Contacts of the strand formed by residues 207 - 216 (chain A) in PDB entry 2AEW
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 GLU 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.9 8.0 + - - +
181A VAL* 3.1 48.9 + - + +
206A LYS* 1.3 72.9 - - - +
208A TYR* 1.3 66.3 + - - +
230A TYR* 4.5 12.1 - - + -
231A VAL 3.5 4.0 - - - +
232A THR* 3.7 32.0 - - + +
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Residues in contact with TYR 208 (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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178A TYR* 4.1 19.5 - + + -
179A LYS* 3.5 18.6 - - - -
180A GLU* 3.9 16.8 + - + -
181A VAL* 4.0 0.8 - - - +
187A LYS* 5.1 9.0 + - - -
202A LEU* 3.9 27.9 - - + -
203A LYS* 3.1 55.6 + - - +
206A LYS* 3.7 24.7 - - + +
207A GLU* 1.3 75.1 - - - +
209A GLU* 1.3 63.4 + - - +
210A VAL* 5.3 1.8 - - + -
230A TYR* 3.4 8.8 - - - +
231A VAL* 2.5 55.5 + - + +
233A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 209 (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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178A TYR* 3.1 28.6 - - - +
179A LYS* 2.5 45.5 + - - +
181A VAL* 3.6 22.4 - - + +
186A TRP* 3.7 18.2 - - + -
208A TYR* 1.3 73.9 - - - +
210A VAL* 1.3 62.8 + - - +
228A VAL* 4.1 8.8 - - + +
229A LEU 3.6 3.4 - - - -
230A TYR* 3.2 44.0 + - + -
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Residues in contact with VAL 210 (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 LEU* 4.4 9.9 - - + -
153A ILE* 5.4 2.2 - - + -
155A VAL* 4.1 23.8 - - + -
176A LEU* 3.9 27.4 - - + -
177A GLN 3.4 5.4 - - - +
178A TYR* 4.2 10.8 - - + -
199A VAL* 6.2 0.7 - - + -
208A TYR* 5.3 2.0 - - + -
209A GLU* 1.3 79.9 - - - +
211A ARG* 1.3 67.9 + - - +
227A GLU 4.1 0.2 - - - +
228A VAL* 3.2 8.6 - - - +
229A LEU* 2.7 48.1 + - + +
231A VAL* 3.6 25.8 - - + -
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Residues in contact with ARG 211 (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 LEU* 4.8 1.1 - - - -
175A GLU 3.9 0.3 - - - +
176A LEU 3.7 0.2 - - - -
177A GLN* 2.8 57.0 + - + +
186A TRP* 3.4 57.7 - - + +
210A VAL* 1.3 79.4 - - - +
212A VAL* 1.3 64.1 + - - +
225A PHE* 3.1 57.2 - - + +
226A SER* 3.8 10.5 - - - +
228A VAL* 4.5 15.1 - - + +
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Residues in contact with VAL 212 (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 PRO* 3.2 28.8 - - + +
137A LEU* 3.8 19.3 - - + -
155A VAL* 5.0 0.2 - - + -
157A TRP* 3.9 22.0 - - + -
174A TYR* 3.5 32.1 - - + -
175A GLU 3.5 11.0 - - - +
176A LEU* 4.0 20.6 - - + +
210A VAL* 4.6 0.9 - - + -
211A ARG* 1.3 79.7 - - - +
213A ARG* 1.3 62.1 + - - +
225A PHE* 3.8 2.2 - - - -
226A SER* 3.0 29.6 + - - +
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Residues in contact with ARG 213 (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 PRO* 4.4 1.3 - - - -
174A TYR* 3.6 4.2 - - - -
175A GLU* 2.9 58.4 + - - +
177A GLN* 3.8 5.4 - - - +
212A VAL* 1.3 76.6 - - - +
214A SER* 1.3 59.8 + - - +
222A TYR* 3.2 50.4 - - + +
223A GLY 3.8 18.4 + - - +
224A GLU 3.8 7.0 - - - +
225A PHE* 3.2 46.9 - - + -
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Residues in contact with SER 214 (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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131A PRO* 3.5 18.2 - - - +
132A ASP 3.0 28.8 + - - -
133A PRO* 4.5 0.2 - - - +
134A PRO* 3.9 6.4 - - - +
160A PRO* 4.1 0.3 - - - +
172A LEU* 3.9 8.4 - - - +
173A GLU 4.2 2.7 - - - -
174A TYR* 3.2 27.4 - - - -
213A ARG* 1.3 72.6 - - - +
215A LYS* 1.3 64.2 + - - +
222A TYR* 3.4 2.6 - - - -
223A GLY* 3.0 26.8 + - - +
224A GLU 4.3 5.7 + - - -
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Residues in contact with LYS 215 (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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131A PRO* 4.1 6.1 - - - -
172A LEU* 3.3 5.7 - - - +
173A GLU* 2.9 68.7 + - + +
191A PRO* 3.9 8.3 - - + +
214A SER* 1.3 79.9 - - - +
216A GLN* 1.3 66.8 + - - +
218A ASN 3.8 19.0 + - - +
220A GLY 4.3 14.4 - - - +
221A ASN 3.8 6.3 - - - +
222A TYR* 3.4 47.4 + - + +
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Residues in contact with GLN 216 (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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43A ARG* 4.2 26.0 - - - +
126A ASP* 5.0 2.3 - - - +
129A VAL* 3.7 37.0 - - + +
131A PRO* 3.9 5.4 - - + +
170A MET* 3.8 21.7 - - + +
171A VAL 4.0 3.8 - - - +
172A LEU* 4.6 5.4 - - - -
215A LYS* 1.3 82.3 - - - +
217A ARG* 1.3 75.8 + - - +
218A ASN* 3.0 15.0 + - - +
219A SER 3.7 18.4 + - - +
220A GLY* 3.6 10.7 - - - -
221A ASN 4.0 3.6 + - - +
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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