Contacts of the strand formed by residues 164 - 175 (chain E) in PDB entry 1R8Y
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 VAL 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E ASP 5.2 0.2 - - - +
129E GLY* 4.3 1.7 - - - -
130E PHE 4.0 5.2 - - - +
133E VAL* 3.9 13.0 - - + -
160E ILE 4.1 5.6 - - - +
161E ALA* 2.9 21.4 + - - +
162E SER 4.1 4.2 - - - +
163E MET* 1.3 77.6 - - - +
165E ARG* 1.3 75.6 + - - +
166E PRO* 4.5 0.3 - - - +
168E GLY* 3.4 29.6 - - - +
169E LEU 3.5 12.3 - - - +
170E LEU* 3.8 26.7 - - + +
258E PHE* 4.4 8.5 - - + -
290E LYS* 3.9 18.8 - - + +
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Residues in contact with ARG 165 (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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128E ASP* 3.6 18.5 - - - +
129E GLY* 3.6 19.3 + - - -
130E PHE 3.1 22.3 + - - +
131E ASP* 3.1 29.5 + - - +
164E VAL* 1.3 80.7 - - - +
166E PRO* 1.3 93.1 + - + +
167E GLY 3.5 1.5 + - - -
168E GLY* 3.1 18.1 + - - +
290E LYS* 4.0 3.9 - - - +
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Residues in contact with PRO 166 (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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128E ASP 4.0 9.4 - - - +
164E VAL 4.5 1.3 - - - +
165E ARG* 1.3 112.0 + - + +
167E GLY* 1.3 58.8 + - - +
261E ARG* 5.7 1.3 - - - +
290E LYS* 4.5 20.6 - - + -
291E THR 4.5 2.5 - - - +
292E ASP 4.4 22.0 - - - -
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Residues in contact with GLY 167 (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 ARG* 3.5 3.0 + - - -
166E PRO* 1.3 72.3 - - - +
168E GLY* 1.3 59.0 + - - +
169E LEU* 5.5 1.6 - - - +
289E LYS* 5.5 2.2 - - - -
290E LYS 3.2 24.4 + - - -
291E THR* 4.3 4.1 - - - +
292E ASP 5.0 1.3 - - - +
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Residues in contact with GLY 168 (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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130E PHE 4.6 0.9 - - - -
131E ASP 3.5 13.0 - - - -
164E VAL* 3.4 10.7 - - - +
165E ARG* 3.1 20.3 + - - -
166E PRO 3.3 0.2 - - - -
167E GLY* 1.3 79.7 - - - +
169E LEU* 1.3 63.6 + - - +
289E LYS* 3.0 25.8 - - - -
290E LYS 3.2 5.9 + - - +
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Residues in contact with LEU 169 (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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51E LEU* 4.5 13.9 - - + +
52E LEU* 5.0 3.1 - - + -
55E HIS* 3.5 49.6 - - + +
57E CYS* 3.8 12.6 - - - -
131E ASP 3.1 12.7 + - - +
132E ALA* 3.2 10.8 - - + -
133E VAL* 2.7 30.9 + - - -
164E VAL* 3.5 10.5 - - - +
167E GLY 5.5 1.3 - - - +
168E GLY* 1.3 82.0 - - - +
170E LEU* 1.3 55.4 + - - +
171E VAL* 4.6 6.5 - - + -
287E VAL* 4.2 15.0 - - + -
288E LEU 3.3 16.4 - - - +
289E LYS* 3.6 14.8 - - + -
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Residues in contact with LEU 170 (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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133E VAL* 2.9 45.1 - - + +
134E ILE* 5.1 2.0 - - - -
135E CYS* 5.4 0.4 - - + -
157E LEU* 5.4 2.9 - - + +
160E ILE* 3.3 26.2 - - + -
161E ALA* 4.6 4.9 - - + +
164E VAL* 3.8 6.8 - - + +
