Contacts of the strand formed by residues 164 - 173 (chain P) in PDB entry 5IYB
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 GLN 164 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162P VAL* 2.0 58.4 + - + +
163P PRO* 1.3 79.9 + - - +
165P LEU* 1.3 65.5 + - - +
166P GLN* 3.7 15.2 - - - +
260P GLY* 3.6 1.5 - - - -
261P SER 3.0 40.8 + - - +
262P CYS* 5.9 1.6 - - + -
321P ILE* 6.5 0.4 - - - -
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Residues in contact with LEU 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P PRO 4.7 1.8 - - - +
164P GLN* 1.3 74.4 - - - +
166P GLN* 1.3 67.0 + - - +
167P ASN 5.1 0.2 - - - +
168P ILE* 3.9 26.7 - - + -
225P LYS* 3.5 30.6 + - - +
226P SER* 5.2 0.2 - - - -
227P GLU* 5.2 1.3 - - - +
258P MET* 4.6 5.8 - - + -
259P VAL 3.9 9.9 - - - +
260P GLY* 4.2 3.1 - - - -
318P ARG* 3.7 56.8 - - + +
321P ILE* 5.7 11.0 - - + -
322P TYR* 4.0 18.2 - - + +
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Residues in contact with GLN 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P GLN* 3.7 23.2 + - - +
165P LEU* 1.3 83.0 - - - +
167P ASN* 1.3 66.8 + - + +
223P GLY 4.7 1.2 - - - +
224P ALA 4.5 0.6 - - - +
225P LYS* 3.3 36.5 + - - +
259P VAL* 3.0 12.0 + - + +
260P GLY 4.3 0.9 - - - -
261P SER* 2.9 36.4 + - - +
80Y T 4.0 18.1 - - - +
81Y A 4.1 30.9 + - - +
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Residues in contact with ASN 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P LEU 3.9 0.2 - - - -
166P GLN* 1.3 81.5 - - + +
168P ILE* 1.3 86.5 + - - +
169P VAL* 4.8 1.8 - - - +
223P GLY* 3.3 27.4 + - - -
224P ALA 3.8 4.5 + - - -
225P LYS* 5.1 0.2 - - - +
259P VAL* 2.7 51.9 + - + +
13X A 4.5 3.4 + - - -
79Y T 2.2 41.6 + - - +
80Y T 3.9 26.1 + - - +
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Residues in contact with ILE 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P LEU* 3.9 24.0 - - + -
167P ASN* 1.3 90.2 + - - +
169P VAL* 1.3 67.4 + - - +
170P SER* 4.0 17.3 - - - +
221P CYS 4.0 1.2 - - - +
222P THR* 3.5 4.5 - - - -
223P GLY 3.2 22.3 + - - -
224P ALA* 3.0 26.8 + - + +
225P LYS 4.2 2.0 - - - -
226P SER* 3.9 20.0 - - - +
227P GLU* 4.9 2.5 - - - +
230P SER* 4.6 10.6 - - - +
255P ILE* 4.2 13.9 - - + -
257P ASN 3.6 7.2 - - - +
258P MET* 3.6 28.3 - - + -
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Residues in contact with VAL 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P ASN* 4.8 2.5 - - - +
168P ILE* 1.3 77.2 - - - +
170P SER* 1.3 62.6 + - - +
171P THR* 5.8 0.2 - - + -
220P VAL* 4.7 6.1 - - + -
221P CYS 3.9 2.2 - - - -
222P THR* 3.8 17.5 - - + -
255P ILE* 3.8 0.5 - - - +
256P GLN* 2.6 41.2 + - + -
257P ASN* 2.7 36.6 + - + +
259P VAL* 5.5 2.0 - - + -
13X A 3.9 16.6 - - + -
14X A 3.6 39.0 - - + +
15X A 5.2 2.5 - - + +
79Y T 4.3 7.2 - - - +
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Residues in contact with SER 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ILE* 4.0 4.2 - - - +
169P VAL* 1.3 76.9 - - - +
171P THR* 1.3 63.6 + - - +
220P VAL* 3.2 8.5 - - - +
221P CYS* 2.8 39.6 + - - +
230P SER* 3.9 13.1 + - - -
253P PHE* 4.1 17.7 - - - -
254P LYS 3.3 13.2 - - - -
255P ILE* 3.2 28.8 - - - +
256P GLN* 3.8 1.6 - - - +
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Residues in contact with THR 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P VAL* 5.8 0.4 - - + -
170P SER* 1.3 80.3 - - - +
172P VAL* 1.3 65.0 + - - +
219P MET 3.5 8.3 - - - -
220P VAL* 3.7 27.6 - - + +
221P CYS* 4.5 0.9 - - - +
252P ASP* 3.7 5.1 + - - +
253P PHE* 3.5 4.0 - - - -
254P LYS* 2.9 31.2 + - - +
256P GLN* 2.7 35.5 + - + +
15X A 4.5 18.1 - - - +
16X A 5.1 6.2 - - - -
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Residues in contact with VAL 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P THR* 1.3 78.1 - - - +
173P ASN* 1.3 57.9 + - - +
174P LEU* 5.1 2.9 - - + -
218P LYS* 3.9 1.4 - - - +
219P MET* 2.7 73.4 + - + +
220P VAL* 5.8 0.7 - - - -
221P CYS* 5.9 3.1 - - + -
234P ALA* 4.3 13.9 - - + +
249P LYS 5.3 0.2 - - - +
250P PHE* 4.3 14.6 - - + -
251P LEU 3.1 28.7 - - - +
252P ASP* 3.6 6.1 - - - -
253P PHE* 3.8 24.7 - - + -
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Residues in contact with ASN 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172P VAL* 1.3 75.7 - - - +
174P LEU* 1.3 60.9 + - - +
175P GLY* 2.4 37.7 + - - -
217P GLY* 2.9 15.5 - - - +
218P LYS* 4.2 22.4 - - + +
249P LYS 3.2 11.1 - - - +
251P LEU* 2.9 34.6 + - + +
252P ASP* 3.9 18.7 + - + +
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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