Contacts of the strand formed by residues 269 - 281 (chain C) in PDB entry 4LL1
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C GLU* 4.2 2.4 - - - +
71C ARG* 3.9 9.0 + - - -
219C HIS* 4.4 15.0 - - + +
220C THR 3.5 12.1 - - - +
221C TYR* 4.0 6.7 - - + +
266C GLY* 2.6 35.2 + - - +
267C SER 4.2 0.9 - - - +
268C ASN* 1.3 76.1 + - - +
270C LEU* 1.3 65.1 + - - +
271C ARG* 3.9 9.0 - - - +
272C VAL* 3.6 30.7 - - + -
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Residues in contact with LEU 270 (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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66C THR 4.5 2.4 - - - +
67C SER* 3.9 1.9 - - - -
68C GLU* 2.9 59.0 + - + +
69C TYR 4.8 9.4 - - - +
70C LEU* 5.3 0.2 - - - -
71C ARG* 3.4 35.0 - - + +
220C THR* 2.8 19.8 + - + +
222C LEU* 3.6 35.2 - - + +
227C THR* 5.4 2.5 - - + +
268C ASN 3.2 18.2 - - - +
269C ILE* 1.3 76.3 - - - +
271C ARG* 1.3 68.2 + - + +
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Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR 4.9 2.7 - - - -
67C SER* 3.7 22.0 - - - +
68C GLU 3.3 18.7 + - - +
69C TYR* 3.4 45.7 + - - +
106C PRO* 5.6 4.9 - - - +
108C GLY* 4.3 16.0 - - - +
109C PRO* 3.7 16.4 + - - +
219C HIS* 3.6 0.3 - - - -
220C THR* 2.8 60.3 + - - +
227C THR* 5.5 2.2 - - - +
269C ILE* 3.7 3.9 - - - +
270C LEU* 1.3 83.8 - - - +
272C VAL* 1.3 70.1 + - - +
273C GLU* 3.3 26.6 + - + -
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLN* 2.6 34.5 + - - +
66C THR 5.5 0.6 + - - -
67C SER* 4.8 0.9 + - - -
217C ALA* 3.8 11.7 - - + -
218C ARG 3.4 9.9 - - - +
219C HIS* 3.5 37.2 - - + +
269C ILE* 3.6 15.7 - - + -
271C ARG* 1.3 83.7 - - - +
273C GLU* 1.3 63.2 + - - +
274C TYR* 3.7 33.5 - - + +
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Residues in contact with GLU 273 (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* 4.9 0.7 - - - +
69C TYR* 4.6 4.4 + - - +
109C PRO* 3.8 32.4 - - - +
216C VAL 3.8 1.6 - - - +
217C ALA* 3.5 1.6 - - - -
218C ARG* 2.8 61.2 + - - +
220C THR* 5.5 3.8 - - - +
271C ARG* 3.3 32.6 + - + +
272C VAL* 1.3 76.0 - - - +
274C TYR* 1.3 61.3 + - - +
294C LEU 5.7 0.2 - - - -
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLN* 3.8 12.8 - - - -
215C ILE* 4.2 4.7 - - + -
216C VAL 3.3 4.7 - - - +
217C ALA* 4.1 11.4 - - + -
218C ARG* 4.0 1.6 + - - -
219C HIS* 5.4 1.9 - - - -
234C LEU* 3.9 24.9 - - + -
259C LYS 5.3 5.9 + - - -
272C VAL* 3.7 44.7 - - + +
273C GLU* 1.3 75.4 - - - +
275C SER* 1.3 63.8 + - - +
293C PRO* 3.8 2.4 - - - +
294C LEU* 3.0 39.3 + - + +
296C ILE* 3.6 59.5 - - + +
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Residues in contact with SER 275 (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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214C ALA 3.7 0.2 - - - +
215C ILE* 3.4 3.6 - - - +
216C VAL* 2.8 35.0 + - - +
218C ARG* 2.4 33.5 + - - -
274C TYR* 1.3 74.4 + - - +
276C LEU* 1.3 59.7 + - - +
277C LEU* 3.9 5.3 + - - -
291C ASP* 2.7 30.9 + - - -
292C LEU 3.4 5.4 - - - -
293C PRO* 4.2 5.9 - - - +
294C LEU* 4.0 5.8 - - - +
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Residues in contact with LEU 276 (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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184C ILE* 3.8 32.8 - - + -
