Contacts of the strand formed by residues 139 - 146 (chain H) in PDB entry 3WBR
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 SER 139 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E MET* 3.5 13.0 - - - +
201E PRO* 3.7 23.0 - - - +
138H SER* 1.3 75.7 - - - +
140H TYR* 1.3 62.4 + - - +
182H ILE* 3.4 3.8 - - - +
183H ILE 3.5 4.8 + - - -
184H ASN* 2.9 27.9 + - - +
202H GLN* 2.8 29.4 + - - +
203H LYS* 3.2 24.4 + - - +
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Residues in contact with TYR 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ILE* 3.4 31.2 - - + +
99H THR* 5.9 0.9 - - + -
134H LEU* 3.6 32.3 - - + -
135H LYS* 2.8 33.6 + - - +
138H SER* 3.3 34.5 + - - -
139H SER* 1.3 75.9 + - - +
141H PHE* 1.3 62.4 + - - +
182H ILE* 3.1 6.2 - - - -
183H ILE* 2.7 46.0 + - + +
191H TRP* 4.5 1.3 - + - -
202H GLN* 4.6 0.4 - - - -
203H LYS* 3.2 32.8 - - + +
204H SER 4.0 7.0 - - - -
205H ILE* 3.8 24.0 - - + -
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Residues in contact with PHE 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H GLN 3.3 24.7 - - - -
104H TRP* 3.3 41.1 - + + -
107H SER* 4.0 7.0 - - - -
118H LEU* 4.1 9.2 - - + +
140H TYR* 1.3 73.6 - - - +
142H LEU* 1.3 62.0 + - - +
180H CYS* 3.9 17.9 - - + -
181H ALA 3.6 7.0 - - - -
182H ILE* 3.6 10.9 - - + +
196H ILE* 3.6 22.7 - - + -
197H HIS 4.6 0.4 - - - -
198H CYS 3.7 14.1 - - - -
200H VAL 3.2 22.0 - - - -
202H GLN* 3.6 20.8 - - + +
203H LYS 2.8 13.1 + - - +
204H SER* 4.0 6.7 - - - -
205H ILE* 3.6 23.4 + - - +
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Residues in contact with LEU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F TRP* 4.7 2.0 - - + -
104H TRP* 2.9 21.8 + - - -
118H LEU* 4.1 3.6 - - - -
119H VAL* 3.8 18.4 - - + +
121H ILE* 3.7 24.9 - - + -
141H PHE* 1.3 75.7 - - - +
143H GLY* 1.3 59.3 + - - +
144H LEU* 2.9 21.7 + - + +
181H ALA* 3.0 24.9 + - + +
182H ILE 4.4 2.7 - - - +
183H ILE* 3.7 34.3 - - + +
193H TRP* 3.7 44.0 - - + +
205H ILE* 4.6 1.8 - - + -
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Residues in contact with GLY 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLN 3.7 0.5 - - - +
155F TRP* 3.4 9.2 - - - -
156F VAL* 2.8 36.6 + - - +
104H TRP* 4.2 8.7 - - - -
118H LEU* 3.5 26.7 - - - +
119H VAL 2.9 22.0 + - - -
142H LEU* 1.3 69.1 - - - +
144H LEU* 1.3 56.8 + - - +
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F TRP* 3.6 24.2 - - + -
154F GLN 3.5 20.2 - - - +
155F TRP* 3.7 24.7 - - + -
161F TYR* 3.7 24.9 - - + -
168F TRP* 3.7 35.0 - - + -
104H TRP* 3.9 1.1 + - - -
142H LEU* 2.9 11.8 + - + +
143H GLY* 1.3 77.8 - - - +
145H SER* 1.3 63.2 + - - +
180H CYS* 3.9 0.5 - - - -
181H ALA* 3.0 37.2 + - + +
193H TRP* 4.0 15.3 - - + -
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Residues in contact with SER 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F TRP* 3.5 10.9 - - - -
154F GLN* 2.9 43.0 + - - +
156F VAL* 6.1 0.3 - - - -
104H TRP* 3.7 24.3 - - - -
143H GLY 5.2 0.2 + - - -
144H LEU* 1.3 78.2 - - - +
146H ASP* 1.3 64.3 + - - +
147H PRO* 4.8 2.1 - - - +
179H ARG 3.2 14.1 - - - -
180H CYS* 3.9 15.0 - - - -
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Residues in contact with ASP 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ARG* 3.0 58.6 + - + +
152F HIS* 3.8 17.6 + - - +
153F TRP* 3.7 6.1 - - + -
176F LEU* 5.0 0.3 - - - +
145H SER* 1.3 75.9 - - - +
147H PRO* 1.3 71.4 - - - +
148H GLY* 3.0 23.9 + - - +
176H LEU* 4.7 8.0 - - - +
178H GLU* 3.3 4.5 - - - +
179H ARG* 2.7 35.5 + - + +
198H CYS* 5.1 0.2 - - - -
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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