Contacts of the strand formed by residues 279 - 288 (chain E) in PDB entry 1S9C
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 279 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247E ALA* 3.0 22.4 - - + +
248E LYS* 3.2 18.3 + - - +
270E GLN* 3.2 30.1 - - + +
271E THR 3.6 4.7 - - - +
272E LYS* 3.9 23.1 - - + -
277E GLY 3.6 2.9 + - - +
278E ASP* 1.3 72.7 - - - +
280E VAL* 1.3 59.7 + - - +
281E ILE 3.6 21.1 - - - +
282E SER* 4.0 17.5 - - - -
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Residues in contact with VAL 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E THR* 3.9 9.6 - - + -
246E PHE* 3.8 3.8 - - - +
247E ALA 2.9 22.2 + - - -
248E LYS* 3.3 23.6 - - + +
249E PRO 3.6 5.6 - - - +
250E VAL* 3.2 33.9 - - + -
256E LEU* 4.7 0.2 - - + -
271E THR* 2.8 39.6 + - + +
272E LYS* 4.2 3.6 - - - +
273E VAL* 3.5 17.3 - - + -
278E ASP* 4.1 6.1 - - + +
279E ILE* 1.3 77.2 - - - +
281E ILE* 1.3 65.7 + - + +
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Residues in contact with ILE 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E THR* 3.7 17.0 - - + +
220E PHE* 3.7 38.8 - - + +
223E SER* 4.7 0.9 - - - +
244E ALA* 3.8 22.2 - - + -
245E ARG 3.3 9.9 - - - +
246E PHE* 4.2 14.4 - - + -
269E PHE* 4.1 16.8 - - + -
270E GLN* 3.5 8.0 - - - +
271E THR* 2.9 42.5 + - - +
279E ILE* 3.6 2.4 - - - +
280E VAL* 1.3 91.1 - - + +
282E SER* 1.3 63.5 + - - +
284E ALA* 4.1 4.9 - - + -
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Residues in contact with SER 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E ARG* 2.8 43.6 + - - +
247E ALA* 4.8 8.0 - - - +
270E GLN* 4.4 10.3 - - - +
279E ILE* 4.0 15.9 - - - -
281E ILE* 1.3 74.9 - - - +
283E ASN* 1.3 88.4 + - - +
284E ALA* 3.0 5.9 + - - +
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Residues in contact with ASN 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ALA* 3.6 17.0 - - + +
165E VAL 2.8 46.1 + - - +
166E ALA* 3.2 23.2 - - - +
167E ILE* 4.2 14.3 + - - +
243E LYS* 4.3 2.1 - - - +
244E ALA* 4.8 0.9 - - - -
245E ARG* 3.7 21.5 - - + +
269E PHE 4.4 2.6 + - - -
270E GLN* 5.5 0.2 + - - -
282E SER* 1.3 95.7 + - - +
284E ALA* 1.3 57.4 + - - +
285E TYR* 4.7 0.7 - - - -
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Residues in contact with ALA 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E VAL 4.5 1.8 - - - +
167E ILE* 5.2 0.7 - - - +
243E LYS 3.0 16.6 - - - +
244E ALA* 3.6 13.7 - - + -
268E HIS* 3.5 6.9 + - - +
269E PHE* 2.9 58.9 + - + +
281E ILE* 4.1 3.6 - - + -
282E SER 3.0 4.2 + - - +
283E ASN* 1.3 80.0 - - - +
285E TYR* 1.3 66.3 + - - +
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Residues in contact with TYR 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E TYR* 3.9 20.1 - + - -
162E LYS* 5.7 1.4 - - - +
163E VAL 4.1 5.6 + - - -
165E VAL* 3.6 37.0 - - + -
241E ALA 4.8 3.6 - - - -
242E VAL* 3.2 6.1 - - - +
243E LYS* 2.9 58.8 + - + +
266E ARG* 3.2 49.8 + - + -
267E ILE 3.2 14.4 - - - +
268E HIS* 4.0 6.3 - - - +
269E PHE* 3.5 6.4 - - - -
284E ALA* 1.3 79.3 - - - +
286E VAL* 1.3 68.5 + - - +
287E ASP* 3.2 18.0 + - - -
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Residues in contact with VAL 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ALA* 6.0 1.1 - - + -
227E VAL* 3.1 37.9 - - + -
239E PHE* 3.7 28.9 - - + -
241E ALA 3.0 13.9 - - - +
242E VAL* 4.1 8.3 - - + -
265E ASN 3.8 0.3 - - - +
266E ARG* 3.7 0.2 - - - -
267E ILE* 3.0 38.0 + - + +
269E PHE* 4.3 4.7 - - + -
285E TYR* 1.3 78.1 - - - +
287E ASP* 1.3 67.2 + - - +
288E LEU* 3.8 20.2 + - + -
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Residues in contact with ASP 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LYS* 3.0 34.1 + - + +
241E ALA* 2.7 26.0 + - + +
265E ASN* 3.5 3.9 - - + +
266E ARG* 2.8 54.3 + - - +
285E TYR* 3.2 11.4 + - - -
286E VAL* 1.3 73.4 - - - +
288E LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E VAL* 5.2 4.3 - - + -
228E LEU* 5.6 0.9 - - - -
231E PHE* 3.1 35.7 - - + +
232E ALA* 3.9 16.8 - - + -
238E ARG* 3.1 27.6 - - - +
239E PHE* 4.2 9.2 - - + -
240E LYS* 4.4 9.2 + - - +
265E ASN* 2.7 39.4 + - - +
267E ILE* 3.8 26.9 - - + -
286E VAL* 3.9 17.0 - - + +
287E ASP* 1.3 80.8 - - - +
289E ALA* 1.3 60.6 + - - +
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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