Contacts of the strand formed by residues 173 - 182 (chain B) in PDB entry 3FB7
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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLU* 4.3 16.3 + - - +
138B ASN 3.2 1.2 + - - -
139B PHE* 2.9 43.2 + - + +
140B TYR* 3.5 24.6 - + - -
142B LYS* 3.2 58.6 + - + +
164B THR* 3.7 16.6 - - - +
165B ASP* 4.1 1.3 - - - -
166B GLN* 3.3 64.2 + - + +
167B ASP* 5.1 1.1 - - - +
172B THR* 1.3 77.0 - - - +
174B SER* 1.3 69.5 + - - +
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Residues in contact with SER 174 (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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169A HIS* 3.3 24.7 + - - -
171A PHE* 3.3 9.4 - - - -
136B LEU 3.3 5.8 - - - -
137B ASN* 3.5 17.9 - - - -
138B ASN* 3.1 14.6 + - - -
139B PHE* 3.7 4.5 - - - -
163B TRP* 3.7 2.6 - - - +
164B THR* 3.0 38.7 + - - +
167B ASP* 6.1 0.7 - - - +
172B THR* 5.0 0.9 + - - -
173B TYR* 1.3 82.7 + - - +
175B MET* 1.3 59.7 + - - +
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Residues in contact with MET 175 (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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171A PHE* 3.0 12.9 - - - -
134B CYS 4.1 0.2 - - - +
135B PHE* 3.8 1.2 - - - -
136B LEU* 2.9 42.4 + - + +
139B PHE* 4.2 10.3 - - + -
144B ILE* 4.3 16.6 - - + +
145B ASN* 5.8 0.2 - - - -
146B VAL* 3.5 30.1 - - + +
161B ASN* 3.2 35.0 - - - +
162B SER 3.2 12.3 - - - +
163B TRP* 3.4 41.3 - - + +
174B SER* 1.3 74.1 - - - +
176B SER* 1.3 66.0 + - - +
177B SER 4.2 1.6 - - - -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.3 33.8 - - - +
183A SER* 5.1 6.2 + - - -
133B VAL* 5.4 0.2 - - - -
134B CYS 3.8 4.5 - - - -
135B PHE* 4.1 11.2 - - - -
160B LEU 3.3 7.6 - - - +
161B ASN* 3.5 0.8 - - - -
162B SER* 2.6 46.3 + - - -
175B MET* 1.3 72.6 - - - +
177B SER* 1.3 61.8 + - - +
178B THR* 3.8 6.8 + - - -
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Residues in contact with SER 177 (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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133B VAL* 3.7 1.2 - - - +
134B CYS* 3.0 36.9 + - - +
136B LEU* 5.1 1.3 - - - +
146B VAL* 3.7 20.9 - - - +
148B TRP* 2.8 34.1 + - - -
159B VAL* 3.3 7.4 - - - +
160B LEU 3.6 0.4 - - - -
161B ASN* 2.5 26.7 + - - -
175B MET* 4.2 3.8 - - - +
176B SER* 1.3 72.4 - - - +
178B THR* 1.3 60.6 + - - +
179B LEU 4.2 0.7 - - - -
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Residues in contact with THR 178 (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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146A LEU* 5.2 9.2 - - + +
181A THR* 5.4 7.3 - - + +
183A SER* 4.8 5.7 + - - -
131B SER* 4.5 5.8 - - - -
132B VAL 3.9 2.7 - - - -
133B VAL* 3.8 27.4 - - + +
158B GLY 3.0 13.0 - - - +
159B VAL* 4.2 1.3 - - - -
160B LEU* 2.8 38.7 + - + +
176B SER* 4.3 6.9 + - - -
177B SER* 1.3 76.4 + - - +
179B LEU* 1.3 60.8 + - - +
180B THR* 3.5 20.6 + - - +
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Residues in contact with LEU 179 (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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130B ALA 3.8 1.2 - - - +
131B SER* 3.4 1.7 - - - -
132B VAL* 2.8 45.5 + - + +
148B TRP* 3.6 36.4 - - + -
150B ILE* 4.2 25.6 - - + -
155B ARG* 4.2 10.1 - - + -
157B ASN 3.5 21.1 - - - +
158B GLY 3.3 3.8 - - - +
159B VAL* 3.8 13.2 - - + -
178B THR* 1.3 71.1 - - - +
180B THR* 1.3 63.3 + - - +
181B LEU* 3.4 28.9 - - + -
192B TYR* 4.5 7.0 - - + -
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Residues in contact with THR 180 (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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148A LYS* 4.9 15.5 + - - +
124B GLN* 5.8 0.2 - - - +
129B GLY* 6.1 0.9 - - - -
130B ALA 3.3 4.3 - - - +
131B SER* 3.0 27.5 + - - +
158B GLY* 2.9 23.1 + - - +
160B LEU* 6.6 0.2 - - - -
178B THR* 3.5 12.5 - - - +
179B LEU* 1.3 74.3 - - - +
181B LEU* 1.3 76.7 + - - +
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Residues in contact with LEU 181 (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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129B GLY* 4.2 1.7 - - - -
130B ALA* 2.7 33.0 + - + +
132B VAL* 5.9 2.0 - - + -
150B ILE* 4.2 7.6 - - + -
155B ARG* 3.3 37.7 - - - +
157B ASN 4.8 0.2 - - - +
179B LEU* 3.4 23.6 - - + -
180B THR* 1.3 82.2 - - - +
182B THR* 1.3 69.9 + - - +
185B GLU* 3.6 27.8 - - + +
186B TYR* 4.1 4.5 - - + +
192B TYR* 3.8 35.7 - - + +
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Residues in contact with THR 182 (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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128B GLY 3.8 11.4 - - - +
130B ALA* 4.0 1.6 - - - -
181B LEU* 1.3 79.9 - - - +
183B LYS* 1.3 67.2 + - - +
184B ASP* 3.4 12.4 - - - +
185B GLU* 3.1 24.7 + - + +
186B TYR* 3.0 20.4 + - - +
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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