168E GLY 4.2 0.2 + - - -
169E LEU* 1.3 72.5 - - - +
171E VAL* 1.3 65.5 + - - +
172E ILE* 4.4 16.8 - - + +
254E VAL* 4.3 16.6 - - + -
258E PHE* 3.8 38.6 - - + -
286E HIS 3.4 3.5 - - - +
287E VAL* 3.4 1.2 - - - -
288E LEU* 2.8 38.0 + - + +
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Residues in contact with VAL 171 (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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47E TRP* 3.7 31.4 - - + -
48E LEU* 5.1 2.7 - - + -
51E LEU* 3.9 21.3 - - + -
52E LEU* 5.2 5.6 - - + -
132E ALA* 5.6 0.7 - - + -
133E VAL 2.9 8.7 + - - +
134E ILE* 3.3 21.1 - - + +
135E CYS 2.8 27.2 + - - +
136E LEU* 3.9 14.4 - - + +
169E LEU* 4.6 14.6 - - + -
170E LEU* 1.3 76.3 - - - +
172E ILE* 1.3 60.1 + - - +
285E ILE* 3.9 8.7 - - + -
286E HIS 3.4 3.8 - - - +
287E VAL* 4.6 6.5 - - + -
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Residues in contact with ILE 172 (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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135E CYS* 3.2 36.3 - - + +
136E LEU* 4.5 0.9 - - - -
140E PHE* 4.2 12.8 - - + -
157E LEU* 4.0 24.9 - - + -
160E ILE* 5.0 11.2 - - + -
170E LEU* 4.4 13.2 - - + +
171E VAL* 1.3 75.0 - - - +
173E ASP* 1.3 69.1 + - - +
250E PHE* 3.9 26.2 - - + -
254E VAL* 4.1 16.2 - - + -
285E ILE* 4.8 0.2 - - - -
286E HIS* 2.8 39.3 + - + +
288E LEU* 6.6 0.2 - - + -
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Residues in contact with ASP 173 (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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135E CYS 3.2 4.9 + - - +
136E LEU* 3.2 17.5 - - + -
137E GLY 3.0 16.8 + - - -
138E ASN* 3.0 24.9 + - - -
139E SER 4.5 0.7 + - - -
140E PHE* 4.9 7.6 + - - +
172E ILE* 1.3 83.0 - - - +
174E HIS* 1.3 68.6 + - - +
193E TYR* 2.7 34.0 + - - +
250E PHE* 5.1 1.5 - - - -
283E TYR* 3.5 7.1 - - + -
284E PHE 3.2 13.9 - - - +
285E ILE* 4.0 8.5 - - + -
286E HIS* 4.8 0.2 - - - -
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Residues in contact with HIS 174 (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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138E ASN* 3.2 15.0 - - - +
140E PHE* 6.2 0.9 - - + -
141E ALA* 5.5 2.7 - - + +
173E ASP* 1.3 76.8 - - - +
175E ARG* 1.3 80.6 + - - +
177E TYR* 5.1 2.2 - - + -
178E ASP* 5.0 0.9 - - - -
245E HIS* 3.7 31.6 + - + +
246E CYS 4.7 0.7 - - - -
247E LEU* 4.2 12.7 - - - +
250E PHE* 3.6 31.2 - + + +
283E TYR* 3.6 5.9 - - - +
284E PHE* 2.7 59.8 + + + +
286E HIS* 3.0 33.8 + + - -
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Residues in contact with ARG 175 (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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138E ASN* 3.0 30.9 + - + +
174E HIS* 1.3 91.8 + - - +
176E ASN* 1.3 62.9 + - - +
177E TYR* 2.9 27.3 + - + -
180E ILE* 3.9 19.3 - - + +
186E ALA* 3.4 8.5 + - - +
187E PRO* 2.7 51.5 + - - +
190E LYS* 5.0 7.6 - - - +
202E ILE* 5.9 1.8 - - - +
218E LEU* 4.4 19.2 - - - +
220E TYR* 5.1 3.6 + - - -
242E TYR* 6.1 1.4 - - - -
282E CYS* 3.5 14.9 + - - +
283E TYR* 4.2 28.0 + - + +
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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