Contacts of the strand formed by residues 138 - 146 (chain F) in PDB entry 2WNU
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 TYR 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F SER* 3.3 39.5 + - - -
122F ASP* 4.7 0.7 + - - -
130F PHE* 3.6 21.4 - + - -
132F CYS* 4.1 12.2 - - - -
133F LYS 4.8 0.3 + - - -
134F VAL* 2.5 39.5 + - - +
136F GLY 3.2 24.9 - - - -
137F LEU* 1.3 79.1 - - - +
139F TYR* 1.3 59.8 - - - +
140F PHE* 3.4 28.8 - + + -
179F VAL 3.9 0.3 - - - +
180F LEU* 3.2 6.1 - - - +
181F LEU 2.7 33.8 + - - +
183F LEU* 3.9 11.9 - - + -
212F PHE* 3.4 9.2 - - - -
213F LEU* 3.5 27.2 - - + +
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Residues in contact with TYR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 4.9 4.7 - + - -
142E TYR* 4.4 10.5 + + - -
144E THR* 3.6 34.6 + - + +
146E HIS* 4.5 4.3 + - - -
216E SER* 5.1 2.0 - - - -
218E PHE* 4.1 15.0 - + - -
138F TYR* 1.3 73.0 - - - +
140F PHE* 1.3 73.5 + - - +
141F VAL* 3.6 39.8 - - + +
178F GLY* 4.7 1.1 - - - -
179F VAL* 3.6 16.8 - - - -
180F LEU* 3.6 26.0 - - + -
211F GLY* 3.1 5.4 - - - -
212F PHE* 2.9 65.7 + + + -
214F LEU* 4.0 12.7 - - + +
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Residues in contact with PHE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.9 22.0 - + - -
130F PHE* 4.0 19.3 - + - -
138F TYR* 3.4 32.1 - + + -
139F TYR* 1.3 78.0 - - - +
141F VAL* 1.3 61.6 + - - +
154F LEU* 4.0 18.8 - - + -
178F GLY* 2.9 4.8 - - - -
179F VAL 2.8 41.8 + - - +
181F LEU* 4.3 17.7 - - + -
183F LEU* 3.8 23.6 - - + -
189F VAL* 4.0 20.9 - - + -
209F PHE* 3.9 18.4 - + + -
210F SER 3.4 1.6 - - - +
211F GLY* 3.8 14.6 - - - -
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.1 30.5 - - + +
146E HIS* 4.3 8.5 - - + +
139F TYR* 3.6 36.6 - - + +
140F PHE* 1.3 75.7 - - - +
142F TYR* 1.3 63.7 + - - +
143F HIS* 3.8 20.6 - - + +
177F GLY 3.2 19.5 - - - +
178F GLY* 4.0 0.4 - - - -
208F VAL* 5.8 0.2 - - - +
209F PHE* 3.4 5.6 - - - -
210F SER* 2.8 43.8 + - - +
212F PHE* 5.2 0.9 - - + -
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Residues in contact with TYR 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PHE* 5.3 1.1 - - + -
141F VAL* 1.3 75.4 - - - +
143F HIS* 1.3 76.0 + - - +
144F ALA* 3.9 11.2 - - + -
152F VAL* 3.3 35.8 + - + +
154F LEU* 5.7 6.3 - - + -
162F VAL* 6.5 0.2 - - + -
164F PHE* 3.5 24.8 - + - +
175F ASN* 2.8 41.4 + - - -
176F SER* 3.5 3.5 - - - -
177F GLY* 3.0 48.5 + - - +
178F GLY* 4.5 0.9 - - - -
191F LEU* 3.7 37.5 - - + -
208F VAL* 3.1 14.8 - - - +
209F PHE* 4.1 2.9 - + + -
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Residues in contact with HIS 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.8 19.0 + - - -
140D THR* 4.2 6.9 + - - -
142D GLN* 5.3 1.8 - - - -
167D PHE* 3.9 13.2 - - + -
180D SER* 3.2 32.5 + - - -
181D GLY* 3.6 18.4 + - - -
182D GLY 3.7 13.5 - - - -
146E HIS* 5.3 1.6 - + - -
182E THR* 4.9 4.7 - - + -
141F VAL* 3.8 15.1 - - + +
142F TYR* 1.3 81.9 + - - +
144F ALA* 1.3 59.0 - - - +
174F VAL* 4.0 8.3 - - + -
175F ASN 3.5 5.2 - - - -
176F SER* 3.8 9.8 - - - -
206F ASP 3.7 3.6 - - - +
207F SER* 3.3 4.2 - - - -
208F VAL* 2.8 49.2 + - + +
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PHE* 6.1 1.8 - - + -
142F TYR* 4.1 14.1 - - + -
143F HIS* 1.3 71.3 - - - +
145F SER* 1.3 63.4 + - - +
146F HIS* 3.4 5.9 + - - -
150F LEU* 3.8 21.3 - - + -
152F VAL* 4.4 3.6 - - + -
174F VAL* 3.4 3.9 - - - +
175F ASN 2.7 41.0 + - - +
199F MET* 4.1 13.7 - - + -
207F SER* 3.6 10.8 - - - +
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Residues in contact with SER 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PHE* 4.5 0.5 - - - -
144F ALA* 1.3 70.3 - - - +
146F HIS* 1.3 61.0 + - - +
172F ASN* 4.1 0.4 - - - -
173F GLN 3.4 7.9 - - - -
174F VAL* 3.9 8.2 - - - +
199F MET* 3.3 28.1 - - - +
201F GLY* 3.8 10.9 + - - -
205F SER* 2.5 41.9 + - - -
206F ASP 2.8 25.5 + - - -
207F SER* 3.1 8.3 + - - -
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Residues in contact with HIS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ALA 3.4 11.3 + - - -
145F SER* 1.3 72.0 - - - +
147F THR* 1.3 63.7 + - - +
148F ALA 2.8 24.7 - - - +
150F LEU* 3.6 12.1 - - + +
166F GLY* 3.3 30.8 + - - -
167F HIS 4.8 0.2 - - - -
168F THR* 3.5 23.4 - - + +
172F ASN* 3.6 2.1 + - - -
173F GLN* 3.1 46.1 + - + +
174F VAL 4.1 1.3 - - - -
175F ASN* 3.6 31.2 - - + -
198F ASP* 3.1 29.4 - - - +
200F VAL 3.8 3.4 - - - -
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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