Contacts of the strand formed by residues 148 - 157 (chain B) in PDB entry 3EYO
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 ALA 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE* 4.5 4.3 - - - -
138B PRO* 4.2 7.4 - - + -
139B SER 4.2 13.5 - - - +
147B THR* 1.3 74.1 - - - +
149B ALA* 1.3 62.7 + - - +
195B THR* 3.2 8.3 - - - +
196B VAL* 2.7 44.2 + - + +
198B SER* 3.9 7.3 + - - -
201B LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 149 (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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117A PHE* 3.5 47.1 - - + -
119A PHE* 3.6 14.6 - - + -
136A LEU* 4.2 7.4 - - + -
138B PRO* 3.1 24.4 - - - +
148B ALA* 1.3 76.8 - - - +
150B LEU* 1.3 62.0 + - - +
193B VAL* 5.8 0.2 - - + -
194B VAL 3.5 6.3 - - - +
195B THR* 4.1 7.9 - - + -
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Residues in contact with LEU 150 (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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119A PHE* 4.2 3.3 - - - -
136B LEU* 3.3 14.8 - - - +
138B PRO* 3.7 24.5 - - + -
149B ALA* 1.3 76.0 - - - +
151B GLY* 1.3 61.6 + - - +
166B TRP* 3.7 19.7 - - + -
193B VAL* 3.2 7.4 - - - +
194B VAL* 2.8 62.5 + - + +
196B VAL* 4.4 8.1 - - + -
201B LEU* 4.2 11.2 - - + -
206B TYR* 3.8 35.2 - - + -
223B VAL* 4.3 11.4 - - + +
224B GLU* 6.1 0.2 - - - -
225B PRO* 6.1 0.2 - - + -
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Residues in contact with GLY 151 (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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136B LEU* 2.8 42.7 + - - +
150B LEU* 1.3 77.9 - - - +
152B CYS* 1.3 58.4 - - - -
166B TRP* 3.6 13.5 - - - -
192B SER 2.9 14.4 - - - -
193B VAL* 3.9 1.3 - - - -
223B VAL* 3.6 12.8 - - - +
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Residues in contact with CYS 152 (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* 4.0 7.4 - - + -
134B PHE 3.3 4.7 - - - +
136B LEU* 3.8 6.3 - - - +
151B GLY* 1.3 73.6 - - - -
153B LEU* 1.3 60.3 + - - +
154B VAL* 3.7 8.0 + - + +
164B VAL* 5.5 0.2 - - + -
166B TRP* 3.8 2.0 - - + -
191B SER* 3.6 4.0 - - - -
192B SER* 2.8 33.8 + - - +
208B CYS* 2.0 52.7 - - + -
210B VAL* 5.3 0.2 - - + -
221B LYS* 3.9 11.9 - - - -
223B VAL* 3.7 24.5 - - - -
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Residues in contact with LEU 153 (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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125A GLN* 4.5 3.1 - - - +
132A SER* 3.6 33.9 - - - +
134A VAL* 4.4 15.9 - - + -
179A THR* 4.9 10.5 - - + +
132B SER 3.2 6.2 - - - +
133B VAL* 3.5 1.1 - - - -
134B PHE* 2.7 54.0 + - + +
136B LEU* 4.2 12.9 - - + +
152B CYS* 1.3 72.5 - - - +
154B VAL* 1.3 61.5 + - - +
155B LYS* 3.3 13.4 + - + -
189B SER* 3.8 19.1 - - - +
190B LEU 3.2 19.7 - - - +
191B SER* 4.6 5.4 - - - +
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Residues in contact with VAL 154 (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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131B PRO* 3.5 27.4 - - + -
132B SER 3.8 2.2 - - - -
133B VAL* 4.5 7.0 - - + +
152B CYS* 4.4 9.2 - - + +
153B LEU* 1.3 71.2 - - - +
155B LYS* 1.3 58.7 + - - +
157B TYR* 3.6 15.6 - - + -
162B VAL* 4.5 6.5 - - + -
164B VAL* 4.4 6.7 - - + -
189B SER* 3.3 4.1 - - - -
190B LEU* 2.7 61.5 + - + +
192B SER* 5.5 0.4 - - - -
210B VAL* 3.9 37.0 - - + -
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Residues in contact with LYS 155 (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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125A GLN* 3.6 24.5 - - - +
130A THR* 4.5 15.2 - - - +
132A SER* 3.8 13.4 + - - +
179A THR* 6.3 0.2 - - - +
181A THR* 4.8 6.9 + - - +
131B PRO* 3.6 1.7 - - - +
132B SER* 2.8 43.7 + - - +
134B PHE* 4.4 15.5 - - + -
153B LEU* 3.3 14.6 + - + +
154B VAL* 1.3 75.6 - - - +
156B ASP* 1.3 92.7 + - - +
157B TYR 3.7 1.3 - - - -
183B GLN* 2.8 29.9 + - - -
189B SER* 3.4 16.3 + - - +
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Residues in contact with ASP 156 (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 LYS* 3.6 23.8 + - - +
130B GLY 3.5 13.5 - - - +
132B SER* 5.5 3.4 - - - +
155B LYS* 1.3 99.2 + - - +
157B TYR* 1.3 57.6 - - - +
183B GLN* 2.6 33.6 + - - -
185B SER* 4.3 1.7 + - - -
187B LEU* 3.5 31.0 - - + +
188B TYR 2.9 14.9 + - - -
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Residues in contact with TYR 157 (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 LYS 3.3 13.7 - - - +
131B PRO* 3.8 20.6 - - + -
154B VAL* 3.6 34.5 - - + -
156B ASP* 1.3 77.3 - - - +
158B PHE* 1.3 62.2 + - - +
159B PRO 3.6 20.0 - - - -
160B GLU* 2.8 30.6 + - - -
162B VAL* 3.6 38.1 - - + +
180B ALA* 2.9 18.4 - - - +
187B LEU* 3.7 2.4 - - - -
188B TYR* 2.7 53.3 + + + +
189B SER* 4.0 2.2 - - - -
190B LEU* 3.7 5.6 - - + +
212B HIS* 3.8 2.0 - - + -
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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