Contacts of the strand formed by residues 210 - 223 (chain A) 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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ILE* 5.1 4.0 - - + +
209A VAL* 1.3 78.9 - - - +
211A PRO* 1.3 76.5 - - + +
212A LYS* 4.1 18.3 - - - +
238A ARG* 3.8 33.0 - - + +
239A GLY 3.8 13.9 - - - +
241A HIS* 4.2 16.6 - - + +
280A VAL* 4.1 2.5 - - - -
281A SER* 2.8 42.7 + - - +
283A PRO* 6.2 2.5 - - + -
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Residues in contact with PRO 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 3.4 40.2 - - + -
210A VAL* 1.3 88.5 - - + +
212A LYS* 1.3 64.4 + - - +
239A GLY* 2.8 38.2 + - - +
240A ASN 3.4 22.2 - - - +
242A ILE* 3.4 21.8 - - + -
248A ALA* 6.2 0.7 - - + -
250A TRP* 4.0 10.1 - - + +
279A TYR 3.4 6.1 - - - +
280A VAL* 4.1 2.7 - - + -
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 4.1 20.9 - - + +
211A PRO* 1.3 79.9 - - - +
213A ALA* 1.3 66.3 + - - +
237A VAL 3.6 12.1 - - - +
238A ARG* 4.3 25.6 - - + +
250A TRP* 3.8 6.6 - - - -
278A ILE* 3.4 6.4 - - - +
279A TYR* 2.8 70.7 + - + +
281A SER* 4.0 24.2 + - - -
287A LYS* 6.2 0.8 - - - +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.3 15.5 - - + -
212A LYS* 1.3 79.4 - - - +
214A ALA* 1.3 63.1 + - - +
236A SER* 3.1 22.2 - - - -
237A VAL* 3.0 25.9 + - + +
250A TRP* 3.8 19.7 - - + -
255A LEU* 4.3 5.8 - - + -
276A LEU* 4.4 0.7 - - + -
277A LEU 3.0 11.9 - - - +
278A ILE* 4.3 4.7 - - + -
279A TYR* 4.3 3.9 + - - -
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA* 1.3 77.9 - - - +
215A ILE* 1.3 67.8 + - - +
216A VAL* 3.9 3.5 + - + -
233A LYS* 4.3 7.4 - - + -
235A SER 3.5 12.1 - - - +
236A SER* 3.9 8.7 - - - +
255A LEU* 4.3 1.3 - - - -
275A SER 3.7 0.2 - - - +
276A LEU* 3.6 4.6 - - - +
277A LEU* 2.7 38.9 + - + +
279A TYR* 4.4 5.6 - - + +
83C THR* 4.2 24.2 - - + -
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ILE* 3.6 31.4 - - + -
214A ALA* 1.3 74.1 - - - +
216A VAL* 1.3 68.6 + - - +
234A LEU* 2.9 49.5 + - + +
235A SER* 3.2 16.2 + - - +
255A LEU* 4.0 20.4 - - + +
256A ARG 3.6 24.7 - - - +
257A VAL* 4.3 12.3 - - + -
274A TYR* 4.6 9.0 - - + -
275A SER 3.2 9.9 - - - +
276A LEU* 4.3 3.8 - - + -
294A LEU* 4.3 9.0 - - + -
296A ILE* 5.0 3.1 - - + -
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA* 4.4 4.5 - - + +
215A ILE* 1.3 83.2 - - - +
217A ALA* 1.3 63.1 + - - +
218A ARG* 3.8 15.9 - - - +
231A THR* 4.4 7.2 - - + -
232A GLN 3.3 11.4 - - - +
233A LYS* 4.2 6.3 - - - -
273A GLU 3.8 0.2 - - - +
274A TYR* 3.2 9.5 - - - -
275A SER* 2.8 51.1 + - - +
277A LEU* 3.7 33.2 - - + -
82C PRO 4.2 1.6 - - - +
83C THR* 4.1 25.8 - - + -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL* 1.3 74.7 - - - +
218A ARG* 1.3 61.6 + - - +
219A HIS* 3.9 11.8 - - - +
230A LEU 3.4 1.7 - - - +
231A THR* 3.3 3.5 - - - +
232A GLN* 2.7 46.5 + - + +
234A LEU* 4.3 6.3 - - + +
260A ILE* 4.1 15.5 - - + -
272A VAL* 3.9 18.6 - - + -
273A GLU 3.5 3.4 - - - -
274A TYR* 4.2 8.7 - - + -
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL* 3.8 19.0 - - - +
217A ALA* 1.3 75.2 - - - +
219A HIS* 1.3 62.1 + - - +
220A THR* 3.4 5.2 + - - -
229A VAL* 3.8 16.8 - - + -
230A LEU 3.3 4.5 - - - -
231A THR* 4.3 19.8 + - + +
271A ARG 3.7 0.2 - - - +
272A VAL* 3.4 3.0 - - - +
273A GLU* 2.6 56.8 + - + +
274A TYR 4.4 3.4 + - - -
275A SER* 2.9 32.7 + - - +
277A LEU* 4.2 4.2 - - - +
291A ASP* 3.1 22.1 + - - -
82C PRO* 4.8 7.1 + - - +
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA* 4.0 6.4 - - - +
218A ARG* 1.3 71.2 - - - +
220A THR* 1.3 60.6 + - - +
221A TYR* 3.7 5.0 - - + -
228A LYS 3.5 1.0 - - - +
229A VAL* 2.9 5.2 - - - -
230A LEU* 2.7 72.4 + - + +
232A GLN* 3.1 34.1 + - + +
260A ILE* 4.1 16.8 - - + -
269A ILE* 4.3 23.5 - - + +
271A ARG 3.5 7.4 - - - +
272A VAL* 3.7 26.9 - - + +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG* 3.9 5.4 + - - +
219A HIS* 1.3 73.5 - - - +
221A TYR* 1.3 59.0 + - - +
227A THR* 5.7 2.2 - - - -
228A LYS 3.0 15.9 - - - +
229A VAL* 4.2 10.3 - - + +
269A ILE* 3.4 4.3 - - - +
270A LEU* 2.8 35.4 + - + -
271A ARG* 2.9 59.0 + - - +
273A GLU* 4.4 3.8 + - - -
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A HIS* 3.7 11.9 - - + -
220A THR* 1.3 75.0 - - - +
222A LEU* 1.3 65.8 + - - +
223A ALA* 3.6 28.9 + - + -
226A GLN 3.6 0.5 - - - +
227A THR 3.5 4.3 + - - -
228A LYS* 2.6 83.2 + - + +
229A VAL 4.1 0.4 - - - -
230A LEU* 3.9 27.2 - - + +
268A ASN* 3.4 7.6 - - + +
269A ILE* 3.5 24.5 - - + +
270A LEU* 4.2 3.4 - - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 3.8 42.8 - - + +
221A TYR* 1.3 73.5 - - - +
223A ALA* 1.3 62.7 + - - +
226A GLN 3.1 7.0 - - - +
227A THR 4.2 6.1 - - - +
268A ASN* 2.6 48.4 + - - +
270A LEU* 4.1 28.3 - - + -
224C ASN* 3.8 13.7 - - + +
225C GLY* 3.4 38.6 - - - +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.6 29.9 + - + -
222A LEU* 1.3 74.8 - - - +
224A ASN* 1.3 73.1 + - + +
225A GLY 3.4 2.0 - - - -
226A GLN* 2.7 39.5 + - - +
228A LYS* 4.6 9.4 - - + +
224C ASN* 4.5 5.2 - - - -
225C GLY* 4.4 0.6 - - - -
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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