Contacts of the strand formed by residues 158 - 171 (chain B) in PDB entry 2EX4
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASP* 4.2 9.0 + - - +
130B TYR 3.4 13.0 - - - +
131B ASP 4.5 0.7 - - - +
133B ILE* 3.6 23.3 - - + -
154B CYS 3.5 10.3 - - - +
155B LYS* 3.3 19.1 + - + +
156B GLY 3.5 1.8 - - - +
157B SER* 1.3 78.5 - - - +
159B ARG* 1.3 69.4 + - - +
160B PRO* 4.6 0.5 - - - +
162B GLY* 3.6 17.3 - - - +
163B ILE* 3.6 27.6 - - - +
164B ILE* 4.1 20.6 - - + -
224B ARG* 4.3 14.1 - - + -
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 2.5 32.5 + - - -
65B CYS* 3.6 13.3 - - - +
113B ARG* 5.0 7.5 - - - +
128B ASP* 3.7 31.3 + - - +
129B SER* 2.9 27.3 + - - +
130B TYR 2.8 18.0 + - - +
131B ASP* 3.6 26.1 + - - +
157B SER 3.6 0.2 + - - -
158B LEU* 1.3 78.9 - - - +
160B PRO* 1.4 70.2 - - + +
161B ASN 3.2 0.2 + - - -
162B GLY* 2.8 22.2 + - - -
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS 4.9 0.5 - - - +
62B GLY 5.0 3.1 + - - -
128B ASP* 3.8 12.3 - - - +
131B ASP* 4.7 4.3 - - - +
158B LEU 4.6 0.7 - - - +
159B ARG* 1.4 92.9 - - + +
161B ASN* 1.3 73.8 + - - +
162B GLY* 3.2 2.9 + - - -
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Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS 3.4 37.5 + - - +
61B THR* 2.8 26.8 + - - -
159B ARG 3.2 0.4 + - - -
160B PRO* 1.3 78.0 + - - +
162B GLY* 1.3 61.3 + - - +
224B ARG* 2.9 28.8 + - - +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 4.2 2.7 - - - -
131B ASP* 3.1 21.8 - - - -
158B LEU* 3.6 13.9 - - - +
159B ARG 2.8 19.0 + - - -
160B PRO 3.1 2.3 + - - -
161B ASN* 1.3 78.9 - - - +
163B ILE* 1.3 59.2 + - - -
224B ARG* 3.0 27.7 + - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.9 14.8 - - + -
52B PHE* 3.7 36.8 - - + -
61B THR* 3.9 7.6 - - - +
131B ASP 2.9 7.3 + - - -
132B VAL* 3.3 16.2 - - + +
133B ILE 3.0 23.2 + - - +
158B LEU* 3.6 6.4 - - - +
162B GLY* 1.3 78.4 - - - +
164B ILE* 1.3 65.3 + - - +
165B VAL* 3.8 24.5 - - + -
203B LEU* 3.5 19.5 - - + -
222B ALA* 4.5 1.8 - - + -
223B LEU 3.3 7.2 - - - +
224B ARG* 3.4 23.8 - - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.3 13.5 - - + +
135B ILE* 3.7 29.2 - - + -
151B LEU* 4.1 13.2 - - + +
154B CYS* 3.7 28.0 - - + -
155B LYS 3.9 8.5 - - - +
158B LEU* 4.1 13.9 - - + +
163B ILE* 1.3 76.9 - - - +
165B VAL* 1.3 68.8 + - - +
166B ILE* 4.6 0.7 - - + +
200B LEU* 3.9 32.1 - - + -
221B PHE 3.6 1.0 - - - +
222B ALA* 3.4 2.3 - - - -
223B LEU* 2.7 51.7 + - + +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 4.1 23.1 - - + -
49B LEU* 4.8 0.9 - - + -
132B VAL* 4.6 2.9 - - + -
133B ILE 2.8 10.3 + - - +
134B TRP* 3.6 52.7 - - + -
135B ILE* 2.7 35.0 + - - +
