Contacts of the strand formed by residues 162 - 170 (chain E) in PDB entry 5ZR1
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 162 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E LEU* 3.7 36.8 - - + -
89E TYR* 5.2 1.3 - - + -
116E PHE* 3.7 44.7 + - + +
119E TYR* 3.7 30.7 - - + -
122E LEU* 4.2 15.5 - - + -
126E THR* 3.3 10.8 - - + +
128E LEU* 4.4 22.0 - - + +
160E SER* 3.3 15.0 + - - +
161E LYS* 1.3 81.2 - - + +
163E ASN* 1.3 65.8 + - - +
164E ILE* 3.9 0.8 + - - +
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Residues in contact with ASN 163 (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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26E PRO* 3.4 29.6 - - + +
125E LYS* 3.4 29.5 - - - +
126E THR 3.0 12.3 + - - +
127E CYS* 3.3 8.5 - - - +
128E LEU 3.3 18.2 + - - -
157E PRO 4.4 4.9 - - - +
158E LYS 4.2 10.8 + - - +
160E SER* 3.7 15.0 + - - +
161E LYS 4.9 0.2 + - - -
162E ILE* 1.3 77.0 - - - +
164E ILE* 1.3 66.2 + - - +
165E LYS* 3.6 11.4 + - - +
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Residues in contact with ILE 164 (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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31E SER* 5.0 4.7 - - - +
77E ILE* 4.9 0.7 - - + -
81E VAL* 4.2 18.4 - - + -
112E LEU* 4.5 15.7 - - + -
116E PHE* 4.3 13.8 - - + -
128E LEU* 3.5 17.5 - - + +
130E LEU* 3.7 37.5 - - + -
152E LEU* 6.1 0.4 - - + -
153E ASN* 5.5 8.5 - - - +
156E LEU* 3.7 28.2 - - + +
162E ILE* 3.9 4.2 + - - +
163E ASN* 1.3 74.2 - - - +
165E LYS* 1.3 69.4 + - - +
166E PHE* 4.1 25.6 - - + -
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Residues in contact with LYS 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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26E PRO* 3.6 17.8 + - - +
29E THR* 3.3 29.2 + - + -
30E PRO 3.6 17.7 - - - +
31E SER* 3.9 18.6 - - - +
127E CYS* 3.9 22.0 - - + -
128E LEU 2.9 7.3 + - - +
129E PHE* 3.4 29.2 - - + +
130E LEU* 2.6 35.1 + - - +
163E ASN* 3.6 21.8 - - - +
164E ILE* 1.3 80.1 - - - +
166E PHE* 1.3 59.9 + - - +
167E ILE* 3.9 0.6 + - + -
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Residues in contact with PHE 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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30E PRO 5.2 0.9 - - - +
31E SER* 3.3 15.4 + - - +
32E ASN* 3.5 9.1 + - - +
33E LEU* 3.2 22.2 + - - +
77E ILE* 4.9 2.0 - - + -
112E LEU* 5.9 1.8 - - + -
130E LEU* 3.5 37.9 - - + -
132E LEU* 4.3 10.5 - - + -
149E TYR* 4.1 26.7 - + - -
152E LEU* 3.6 32.3 - - + -
153E ASN* 5.1 7.0 - - + -
164E ILE* 4.1 28.0 - - + -
165E LYS* 1.3 76.0 - - - +
167E ILE* 1.3 64.2 + - - +
168E TYR* 3.3 36.1 - + + +
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Residues in contact with ILE 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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22E ILE* 3.8 26.0 - - + -
33E LEU* 3.4 21.8 - - + +
35E LEU* 4.4 20.6 - - + -
47E LEU* 4.6 12.3 - - + -
51E PHE* 4.1 9.6 - - + -
129E PHE* 3.6 39.7 - - + -
130E LEU 3.1 6.7 + - - -
131E ILE* 3.5 16.2 - - + +
132E LEU* 2.9 27.0 + - - +
166E PHE* 1.3 76.8 - - - +
168E TYR* 1.3 69.9 + - - +
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Residues in contact with TYR 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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32E ASN* 3.1 28.8 + - + -
33E LEU 2.7 25.2 + - - +
34E ILE* 4.1 3.8 - - + -
35E LEU* 2.7 33.9 + - - +
132E LEU* 3.6 37.7 - - + +
135E PHE* 4.4 8.1 - + + -
146E PHE* 3.5 36.6 - + - -
149E TYR* 3.1 38.8 + - + +
150E ILE* 4.0 0.4 + - + -
166E PHE* 3.3 18.7 - - + +
167E ILE* 1.3 74.7 - - - +
169E THR* 1.3 59.9 + - - +
170E MET* 3.9 18.2 - - + -
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Residues in contact with THR 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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35E LEU* 3.5 8.5 - - - +
43E LYS* 3.6 34.0 + - + -
44E THR* 4.7 3.8 - - + -
47E LEU* 3.7 17.3 - - - +
131E ILE* 5.1 0.5 - - - +
132E LEU 3.1 5.3 + - - -
133E ASP* 3.5 24.8 + - - +
134E GLY* 3.1 21.6 + - - +
135E PHE* 2.8 28.1 + - - +
167E ILE 5.1 0.7 + - - -
168E TYR* 1.3 76.9 + - - +
170E MET* 1.3 64.0 + - - +
2001E AGS 5.8 0.4 - - - +
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Residues in contact with MET 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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34E ILE* 3.7 19.3 - - + -
35E LEU 3.3 4.3 + - - +
36E GLN* 3.3 13.5 - - + +
37E GLY 3.1 25.9 + - - +
43E LYS* 3.8 2.6 - - - -
134E GLY* 5.2 1.3 - - - -
135E PHE* 4.6 6.7 - - + -
136E ASP* 3.7 18.2 - - + +
146E PHE* 3.8 26.9 - - + -
168E TYR* 3.9 18.2 - - + -
169E THR* 1.3 73.4 - - - +
171E LEU* 1.3 65.0 + - - +
172E GLU 5.6 0.4 - - - +
173E THR 6.3 0.2 - - - +
175E PHE* 3.6 35.4 - - + -
176E LEU* 3.8 27.4 - - + -
179E TYR* 6.1 0.2 - - - -
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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