Contacts of the strand formed by residues 158 - 170 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP* 3.5 14.3 + - - +
130A TYR 3.4 10.1 - - - +
131A ASP 4.3 0.9 - - - +
133A ILE* 3.8 19.1 - - + -
154A CYS 3.6 10.3 - - - +
155A LYS* 3.2 19.1 + - + +
156A GLY 4.6 1.6 - - - +
157A SER* 1.3 79.4 - - - +
159A ARG* 1.3 67.9 + - - +
160A PRO* 4.5 0.3 - - - +
162A GLY 3.5 17.9 - - - +
163A ILE* 3.4 33.0 - - - +
164A ILE* 4.1 20.2 - - + -
224A ARG* 4.0 19.5 - - + -
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Residues in contact with ARG 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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64A SER* 3.2 33.7 + - - -
65A CYS* 3.7 8.7 - - - +
113A ARG* 5.7 4.0 - - - +
128A ASP* 3.6 24.3 + - - +
129A SER* 3.5 24.5 + - - +
130A TYR 2.8 21.6 + - - +
131A ASP* 3.2 29.1 + - - +
157A SER 3.7 0.2 + - - -
158A LEU* 1.3 78.3 - - - +
160A PRO* 1.3 79.2 - - + +
161A ASN 3.2 0.5 + - - -
162A GLY* 2.7 16.8 + - - +
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Residues in contact with PRO 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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62A GLY 5.2 1.9 + - - -
128A ASP* 3.1 19.5 - - - +
131A ASP* 4.7 3.8 - - - +
158A LEU 4.5 0.2 - - - +
159A ARG* 1.3 92.6 - - + +
161A ASN* 1.3 76.4 + - - +
162A GLY* 3.1 2.4 + - - -
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Residues in contact with ASN 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 LYS 3.3 35.5 + - - +
61A THR* 2.9 27.2 + - - -
159A ARG 3.2 0.4 + - - -
160A PRO* 1.3 80.7 + - - +
162A GLY* 1.3 60.6 + - - +
224A ARG* 3.1 28.1 + - - +
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Residues in contact with GLY 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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61A THR* 4.2 1.8 - - - -
131A ASP* 3.0 24.5 - - - -
158A LEU* 3.5 13.9 - - - +
159A ARG 2.7 23.6 + - - +
160A PRO 3.1 2.4 + - - -
161A ASN* 1.3 72.9 - - - +
163A ILE* 1.3 58.6 + - - -
224A ARG* 3.0 27.4 + - - +
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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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49A LEU* 3.9 10.5 - - + -
52A PHE* 3.6 40.6 - - + -
61A THR* 3.9 5.2 - - - +
131A ASP 2.9 7.4 + - - +
132A VAL* 3.3 20.8 - - + -
133A ILE 3.0 22.5 + - - -
158A LEU* 3.4 9.4 - - - +
161A ASN 3.9 2.5 - - - +
162A GLY* 1.3 75.0 - - - +
164A ILE* 1.3 60.4 + - - +
165A VAL* 3.8 24.2 - - + -
203A LEU* 3.6 17.5 - - + -
222A ALA* 4.2 2.0 - - + -
223A LEU 3.2 8.3 - - - +
224A ARG* 3.3 29.8 - - - +
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Residues in contact with ILE 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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133A ILE* 3.3 15.3 - - + +
135A ILE* 3.7 30.1 - - + -
151A LEU* 4.0 7.2 - - + +
154A CYS* 3.5 30.5 - - + -
155A LYS* 3.7 15.5 - - - +
158A LEU* 4.1 10.1 - - + -
163A ILE* 1.3 76.8 - - - +
165A VAL* 1.3 67.8 + - - +
166A ILE* 4.7 0.2 - - + -
200A LEU* 4.0 28.0 - - + -
221A PHE 3.5 1.0 - - - +
222A ALA* 3.4 3.1 - - - -
223A LEU* 2.8 49.0 + - + +
