Contacts of the strand formed by residues 269 - 281 (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 ILE 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLU* 4.3 1.3 - - - +
71A ARG* 4.3 14.1 + - - -
219A HIS* 4.3 19.1 - - + +
220A THR 3.4 9.4 - - - +
221A TYR* 3.5 20.4 - - + +
268A ASN* 1.3 82.5 + - - +
270A LEU* 1.3 64.5 + - - +
271A ARG* 4.7 5.2 - - - +
272A VAL* 4.3 23.8 - - + -
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Residues in contact with LEU 270 (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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66A THR 4.7 1.6 - - - +
67A SER* 4.1 2.4 - - - -
68A GLU* 3.1 63.5 + - + +
69A TYR* 4.7 4.0 - - - +
70A LEU* 4.7 2.2 - - - +
71A ARG* 4.5 16.2 - - + +
220A THR* 2.8 35.0 + - + +
221A TYR 4.4 2.9 - - - +
222A LEU* 4.1 39.7 - - + -
227A THR* 5.7 2.5 - - - +
269A ILE* 1.3 75.9 - - - +
271A ARG* 1.3 69.0 + - + +
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Residues in contact with ARG 271 (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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66A THR 5.2 1.6 - - - -
67A SER* 3.5 24.0 - - - +
68A GLU 3.1 18.2 + - - +
69A TYR* 3.6 46.6 + - - +
106A PRO* 5.6 6.3 - - - +
109A PRO* 4.5 11.1 + - - +
219A HIS* 3.5 2.8 - - - +
220A THR* 2.9 62.2 + - - +
269A ILE* 4.7 5.3 - - - +
270A LEU* 1.3 83.5 - - - +
272A VAL* 1.3 67.9 + - - +
273A GLU* 2.7 41.1 + - + +
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Residues in contact with VAL 272 (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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65A GLN* 3.5 12.2 + - - +
66A THR 5.7 0.6 + - - -
67A SER* 5.2 1.1 + - - -
217A ALA* 3.9 19.3 - - + -
218A ARG 3.4 7.4 - - - +
219A HIS* 3.7 30.1 - - + +
260A ILE* 4.9 2.0 - - + -
269A ILE* 4.3 15.9 - - + -
271A ARG* 1.3 81.0 - - - +
273A GLU* 1.3 61.8 + - - +
274A TYR* 3.4 43.8 - - + +
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Residues in contact with GLU 273 (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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69A TYR* 5.2 2.7 + - - +
109A PRO* 4.7 8.2 - - - +
217A ALA* 3.5 0.5 - - - -
218A ARG* 2.6 65.2 + - + +
220A THR* 4.8 4.5 - - - -
271A ARG* 2.7 42.1 + - - -
272A VAL* 1.3 74.0 - - - +
274A TYR* 1.3 60.5 + - - +
294A LEU 5.5 0.7 - - - -
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Residues in contact with TYR 274 (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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65A GLN* 3.7 18.4 - - - -
191A GLU* 5.3 3.8 + - - -
215A ILE* 4.6 8.3 - - + -
216A VAL 3.2 14.1 - - - -
217A ALA* 4.2 16.8 - - + -
218A ARG* 4.4 1.4 + - - -
234A LEU* 4.2 13.5 - - + -
257A VAL* 6.2 0.7 - - + -
258A GLN 5.8 1.3 - - - -
260A ILE* 3.9 16.9 - - + +
272A VAL* 3.4 40.2 - - + +
273A GLU* 1.3 73.2 - - - +
275A SER* 1.3 66.4 + - - +
293A PRO* 3.8 2.6 - - - +
294A LEU* 3.0 34.0 + - + +
296A ILE* 3.7 55.3 + - + +
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Residues in contact with SER 275 (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 3.7 0.3 - - - +
215A ILE* 3.2 5.2 - - - -
216A VAL* 2.8 42.4 + - - +
218A ARG* 2.9 26.2 + - - -
274A TYR* 1.3 77.3 + - - +
276A LEU* 1.3 60.3 + - - +
277A LEU* 3.9 6.1 - - - -
291A ASP* 2.6 28.1 + - - -
292A LEU 3.6 4.5 - - - -
293A PRO* 4.0 5.9 - - - +