195C ILE* 4.2 15.0 - - + -
197C ILE* 4.0 19.7 - - + -
213C ALA* 4.3 0.2 - - + -
214C ALA 3.5 12.3 - - - +
215C ILE* 4.5 6.5 - - + +
255C LEU* 4.1 15.9 - - + -
275C SER* 1.3 72.6 - - - +
277C LEU* 1.3 66.5 + - - +
278C ILE* 3.8 22.3 + - + -
290C LEU 3.6 1.6 - - - +
291C ASP* 3.7 0.5 - - - -
292C LEU* 2.8 44.3 + - + +
294C LEU* 3.8 16.8 - - + +
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Residues in contact with LEU 277 (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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82A PRO* 3.4 48.2 - - + +
83A THR* 4.5 4.3 - - + +
213C ALA* 3.0 7.7 - - - +
214C ALA* 2.6 39.6 + - + +
216C VAL* 3.5 23.6 - - + -
218C ARG* 6.1 1.1 - - - +
275C SER* 4.6 4.7 - - - +
276C LEU* 1.3 73.7 - - - +
278C ILE* 1.3 59.8 + - - +
279C TYR* 4.0 16.6 - - + -
289C ILE* 4.3 9.9 - - + -
290C LEU 3.3 7.6 - - - +
291C ASP* 3.8 33.7 - - + +
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Residues in contact with ILE 278 (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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180C VAL* 4.1 22.5 - - + +
182C ALA* 3.4 31.4 - - + -
184C ILE* 5.3 0.7 - - + -
197C ILE* 4.0 11.9 - - + -
199C ALA* 4.7 0.9 - - + -
201C PHE* 4.3 11.7 - - + -
212C LYS 3.6 9.0 - - - +
213C ALA* 4.1 7.4 - - + -
250C TRP* 4.3 12.8 - - + -
276C LEU* 3.8 29.1 + - + -
277C LEU* 1.3 73.9 - - - +
279C TYR* 1.3 59.6 + - - +
288C VAL 4.2 0.3 - - - +
290C LEU* 2.7 48.6 + - + +
292C LEU* 3.9 17.0 - - + -
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Residues in contact with TYR 279 (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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82A PRO* 5.1 2.7 - - + -
83A THR* 3.7 26.9 - - + +
180C VAL* 5.2 1.1 - - - -
201C PHE* 4.7 1.4 - - - -
210C VAL 3.9 0.3 - - - +
211C PRO* 3.4 3.1 - - - +
212C LYS* 2.8 74.0 + - + +
213C ALA* 4.5 3.3 + - - -
214C ALA* 4.5 6.4 - - + +
233C LYS* 4.7 7.1 + - - -
236C SER* 6.1 0.3 - - - -
277C LEU* 4.0 26.0 - - + -
278C ILE* 1.3 78.7 - - - +
280C VAL* 1.3 65.6 + - - +
281C SER* 3.8 19.7 - - - -
287C LYS* 3.7 32.2 - - + -
288C VAL 3.1 14.1 - - - +
289C ILE* 3.7 17.0 - - + -
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Residues in contact with VAL 280 (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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178C VAL* 3.7 22.7 - - + -
179C SER 4.7 1.1 - - - +
180C VAL* 4.2 12.3 - - + -
201C PHE* 3.5 34.3 - - + -
209C VAL* 3.4 40.4 - - + -
210C VAL 3.5 8.5 - - - +
211C PRO* 4.3 3.6 - - + -
242C ILE* 6.0 0.2 - - + -
279C TYR* 1.3 80.5 - - - +
281C SER* 1.3 63.4 + - - +
282C VAL* 3.6 3.1 + - + +
287C LYS* 3.5 5.9 - - - -
288C VAL* 2.8 34.4 + - + +
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Residues in contact with SER 281 (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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209C VAL* 3.3 7.8 - - - +
210C VAL* 2.9 40.1 + - - +
212C LYS* 3.3 34.0 + - - +
279C TYR* 3.8 10.6 - - - -
280C VAL* 1.3 70.9 - - - +
282C VAL* 1.3 59.5 + - - +
283C PRO* 3.6 5.5 - - - +
287C LYS* 4.3 14.8 - - - -
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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