Contacts of the strand formed by residues 161 - 167 (chain E) in PDB entry 2V8W
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 ASP 161 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E THR* 3.2 7.4 - - - +
117E LEU* 2.7 43.1 + - + +
118E ASN 4.3 9.7 - - - +
119E LYS* 3.0 34.4 + - - +
126E LEU* 3.8 43.0 - - + +
155E ASN 3.4 7.6 - - - +
156E VAL* 3.4 16.3 - - - +
157E ARG 3.4 4.0 + - - -
160E GLY* 1.3 73.9 - - - -
162E LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E ARG* 5.1 8.9 - - - +
114E LEU* 3.7 32.5 - - + -
115E ILE 3.4 3.6 - - - -
116E THR* 3.9 15.3 - - + +
117E LEU* 5.0 0.2 - - - -
153E VAL 3.8 0.6 - - - +
154E VAL* 3.1 8.5 - - - +
155E ASN* 2.7 59.6 + - + +
157E ARG* 5.3 2.0 - - + -
159E LYS* 4.6 11.9 - - - +
160E GLY 5.1 2.0 - - - +
161E ASP* 1.3 80.7 - - - +
163E ILE* 1.3 62.9 + - - +
164E ALA 4.4 0.2 - - - -
1218E MGO 2.8 53.8 + - - -
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Residues in contact with ILE 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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113E TRP 3.7 0.6 - - - +
114E LEU* 3.4 3.8 - - - +
115E ILE* 2.8 46.7 + - + +
117E LEU* 4.2 10.0 - - + +
126E LEU* 3.9 16.2 - - + -
129E PHE* 3.8 15.7 - - + -
130E TRP* 3.5 46.9 - - + +
133E THR* 3.5 13.7 - - + +
153E VAL 3.4 3.6 - - - +
154E VAL* 3.8 11.7 - - + -
162E LYS* 1.3 79.9 - - - +
164E ALA* 1.3 62.2 - - - +
183E TYR* 3.1 21.5 - - - +
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Residues in contact with ALA 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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112E ARG* 4.0 22.4 - - + +
113E TRP 3.0 13.2 - - - +
114E LEU* 4.2 7.2 - - + -
152E ALA* 3.1 8.1 - - - +
153E VAL* 2.9 36.1 + - + +
155E ASN* 6.1 0.9 - - - +
163E ILE* 1.3 77.7 - - - +
165E ILE* 1.3 63.1 + - - +
166E TRP* 4.0 20.6 + - + +
183E TYR* 5.1 0.7 - - - -
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Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E ARG* 3.2 2.4 - - - -
113E TRP* 2.9 39.1 + - + +
133E THR* 4.0 14.4 - - + -
136E CYS* 5.0 1.3 - - + -
137E LEU* 4.4 5.4 - - + -
142E PHE* 3.7 22.4 - - + -
149E VAL* 4.3 14.4 - - + -
151E GLY 3.7 8.7 - - - +
152E ALA* 4.4 3.1 - - + -
164E ALA* 1.3 74.4 - - - +
166E TRP* 1.3 68.9 + - - +
167E THR* 3.8 7.0 + - + +
179E ILE* 4.1 20.0 - - + -
183E TYR* 3.4 48.4 - - + -
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Residues in contact with TRP 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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94E PHE* 3.4 24.9 - + + -
100E PRO 4.1 4.9 - - - -
101E MET* 3.5 33.7 - - - -
102E TRP* 3.5 28.3 - + - -
107E ASN* 3.7 10.8 - - - +
111E GLY 3.4 4.9 - - - +
112E ARG* 3.8 29.9 - - + +
149E VAL* 3.7 5.4 - - - +
150E CYS* 2.9 30.3 + - + -
151E GLY 2.8 19.0 + - - +
153E VAL* 3.5 28.5 - - + +
164E ALA* 4.0 15.5 - - + +
165E ILE* 1.3 73.1 - - - +
167E THR* 1.3 56.3 + - - +
200E HIS* 3.4 29.4 - + + -
1218E MGO 3.9 23.3 - - - -
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Residues in contact with THR 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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106E LYS 4.6 0.5 - - - +
107E ASN* 4.7 1.0 - - - +
110E GLY* 3.2 3.5 - - - -
111E GLY 2.9 28.2 + - - +
113E TRP* 4.5 2.9 - - + -
148E ASP* 3.1 16.1 + - - +
149E VAL* 5.0 0.4 - - - -
150E CYS* 3.9 5.4 - - - -
165E ILE* 4.1 10.1 - - + +
166E TRP* 1.3 76.9 - - - +
168E THR* 1.3 60.6 + - - +
169E GLU 4.1 2.6 + - - -
176E VAL* 3.6 13.1 - - + +
179E ILE* 3.9 35.2 - - + -
197E TYR* 2.7 39.6 + - + -
200E HIS* 4.5 4.0 - - - -
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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