294A LEU* 3.6 7.9 - - - +
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Residues in contact with LEU 276 (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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184A ILE* 4.0 34.3 - - + -
195A ILE* 4.0 17.7 - - + -
197A ILE* 4.2 12.1 - - + -
213A ALA* 4.4 1.1 - - + -
214A ALA 3.6 9.4 - - - +
215A ILE* 4.3 4.7 - - + +
255A LEU* 3.6 30.3 - - + -
275A SER* 1.3 73.4 - - - +
277A LEU* 1.3 66.7 + - - +
278A ILE* 4.0 18.7 + - + -
290A LEU 3.5 1.6 - - - +
291A ASP 3.5 0.5 - - - -
292A LEU* 2.6 50.8 + - + +
294A LEU* 3.6 12.5 - - + +
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Residues in contact with LEU 277 (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* 3.0 8.3 - - - +
214A ALA* 2.7 38.7 + - - +
216A VAL* 3.7 22.7 - - + -
218A ARG* 4.2 2.5 - - - +
275A SER* 3.9 11.2 - - - -
276A LEU* 1.3 75.3 - - - +
278A ILE* 1.3 61.6 + - - +
279A TYR* 4.1 12.9 - - + -
289A ILE* 4.6 7.2 - - + -
290A LEU 3.1 4.7 - - - +
291A ASP* 3.6 38.6 - - + +
82C PRO* 3.5 45.8 - - + +
83C THR* 4.5 4.9 - - + +
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Residues in contact with ILE 278 (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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180A VAL* 3.8 23.4 - - + +
182A ALA* 3.4 27.4 - - + -
184A ILE* 5.4 1.1 - - + -
197A ILE* 4.4 15.9 - - + -
199A ALA* 4.9 2.7 - - + -
201A PHE* 4.3 15.7 - - + -
212A LYS 3.4 8.5 - - - +
213A ALA* 4.3 10.8 - - + -
250A TRP* 4.6 5.4 - - + -
276A LEU* 4.1 15.9 - - + -
277A LEU* 1.3 75.8 - - - +
279A TYR* 1.3 60.7 + - - +
288A VAL 4.0 0.3 - - - +
290A LEU* 2.6 48.6 + - + +
292A LEU* 3.8 22.2 - - + -
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Residues in contact with TYR 279 (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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180A VAL* 5.5 0.4 - - - -
201A PHE* 4.6 1.8 - - - -
210A VAL 4.0 0.2 - - - +
211A PRO* 3.4 3.3 - - - +
212A LYS* 2.8 81.3 + - + +
213A ALA* 4.2 11.1 + - - -
214A ALA* 4.4 3.3 - - - +
233A LYS* 5.0 5.7 + - - -
277A LEU* 4.1 17.9 - - + -
278A ILE* 1.3 78.6 - - - +
280A VAL* 1.3 64.8 + - - +
281A SER* 4.6 4.7 - - - -
287A LYS* 3.5 39.9 - - + -
288A VAL 3.0 12.3 - - - +
289A ILE* 3.7 18.8 - - + -
82C PRO* 5.0 4.9 - - + -
83C THR* 4.0 24.7 + - + +
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Residues in contact with VAL 280 (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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178A VAL* 4.0 23.8 - - + -
179A SER 4.5 1.6 - - - +
180A VAL* 4.0 15.5 - - + -
201A PHE* 3.7 30.1 - - + -
209A VAL* 3.6 38.1 - - + -
210A VAL 3.4 10.5 - - - +
211A PRO* 4.6 1.8 - - + -
242A ILE* 5.6 0.4 - - + -
279A TYR* 1.3 79.6 - - - +
281A SER* 1.3 64.5 + - - +
282A VAL* 3.7 4.7 + - + +
287A LYS* 3.6 1.7 - - - -
288A VAL* 2.7 32.5 + - + +
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Residues in contact with SER 281 (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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209A VAL* 3.6 8.1 - - - +
210A VAL* 2.8 40.4 + - - +
212A LYS* 4.0 24.2 + - - -
279A TYR* 3.9 7.9 - - - -
280A VAL* 1.3 73.6 - - - +
282A VAL* 1.3 59.3 + - - +
283A PRO* 4.0 3.5 - - - +
287A LYS* 4.4 20.0 - - - -
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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