Contacts of the strand formed by residues 143 - 151 (chain B) in PDB entry 3DI3
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 LEU 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B PRO* 4.1 8.5 - - + -
132B THR* 3.6 25.8 - - + +
134B HIS* 3.7 20.2 - - + +
140B VAL* 3.7 25.6 - - + +
141B LYS 3.4 9.8 + - - +
142B VAL* 1.3 86.5 - - - +
144B MET* 1.3 62.9 + - - +
145B HIS* 3.8 21.9 + - + +
164B SER* 4.4 18.4 + - - +
187B SER* 3.6 21.3 - - - -
188B ILE 3.4 19.7 - - - +
189B PRO* 4.1 0.2 - - + -
190B ASP* 3.7 8.0 - - - +
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Residues in contact with MET 144 (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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143B LEU* 1.3 72.9 - - - +
145B HIS* 1.3 67.2 + - - +
162B ASN* 3.4 39.3 - - - +
163B LEU 3.7 18.6 - - - +
164B SER* 4.3 6.3 - - - +
187B SER* 3.7 1.4 - - - -
188B ILE* 3.0 45.3 + - + +
190B ASP* 3.1 37.2 - - + +
197B TRP* 3.8 7.7 - - + -
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Residues in contact with HIS 145 (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 PHE* 3.7 32.4 - + + -
132B THR* 4.3 13.8 - - + +
135B LEU* 5.9 2.0 - - - +
143B LEU* 3.8 29.8 + - + +
144B MET* 1.3 75.5 - - - +
146B ASP* 1.3 60.9 + - - +
147B VAL* 4.2 0.9 - - + +
162B ASN* 3.4 7.4 - - - +
163B LEU* 3.0 35.4 + - + +
164B SER 4.2 4.6 + - - -
165B SER* 3.1 37.3 + - - -
166B THR* 4.0 10.3 - - - +
185B VAL* 4.3 2.0 - - + -
186B ARG 3.4 6.5 - - - +
187B SER* 2.9 26.5 + - - -
197B TRP* 4.6 0.2 - - - -
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Residues in contact with ASP 146 (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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145B HIS* 1.3 76.3 - - - +
147B VAL* 1.3 63.3 + - - +
148B ALA 3.6 1.4 + - - -
160B HIS* 3.0 44.7 + - - +
161B VAL 3.6 2.5 + - - -
162B ASN* 3.6 10.0 - - - +
185B VAL* 3.5 5.9 - - - +
186B ARG* 2.9 52.0 + - + +
197B TRP* 3.5 28.3 - - + -
200B TRP* 3.6 5.5 - - - -
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Residues in contact with VAL 147 (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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115B LEU* 6.0 0.2 - - + -
128B VAL* 5.1 3.1 - - + -
130B PHE* 4.2 17.5 - - + -
145B HIS* 5.6 0.2 - - + -
146B ASP* 1.3 71.4 - - - +
148B ALA* 1.3 63.0 + - - +
149B TYR* 4.4 6.3 - - + -
159B THR 3.6 1.4 - - - +
160B HIS* 3.1 4.0 - - - -
161B VAL* 2.7 43.7 + - + +
163B LEU* 5.2 5.6 - - + -
168B LEU* 4.1 29.8 - - + -
183B ILE* 3.4 34.8 - - + -
184B LYS 3.4 4.9 - - - +
185B VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 148 (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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146B ASP 3.6 0.4 + - - -
147B VAL* 1.3 74.4 - - - +
149B TYR* 1.3 62.2 + - - +
158B TRP* 3.4 16.7 - - + -
159B THR 3.5 5.6 - - - +
160B HIS* 3.2 33.0 - - + +
183B ILE* 3.3 3.7 - - - +
184B LYS* 2.8 33.6 + - + -
200B TRP* 3.8 19.7 - - + -
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Residues in contact with TYR 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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147B VAL* 4.4 4.3 - - + -
148B ALA* 1.3 76.3 - - - +
150B ARG* 1.3 57.6 + - - +
157B LYS 4.4 0.3 - - - +
158B TRP* 3.2 9.4 - - - -
159B THR* 3.2 51.4 + - + +
161B VAL* 4.1 16.4 - - + +
170B LEU* 3.4 38.1 - - + +
174B LYS* 5.2 9.5 + - - +
175B LEU* 4.0 19.9 - - + +
181B TYR* 3.6 27.8 - + + -
182B GLU 3.1 16.6 - - - +
183B ILE* 3.7 20.0 - - + -
206B PHE* 5.8 1.8 - + + -
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Residues in contact with ARG 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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149B TYR* 1.3 74.6 - - - +
151B GLN* 1.3 83.7 + - - +
152B GLU* 3.6 14.3 + - - +
154B ASP* 3.3 11.2 + - + -
155B GLU* 2.9 42.3 + - - -
157B LYS 3.2 22.4 - - - +
158B TRP* 3.3 35.9 - - + -
180B MET* 6.3 0.6 - - - +
181B TYR* 3.1 10.3 - - - -
182B GLU* 2.5 64.9 + - + +
205B TYR* 5.1 3.0 - - - -
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Residues in contact with GLN 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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150B ARG* 1.3 84.7 + - - +
152B GLU* 1.3 57.9 + - + +
153B LYS* 3.9 36.8 + - - +
154B ASP* 2.6 44.6 + - - +
157B LYS 4.6 0.4 + - - -
176B GLN* 3.1 38.3 + - - +
179B ALA* 3.9 16.9 - - + +
180B MET 4.0 6.5 - - - +
181B TYR* 3.2 23.9 + - + -
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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