Contacts of the strand formed by residues 170 - 176 (chain E) in PDB entry 1S9V
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 170 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E PHE 3.8 0.9 - - - +
133E ARG* 3.8 0.3 - - - -
134E ASN* 2.7 41.5 + - - +
168E GLY 3.7 11.2 - - - +
169E ASP* 1.3 78.9 - - - +
171E TYR* 1.3 62.5 + - - +
172E THR* 4.0 6.5 + - + +
187E GLU* 3.6 44.0 - - + +
188E TRP 3.9 4.3 - - - +
189E ARG* 5.3 5.2 - - + -
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Residues in contact with TYR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LEU* 3.9 21.1 - - + -
131E TRP* 4.0 7.4 - - + -
132E PHE 3.2 11.9 - - - +
133E ARG* 2.8 48.7 + - + -
138E GLU* 5.4 1.1 - - + -
161E LEU* 3.9 22.0 - - + -
163E MET* 3.6 38.4 - - + +
164E THR 3.8 13.8 + - - -
165E PRO* 5.5 0.4 - - + -
169E ASP* 3.5 30.5 + - + -
170E VAL* 1.3 74.3 - - - +
172E THR* 1.3 58.0 + - - +
186E VAL 3.9 0.3 - - - +
187E GLU* 3.1 2.6 - - - -
188E TRP* 2.6 53.6 + + + +
190E ALA* 5.5 2.5 - - + -
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Residues in contact with THR 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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130E ARG 3.7 1.0 - - - +
131E TRP* 3.4 8.5 - - - -
132E PHE* 2.9 62.5 + - + +
134E ASN 5.5 1.6 - - - +
135E ASP 5.6 2.5 - - - +
170E VAL* 4.6 8.5 - - + +
171E TYR* 1.3 76.2 - - - +
173E CYS* 1.3 69.9 + - - +
174E HIS* 3.7 2.6 + - - +
185E THR* 4.0 16.5 - - - +
186E VAL 3.2 8.5 + - - -
187E GLU* 4.2 10.3 - - - -
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Residues in contact with CYS 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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99E VAL* 4.1 8.4 - - + +
101E ILE* 4.1 10.3 - - + -
117E CYS* 2.0 52.5 - - + -
129E VAL* 3.7 22.4 - - - -
130E ARG 3.7 3.6 - - - -
131E TRP* 3.9 9.9 - - + -
172E THR* 1.3 70.7 - - - +
174E HIS* 1.3 59.0 + - - +
175E VAL* 4.1 4.9 - - - +
184E ILE 3.4 2.4 - - - +
185E THR* 3.2 5.7 - - - -
186E VAL* 2.7 35.3 + - - +
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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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128E LYS 3.6 1.1 + - - +
129E VAL* 3.3 4.2 - - - -
130E ARG* 2.8 60.6 + - - +
132E PHE* 3.6 28.8 - + + -
172E THR* 3.7 1.5 + - - +
173E CYS* 1.3 72.0 - - - +
175E VAL* 1.3 60.1 + - - +
176E GLU* 3.1 39.8 - - + +
183E PRO* 3.5 21.2 - - + +
184E ILE 3.5 3.1 - - - -
185E THR* 3.7 22.4 - - + -
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Residues in contact with VAL 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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97E PRO* 4.2 17.3 - - + -
99E VAL* 4.0 17.3 - - + -
119E VAL* 3.9 25.8 - - + -
127E ILE* 3.9 29.8 - - + -
128E LYS 3.4 2.9 - - - +
129E VAL* 4.1 11.2 - - + -
173E CYS* 4.2 7.2 - - - -
174E HIS* 1.3 79.8 - - - +
176E GLU* 1.3 68.9 + - - +
180E LEU* 3.6 5.3 - - + +
183E PRO* 3.2 6.8 - - - +
184E ILE* 2.8 42.8 + - + +
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Residues in contact with GLU 176 (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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127E ILE* 3.3 4.2 - - - +
128E LYS* 2.8 58.4 + - + +
130E ARG* 4.2 15.0 + - - -
174E HIS* 3.1 34.4 - - + +
175E VAL* 1.3 74.3 - - - +
177E HIS* 1.3 63.5 + - - +
180E LEU* 4.7 0.7 - - - -
183E PRO* 4.0 11.8 - - + +
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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