Contacts of the strand formed by residues 156 - 161 (chain E) in PDB entry 1UCY
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 156 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PRO* 3.6 28.2 - - + +
154E VAL 2.8 25.6 + - - +
155E LEU* 1.3 84.4 + - - +
157E VAL* 1.3 63.5 + - - +
16H ILE* 3.8 27.7 - - + +
19H GLY* 4.1 5.8 - - - +
20H GLN* 3.1 22.7 + - - +
21H ASP* 3.1 26.1 + - - +
139H THR* 3.0 29.5 - - - +
140H GLY 3.0 14.8 + - - +
144H ARG* 3.7 19.0 + - + +
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Residues in contact with VAL 157 (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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156E GLN* 1.3 75.0 - - - +
158E VAL* 1.3 66.7 + - - +
159E ASN* 4.6 1.6 - - - +
16H ILE* 4.4 0.9 - - - -
19H GLY* 2.9 24.1 - - - -
20H GLN* 2.9 23.2 + - + +
21H ASP 4.6 0.7 - - - +
22H ALA* 3.4 25.4 - - + -
26H LEU* 3.4 26.2 - - + -
137H ARG* 3.5 42.4 - - + +
138H VAL 3.3 7.0 - - - +
139H THR* 3.7 4.7 - - + -
14L THR* 5.1 4.0 - - - +
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Residues in contact with VAL 158 (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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157E VAL* 1.3 78.0 - - - +
159E ASN* 1.3 70.1 + - - +
160E LEU* 3.8 31.4 + - + -
184E TYR* 5.6 0.7 - - - +
187E ARG 4.8 3.4 - - - +
188E GLY* 4.2 11.0 - - - -
189E ASP 4.5 6.7 - - - +
16H ILE* 3.4 35.2 - - + -
18H GLU 3.9 17.0 - - - +
19H GLY* 4.0 2.2 - - - -
20H GLN* 6.1 1.6 - - - +
137H ARG* 3.6 0.3 - - - -
138H VAL* 2.9 36.5 + - + +
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Residues in contact with ASN 159 (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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157E VAL* 5.1 1.6 - - - +
158E VAL* 1.3 78.3 - - - +
160E LEU* 1.3 65.6 + - - +
184E TYR* 3.3 19.3 + - - -
20H GLN* 5.8 1.0 - - - +
135H LYS* 4.6 3.8 - - + -
136H GLY 3.1 6.5 - - - +
137H ARG* 2.8 38.1 + - - +
14L GLU* 2.7 87.1 + - + +
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Residues in contact with LEU 160 (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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158E VAL* 3.8 22.2 - - + +
159E ASN* 1.3 83.0 - - - +
161E PRO* 1.3 68.7 - - + +
162E LEU 3.8 0.3 + - - -
183E ALA* 4.4 8.7 - - + +
184E GLY* 4.3 22.9 - - - +
188E GLY* 3.3 32.5 - - - +
189E ASP* 4.6 12.6 - - - +
190E ALA 4.9 0.7 - - - +
199E PHE* 4.0 11.7 - - + -
228E TYR* 3.2 28.5 - - + +
135H LYS* 3.1 3.5 - - - -
136H GLY* 2.8 37.2 + - - -
138H VAL* 4.0 11.0 - - + -
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Residues in contact with PRO 161 (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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160E LEU* 1.3 85.4 - - + +
162E LEU* 1.3 66.1 + - - +
163E VAL* 3.6 0.6 + - + -
183E ALA* 3.2 4.4 - - - +
184E GLY* 2.9 86.4 + - + +
186E GLU* 4.5 5.2 - - + +
133H GLY* 3.9 18.8 - - - +
134H PHE 3.5 5.4 - - - +
135H LYS* 3.9 12.8 - - + -
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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