Contacts of the strand formed by residues 157 - 170 (chain A) in PDB entry 5CVE
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 LEU 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.8 11.5 - - - +
129A TYR 3.4 12.1 - - - +
130A ASP 4.4 0.9 - - - +
132A ILE* 3.8 20.2 - - + +
153A CYS 3.6 9.2 - - - +
154A LYS* 3.3 17.7 + - + +
155A GLY 4.5 2.4 - - - +
156A SER* 1.3 79.6 - - - +
158A ARG* 1.3 69.6 + - - +
159A PRO* 4.7 0.2 - - - +
161A GLY* 3.7 17.5 - - - +
162A ILE* 3.4 31.4 - - - +
163A ILE* 4.0 21.3 - - + -
223A ARG* 4.2 17.7 - - + +
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 4.6 5.9 - - - -
63A SER* 3.7 18.5 + - - -
64A CYS* 5.4 0.4 - - - -
127A ASP* 3.6 10.6 + - - +
128A SER* 3.8 20.0 - - - +
129A TYR 2.8 26.4 + - - +
130A ASP* 2.5 56.3 + - - +
157A LEU* 1.3 78.2 - - - +
159A PRO* 1.3 79.0 + - + +
160A ASN 3.4 0.3 + - - -
161A GLY* 2.9 20.2 + - - -
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Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY 5.0 2.6 + - - -
127A ASP* 3.8 12.6 - - - +
130A ASP* 4.7 4.3 - - - +
158A ARG* 1.3 101.0 + - + +
160A ASN* 1.3 73.2 + - - +
161A GLY* 3.2 4.2 + - - -
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 3.6 39.4 + - - +
59A LYS 3.2 26.9 + - - +
60A THR* 2.8 27.6 + - - -
158A ARG 3.4 0.6 + - - -
159A PRO* 1.3 75.9 + - - +
161A GLY* 1.3 60.4 + - - +
223A ARG* 3.0 24.5 + - - +
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Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.5 1.3 - - - -
130A ASP* 3.1 20.4 - - - -
157A LEU* 3.7 13.7 - - - +
158A ARG 2.9 19.3 + - - -
159A PRO 3.1 2.3 + - - -
160A ASN* 1.3 79.3 - - - +
162A ILE* 1.3 58.7 + - - -
223A ARG* 2.9 29.0 + - - +
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.0 12.1 - - + -
52A PHE* 3.8 38.1 - - + -
60A THR* 4.0 7.0 - - - +
130A ASP 3.0 6.8 + - - +
131A VAL* 3.3 17.6 - - + -
132A ILE 3.0 22.5 + - - +
157A LEU* 3.4 9.7 - - - +
161A GLY* 1.3 78.8 - - - +
163A ILE* 1.3 62.8 + - - +
164A VAL* 3.9 22.7 - - + -
202A LEU* 3.6 20.0 - - + -
221A ALA* 4.6 2.0 - - + -
222A LEU 3.3 7.6 - - - +
223A ARG* 3.3 22.9 - - - +
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.3 11.0 - - + +
134A ILE* 3.7 28.9 - - + -
150A LEU* 4.4 4.9 - - + -
153A CYS* 3.6 29.6 - - + -
154A LYS 3.8 12.6 - - - +
157A LEU* 4.0 17.0 - - + -
162A ILE* 1.3 76.7 - - - +
164A VAL* 1.3 67.5 + - - +
165A ILE* 4.2 0.9 - - + -
199A LEU* 3.9 30.7 - - + -
220A PHE 3.5 1.0 - - - +
221A ALA* 3.5 2.4 - - - -
222A LEU* 2.8 50.3 + - + +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.0 23.6 - - + -
49A LEU* 4.8 0.9 - - + -
131A VAL* 4.8 2.7 - - + -
132A ILE 2.8 10.4 + - - +
133A TRP* 3.6 51.3 - - + -
134A ILE* 2.7 35.7 + - - +