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Residues in contact with VAL 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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48A PHE* 4.1 17.3 - - + -
49A LEU* 4.8 2.0 - - + -
132A VAL* 4.9 1.8 - - + -
133A ILE 2.8 10.7 + - - +
134A TRP* 3.6 51.5 - - + -
135A ILE* 2.7 34.5 + - - +
163A ILE* 3.8 25.4 - - + -
164A ILE* 1.3 80.4 - - - +
166A ILE* 1.3 70.1 + - - +
167A LYS* 4.0 0.8 + - + +
220A SER* 4.7 3.8 - - - -
221A PHE 3.3 7.9 - - - +
222A ALA* 4.3 8.1 - - + -
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Residues in contact with ILE 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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135A ILE* 3.3 20.2 - - + +
139A ILE* 4.1 41.7 - - + -
147A LEU* 5.2 1.8 - - + -
151A LEU* 4.0 24.5 - - + -
164A ILE* 4.1 0.8 - - + -
165A VAL* 1.3 75.9 - - - +
167A LYS* 1.3 68.5 + - - +
168A ASP* 4.4 3.6 - - + -
191A VAL* 5.2 2.2 - - + -
195A ILE* 4.3 13.0 - - + -
220A SER* 3.2 3.6 - - - -
221A PHE* 2.8 57.1 + - + +
223A LEU* 3.9 24.9 - - + -
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Residues in contact with LYS 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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41A ASP* 2.9 22.1 + - - -
44A SER* 4.2 1.6 + - - -
45A SER* 2.6 35.5 + - - +
134A TRP* 4.4 10.5 - - + +
135A ILE 2.9 8.3 + - - +
136A GLN* 3.2 31.0 - - + +
137A TRP* 3.0 24.0 + - - -
165A VAL* 4.0 1.5 + - + -
166A ILE* 1.3 73.9 - - - +
168A ASP* 1.3 64.4 + - - +
208A GLN* 2.8 30.1 + - - -
218A VAL* 3.9 21.8 - - + -
219A TYR 3.4 3.1 - - - +
220A SER* 3.2 25.2 + - - +
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Residues in contact with ASP 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 GLN* 4.9 0.2 - - - -
137A TRP* 3.2 27.4 + - - +
138A VAL 3.1 24.9 + - - -
139A ILE* 3.3 30.2 + - + +
140A GLY* 5.0 2.8 + - - -
166A ILE* 4.2 5.5 - - + +
167A LYS* 1.3 76.9 - - - +
169A ASN* 1.3 86.9 + - - +
170A MET* 3.6 16.3 - - + +
218A VAL* 3.2 5.2 - - - -
219A TYR 3.0 32.6 + - - +
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Residues in contact with ASN 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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137A TRP* 2.8 34.1 + - - -
139A ILE* 5.8 0.7 - - - +
168A ASP* 1.3 87.8 + - - +
170A MET* 1.3 68.0 + - - +
185A CYS* 3.4 14.4 - - - -
186A ARG 4.3 2.3 + - - +
215A ILE* 5.2 6.8 - - - +
216A TYR* 3.3 39.5 - - + +
217A HIS 3.1 7.0 - - - -
218A VAL* 4.0 9.5 - - - +
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Residues in contact with MET 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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139A ILE* 4.9 4.3 - - + -
168A ASP* 3.6 25.8 - - + +
169A ASN* 1.3 89.7 - - - +
171A ALA* 1.3 67.2 + - - +
172A GLN* 4.0 0.3 + - - +
185A CYS* 3.6 2.5 - - - -
186A ARG 3.4 4.9 - - - +
188A LEU* 3.6 28.7 - - + +
191A VAL* 3.7 31.0 - - + -
216A TYR* 3.6 15.4 - - - +
217A HIS* 2.7 23.5 + - + +
219A TYR* 3.5 34.3 - - + -
221A PHE* 3.8 24.7 - - + -
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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