -
280C VAL* 2.8 41.0 + - + +
282C VAL* 4.3 9.2 - - + -
286C LYS 4.6 1.3 - - - +
287C LYS* 1.3 73.7 - - - +
289C ILE* 1.3 60.8 + - - +
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Residues in contact with ILE 289 (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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79A GLU 5.1 2.5 - - - +
80A ASP* 4.3 10.1 - - - +
82A PRO* 4.1 30.3 - - + -
164C LYS* 2.9 36.6 + - - +
277C LEU* 4.4 15.3 - - + -
279C TYR* 3.6 19.7 - - + -
287C LYS* 3.9 24.8 + - + +
288C VAL* 1.3 75.4 - - - +
290C LEU* 1.3 77.8 + - - +
291C ASP* 4.1 6.1 + - + +
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Residues in contact with LEU 290 (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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162C ALA* 3.6 33.0 - - + +
163C LYS* 3.6 9.0 - - - +
164C LYS* 3.5 42.2 - - + +
180C VAL* 3.8 21.5 - - + +
181C SER* 4.1 0.4 - - - -
182C ALA* 3.7 29.2 - - + +
276C LEU 4.6 0.4 - - - -
277C LEU* 3.7 2.3 - - - -
278C ILE* 2.9 40.6 + - + +
288C VAL 4.3 0.2 + - - -
289C ILE* 1.3 82.9 - - - +
291C ASP* 1.3 59.2 + - - +
292C LEU* 4.2 7.0 - - + -
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Residues in contact with ASP 291 (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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162C ALA* 5.6 1.0 - - - +
218C ARG* 4.6 6.2 + - - -
275C SER* 3.2 24.3 + - - -
276C LEU 3.7 2.9 - - - -
277C LEU* 3.6 21.0 - - + +
289C ILE* 4.0 6.8 + - + -
290C LEU* 1.3 73.6 - - - +
292C LEU* 1.3 72.9 + - - +
293C PRO* 3.9 11.8 - - - +
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Residues in contact with LEU 292 (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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160C VAL* 4.0 32.8 - - + +
161C SER* 4.4 4.5 - - - +
162C ALA* 3.9 28.0 - - + +
182C ALA* 5.0 4.3 - - + +
184C ILE* 4.0 26.2 - - + +
276C LEU* 2.8 44.0 + - + +
278C ILE* 4.2 23.3 - - + -
290C LEU* 4.5 6.1 - - + -
291C ASP* 1.3 87.6 + - - +
293C PRO* 1.3 70.0 - - - +
294C LEU* 3.7 1.6 - - - +
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Residues in contact with PRO 293 (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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160C VAL* 4.8 12.7 - - + +
184C ILE* 5.1 0.3 - - - +
187C LYS* 3.7 30.7 - - - +
218C ARG* 5.9 1.8 - - - +
274C TYR 3.5 9.6 - - - +
275C SER* 4.2 2.9 - - - +
291C ASP* 3.9 12.8 - - - +
292C LEU* 1.3 89.6 - - + +
294C LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 294 (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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65C GLN* 4.8 1.0 + - - +
184C ILE* 3.9 25.8 - - + -
187C LYS* 3.5 14.3 - - - +
189C PHE* 4.0 17.5 - - + -
195C ILE* 4.2 11.2 - - + -
215C ILE* 4.7 6.1 - - + -
273C GLU* 5.5 0.2 - - - -
274C TYR* 2.8 29.0 + - + +
275C SER* 3.6 7.9 - - - +
276C LEU* 3.4 37.2 - - + +
292C LEU 4.0 0.4 - - - +
293C PRO* 1.3 81.9 - - - +
295C VAL* 1.3 68.7 + - - +
296C ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 295 (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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54C VAL* 4.2 20.9 - - + -
56C TRP* 3.7 27.6 - - + -
65C GLN* 3.2 24.9 - - + +
156C LEU* 3.8 25.8 - - + -
187C LYS* 3.1 19.7 + - - +
188C GLY* 4.3 0.7 - - - -
189C PHE 3.2 18.4 + - - -
294C LEU* 1.3 80.2 - - - +
296C ILE* 1.3 69.5 + - - +
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Residues in contact with ILE 296 (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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65C GLN* 3.1 26.9 + - - +
189C PHE* 3.4 17.0 - - + +
191C GLU* 4.4 5.8 - - + +
215C ILE* 4.9 4.5 - - + -
257C VAL* 3.7 36.1 - - + -
258C GLN 6.3 0.4 - - - -
274C TYR* 3.6 61.5 + - + +
294C LEU* 3.8 21.3 - - + -
295C VAL* 1.3 79.8 - - - +
297C GLY* 1.3 68.9 + - - +
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Residues in contact with GLY 297 (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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56C TRP* 3.6 14.7 - - - -
63C CYS* 4.4 0.9 - - - -
64C LYS 3.2 23.3 - - - -
65C GLN 3.8 1.6 - - - -
189C PHE 3.1 8.7 + - - -
190C CYS* 3.4 5.5 - - - -
191C GLU* 3.0 27.8 + - - +
296C ILE* 1.3 77.0 - - - +
298C SER* 1.3 61.8 + - - -
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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