162A ILE* 3.9 24.5 - - + -
163A ILE* 1.3 78.2 - - - +
165A ILE* 1.3 71.9 + - - +
166A LYS* 4.4 0.7 - - + +
219A SER* 4.7 3.6 - - - -
220A PHE 3.2 9.6 - - - +
221A ALA* 4.4 1.3 - - - -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE* 3.3 13.0 - - + +
138A ILE* 4.0 39.3 - - + -
146A LEU* 5.7 1.6 - - + -
150A LEU* 4.0 33.2 - - + -
163A ILE* 4.2 1.1 - - + -
164A VAL* 1.3 75.7 - - - +
166A LYS* 1.3 63.5 + - - +
167A ASP* 4.4 5.6 - - + +
169A MET* 4.9 1.1 - - + -
190A VAL* 5.1 4.7 - - + -
194A ILE* 4.3 12.8 - - + -
218A TYR 3.5 1.4 - - - +
219A SER* 3.2 2.8 - - - -
220A PHE* 2.7 52.6 + - + +
222A LEU* 3.8 26.2 - - + -
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 2.9 22.6 + - - -
44A SER* 4.2 1.0 - - - -
45A SER* 2.8 32.6 + - - +
133A TRP* 4.4 10.5 - - + +
134A ILE 2.9 7.7 + - - -
135A GLN* 3.1 35.2 - - + +
136A TRP* 2.9 23.8 + - - -
164A VAL* 4.0 1.7 - - + -
165A ILE* 1.3 74.8 - - - +
167A ASP* 1.3 63.0 + - - +
207A GLN* 2.7 31.4 + - - -
217A VAL* 4.0 18.6 - - + -
218A TYR 3.2 5.6 - - - +
219A SER* 3.3 24.9 + - - +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 4.0 0.3 - - - -
136A TRP* 3.1 32.4 + - - +
137A VAL 2.9 24.0 + - - -
138A ILE* 2.9 39.2 + - + +
139A GLY 4.8 2.4 + - - -
165A ILE* 4.2 3.5 - - + -
166A LYS* 1.3 72.9 - - - +
168A ASN* 1.3 85.3 + - - +
169A MET* 3.6 15.3 - - + +
217A VAL* 3.4 4.3 - - - +
218A TYR 3.0 30.0 + - - -
1D PBE 4.7 2.1 - - - -
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TRP* 2.9 23.3 + - - -
138A ILE* 5.2 2.4 - - - +
167A ASP* 1.3 86.8 + - - +
169A MET* 1.3 70.5 + - - +
184A CYS* 3.8 24.3 - - + +
185A ARG 4.2 4.3 + - - +
215A TYR* 4.0 15.7 - - + +
216A HIS 3.4 5.6 - - - -
217A VAL* 3.6 11.0 - - - +
1D PBE 2.9 31.5 + - - -
2D PRO* 3.7 8.2 - - - +
3D LYS* 4.0 16.1 - - - +
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Residues in contact with MET 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.3 7.2 - - + -
165A ILE* 4.9 1.1 - - + -
167A ASP* 3.6 28.5 - - + +
168A ASN* 1.3 87.5 - - - +
170A ALA* 1.3 66.1 + - - +
171A GLN 3.9 0.3 + - - -
184A CYS* 3.6 3.6 - - - -
185A ARG 3.3 9.2 - - - +
186A ASP 4.6 1.1 - - - +
187A LEU* 3.9 17.5 - - + -
190A VAL* 3.7 30.1 - - + -
215A TYR* 3.8 5.4 - - - -
216A HIS* 2.8 28.9 + - + +
218A TYR* 3.6 35.9 - - + -
220A PHE* 3.6 28.3 - - + -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A MET* 1.3 76.8 - - - +
171A GLN* 1.3 67.0 + - - +
172A GLU 4.1 9.9 - - - +
173A GLY 4.0 6.5 - - - +
175A ILE* 4.4 7.4 - - + -
184A CYS* 3.3 32.0 - - - +
185A ARG 3.0 13.8 + - - -
186A ASP* 3.2 17.8 - - - +
187A LEU* 4.2 3.6 + - - +
215A TYR* 4.1 12.6 - - + -
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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