Contacts of the strand formed by residues 210 - 218 (chain A) in PDB entry 1PS9
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 23.1 - - + -
13A PHE* 3.6 19.6 - - + -
14A THR* 4.1 11.0 - - + -
16A LEU* 4.3 14.1 - - + -
53A LEU* 4.7 15.5 - - + -
96A LYS* 5.0 3.1 - - + -
98A ALA* 5.5 2.0 - - + -
156A ASP* 3.3 27.6 + - + +
157A GLY* 3.0 4.9 - - - -
158A VAL 3.0 26.2 + - - +
209A PHE* 1.3 70.8 - - - +
211A ILE* 1.3 64.2 + - - +
212A ILE* 4.0 24.9 - - + -
243A THR* 3.5 13.7 - - + -
244A ILE* 4.3 9.4 - - + -
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Residues in contact with ILE 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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158A VAL* 3.5 6.7 - - + +
160A VAL* 4.7 12.3 - - + -
198A VAL* 4.3 15.3 - - + +
201A VAL* 3.9 14.4 - - + -
202A ARG* 3.4 66.2 - - + +
205A VAL* 4.5 2.0 - - + -
209A PHE* 3.8 10.1 - - + +
210A ILE* 1.3 78.5 - - - +
212A ILE* 1.3 70.1 + - - +
213A TYR* 5.7 0.2 - - + -
241A GLY 4.2 2.0 - - - +
242A ALA* 3.7 12.4 - - + -
243A THR* 2.7 38.1 + - - +
244A ILE 3.1 7.4 + - - +
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Residues in contact with ILE 212 (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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21A LEU* 4.1 9.0 - - + -
53A LEU* 3.9 26.2 - - + -
55A VAL* 4.0 21.5 - - + -
98A ALA* 4.7 6.7 - - + -
158A VAL 2.9 9.7 + - - +
159A GLU* 3.1 31.1 - - + +
160A VAL* 2.7 33.8 + - - +
210A ILE* 4.0 14.4 - - + -
211A ILE* 1.3 80.3 - - - +
213A TYR* 1.3 59.6 + - - +
214A ARG 4.1 0.2 - - - -
244A ILE* 3.2 24.0 - - + +
246A ASN* 3.8 18.8 - - + +
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Residues in contact with TYR 213 (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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160A VAL* 3.5 27.6 - - + -
162A GLY* 3.7 27.5 + - - -
168A ILE* 3.6 23.1 - - + +
172A LEU* 4.2 2.1 - - - +
194A ALA* 3.8 16.0 - - + +
198A VAL* 4.1 13.0 - - + -
211A ILE* 4.1 0.4 + - + -
212A ILE* 1.3 74.5 - - - +
214A ARG* 1.3 58.7 + - - +
215A LEU* 3.2 43.7 + - + +
233A LEU* 4.0 10.4 - - + +
237A ILE* 3.7 40.6 - - + -
242A ALA* 4.5 3.4 - - + -
244A ILE 3.0 10.4 + - - +
245A ILE* 3.4 7.7 - - + +
246A ASN 2.8 21.4 + - - -
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Residues in contact with ARG 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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23A GLY* 6.0 0.4 - - - -
24A SER* 4.9 4.4 - - - +
159A GLU* 4.0 18.5 + - - +
160A VAL 3.1 13.8 + - - +
161A MET* 4.4 5.5 - - - +
162A GLY* 3.2 32.6 + - - +
163A SER* 3.5 19.0 + - - +
212A ILE 4.1 0.8 + - - -
213A TYR* 1.3 72.2 - - - +
215A LEU* 1.3 58.8 + - - +
246A ASN* 3.5 24.4 - - - +
247A THR 2.9 32.3 + - - +
248A GLY* 4.0 5.4 - - - -
249A ILE 5.5 0.6 - - - +
286A THR* 3.4 19.4 + - - +
287A ASN* 4.3 1.6 + - - -
308A SER* 5.1 1.8 + - - -
702A FMN 2.5 73.6 + - - -
704A MDE 5.5 0.8 + - - -
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Residues in contact with LEU 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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163A SER* 4.2 0.7 - - - -
172A LEU* 5.8 0.2 - - + -
213A TYR* 3.2 24.0 + - + -
214A ARG* 1.3 71.3 - - - +
216A SER* 1.3 63.7 + - - +
217A MET* 3.3 31.7 + - + +
230A THR* 3.8 16.2 - - + +
233A LEU* 3.4 37.5 - - + -
234A ALA* 4.1 13.5 - - + +
245A ILE* 3.9 8.7 - - + -
246A ASN 2.8 15.3 + - - +
247A THR* 3.6 1.6 - - - -
248A GLY 2.7 29.6 + - - -
275A LEU* 3.7 23.6 - - + -
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Residues in contact with SER 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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162A GLY 4.1 4.5 + - - -
163A SER* 3.6 21.0 - - - -
164A GLU 4.6 1.4 + - - -
169A ASN* 3.5 17.8 + - - -
172A LEU* 5.9 3.3 - - - +
214A ARG 3.8 2.6 + - - -
215A LEU* 1.3 79.4 - - - +
217A MET* 1.3 61.4 + - - +
218A LEU 4.2 0.7 + - - -
219A ASP* 2.7 37.6 + - - +
230A THR* 4.1 9.0 + - - -
248A GLY 3.5 10.1 + - - -
250A GLY 4.7 1.2 + - - -
251A TRP* 4.4 1.7 + - - -
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Residues in contact with MET 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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215A LEU* 3.6 30.1 - - + +
216A SER* 1.3 73.0 - - - +
218A LEU* 1.3 61.4 + - - +
219A ASP* 4.1 0.7 - - - -
227A PHE* 6.1 1.7 - - + -
230A THR* 3.9 23.4 + - + +
245A ILE* 4.3 5.8 - - + +
246A ASN 3.8 9.2 - - - +
247A THR* 3.0 45.8 - - + +
248A GLY 3.0 8.7 + - - +
271A VAL* 3.5 18.4 - - + +
272A THR* 4.1 23.1 - - + +
275A LEU* 4.1 18.2 - - + -
283A LEU* 5.5 1.3 - - + -
284A VAL 5.0 0.2 - - - +
537A LEU* 3.9 20.8 - - + +
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Residues in contact with LEU 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 SER* 3.4 1.8 - - - -
217A MET* 1.3 80.8 - - - +
219A ASP* 1.3 59.0 + - - +
220A LEU* 3.3 31.6 - - + -
248A GLY 3.7 2.4 + - - -
249A ILE* 4.0 15.7 - - + -
250A GLY* 2.6 33.7 + - - -
268A PHE* 4.0 32.8 - - + -
270A TRP* 4.5 0.4 - - + -
271A VAL* 4.1 16.2 - - + -
533A ILE* 4.2 11.9 - - + -
537A LEU* 3.6 21.8 - - + -
541A GLY 3.6 13.7 - - - +
542A GLY* 3.6 10.5 - - - +
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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