163B ILE* 3.8 25.6 - - + -
164B ILE* 1.3 79.1 - - - +
166B ILE* 1.3 70.5 + - - +
167B LYS* 4.4 3.1 - - + +
220B SER* 4.8 0.9 - - - -
221B PHE 3.2 9.0 - - - +
222B ALA* 4.4 0.7 - - - -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 3.4 19.1 - - + +
139B ILE* 4.0 44.0 - - + -
147B LEU* 5.3 1.3 - - + -
151B LEU* 4.0 24.5 - - + -
164B ILE* 4.2 1.1 - - + -
165B VAL* 1.3 75.5 - - - +
167B LYS* 1.3 64.1 + - - +
168B ASP* 4.3 7.0 - - + -
170B MET* 4.9 0.9 - - + -
191B VAL* 5.2 2.7 - - + -
195B ILE* 4.3 12.8 - - + -
219B TYR 3.6 1.2 - - - +
220B SER* 3.2 2.6 - - - -
221B PHE* 2.7 54.7 + - + +
223B LEU* 3.8 25.4 - - + -
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 2.9 27.2 + - - -
44B SER* 4.0 1.6 - - - -
45B SER* 3.0 30.2 + - - +
134B TRP* 4.4 4.7 - - + +
135B ILE 3.0 6.9 + - - -
136B GLN* 3.2 32.1 - - + +
137B TRP* 3.0 24.4 + - + -
165B VAL* 4.1 7.5 - - + +
166B ILE* 1.3 74.7 - - - +
168B ASP* 1.3 63.0 + - - +
208B GLN* 2.6 31.3 + - - -
218B VAL* 3.8 20.6 - - + -
219B TYR 3.3 3.1 - - - +
220B SER* 3.2 24.5 + - - +
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Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE 4.7 0.3 - - - +
136B GLN* 4.0 0.5 - - - -
137B TRP* 3.1 30.0 + - - +
138B VAL 2.9 24.8 + - - -
139B ILE* 3.1 32.4 + - + +
140B GLY* 4.8 3.1 + - - -
166B ILE* 4.2 3.1 - - + -
167B LYS* 1.3 75.4 - - - +
169B ASN* 1.3 84.4 + - - +
170B MET* 3.6 14.7 - - + +
218B VAL* 3.3 4.3 - - - +
219B TYR 3.0 31.9 + - - +
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TRP* 2.9 32.7 + - - +
139B ILE* 5.4 2.3 - - - +
168B ASP* 1.3 85.6 + - - +
170B MET* 1.3 71.0 + - - +
185B CYS* 3.6 12.5 - - - -
186B ARG 4.3 2.6 + - - +
191B VAL* 5.7 0.2 - - - +
215B ILE* 6.1 1.0 - - - +
216B TYR* 3.4 38.4 + - + +
217B HIS 3.2 7.0 - - - -
218B VAL* 3.6 9.0 - - - +
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 4.5 4.9 - - + -
166B ILE* 4.9 0.7 - - + -
168B ASP* 3.6 26.7 - - + +
169B ASN* 1.3 87.3 - - - +
171B ALA* 1.3 65.9 + - - +
172B GLN* 4.0 0.9 + - - +
185B CYS* 3.6 2.9 - - - -
186B ARG 3.4 6.5 - - - +
188B LEU* 3.6 40.4 - - + +
191B VAL* 3.7 31.2 - - + -
216B TYR* 3.7 10.2 - - - -
217B HIS* 2.9 24.0 + - + +
219B TYR* 3.7 23.6 - - + -
221B PHE* 3.6 23.6 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B MET* 1.3 76.5 - - - +
172B GLN* 1.3 66.6 + - - +
173B GLU 4.1 2.7 - - - +
174B GLY 4.1 5.2 - - - +
176B ILE* 3.8 27.4 - - + -
185B CYS* 3.3 21.0 - - - +
186B ARG 2.9 23.2 + - - -
187B ASP* 3.3 15.3 - - - +
188B LEU* 4.3 2.8 + - - +
216B TYR* 4.1 7.0 - - + -
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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