Contacts of the strand formed by residues 154 - 162 (chain B) in PDB entry 6MOL
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 ILE 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.0 13.2 - - + -
144B PRO* 4.1 13.7 - - + -
145B PRO* 4.4 8.5 - - + -
148B THR* 4.6 11.0 - - + +
149B PRO 4.6 4.9 - - - +
150B MET 3.4 20.9 - - - +
151B THR* 3.5 21.2 + - - +
152B SER 3.6 0.6 - - - -
153B HIS* 1.3 78.5 - - - +
155B ARG* 1.3 64.0 + - - +
156B TYR* 3.5 46.5 - - + +
176B GLU* 3.6 2.3 - - - -
177B GLY* 3.6 21.3 + - - -
198B ALA* 4.3 4.3 - - + -
199B ARG 3.6 10.5 - - - +
200B MET* 4.2 11.7 - - - -
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Residues in contact with ARG 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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153B HIS 3.8 1.2 + - - -
154B ILE* 1.3 74.3 - - - +
156B TYR* 1.3 63.2 + - - +
173B GLU* 3.7 24.3 + - - +
174B ILE 3.3 20.9 - - - +
175B LEU* 5.4 1.1 - - - +
176B GLU* 4.2 13.5 - - + +
198B ALA* 3.4 4.0 - - - -
199B ARG* 2.8 75.8 + - + +
201B ALA* 4.1 19.4 - - + +
202B GLU* 3.2 28.2 + - - +
209B TRP* 3.8 11.6 - - - -
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Residues in contact with TYR 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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124B PRO* 4.2 7.2 - - + -
142B TRP* 3.2 48.2 - + + -
144B PRO* 3.3 38.3 - - + +
151B THR 5.0 1.5 + - - -
154B ILE* 3.5 40.0 - - + +
155B ARG* 1.3 79.9 - - - +
157B GLU* 1.3 65.1 + - - +
173B GLU* 3.9 2.8 - - - +
174B ILE* 3.0 32.2 + - + +
175B LEU 5.1 1.3 - - - -
177B GLY 5.4 1.6 - - - -
178B ARG 3.7 21.5 - - - -
179B THR* 4.1 7.6 - - + +
196B VAL* 3.9 3.6 - - + -
197B ARG 3.1 23.6 - - - +
198B ALA* 4.1 8.7 - - + -
209B TRP* 3.9 5.9 - - - -
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Residues in contact with GLU 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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156B TYR* 1.3 79.4 - - - +
158B VAL* 1.3 59.1 + - - +
171B ARG* 3.5 33.5 - - + +
172B VAL 3.4 15.3 - - - +
173B GLU* 3.5 24.1 - - + +
174B ILE* 4.3 0.6 - - - +
197B ARG* 2.6 63.1 + - + -
209B TRP* 3.6 29.7 + - + -
212B TRP* 3.3 9.4 - - + -
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Residues in contact with VAL 158 (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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140B LEU* 4.3 18.2 - - + -
142B TRP* 4.0 25.1 - - + -
157B GLU* 1.3 72.1 - - - +
159B ASP* 1.3 61.2 + - - +
160B VAL* 4.1 3.1 + - + -
171B ARG* 3.2 8.5 - - - +
172B VAL* 2.9 56.9 + - + +
174B ILE* 4.2 9.0 - - + -
181B CYS* 4.4 2.7 - - - -
183B LEU* 4.3 16.8 - - + -
195B ALA 3.2 5.8 - - - +
196B VAL* 3.8 26.2 - - + -
212B TRP* 4.3 0.9 - - - -
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Residues in contact with ASP 159 (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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158B VAL* 1.3 73.1 - - - +
160B VAL* 1.3 63.0 + - - +
161B SER* 3.8 20.0 - - - -
167B GLY 5.0 1.4 - - - +
168B SER* 4.9 8.6 + - - -
170B GLN 3.7 9.2 - - - +
171B ARG* 2.7 33.6 + - - +
193B THR 3.2 14.6 - - - +
194B PHE* 3.5 2.2 - - - -
195B ALA* 2.7 27.0 + - + +
212B TRP* 3.6 27.1 - - + -
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Residues in contact with VAL 160 (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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158B VAL* 5.0 4.3 - - + -
159B ASP* 1.3 74.6 - - - +
161B SER* 1.3 58.5 + - - +
168B SER* 4.1 1.0 - - - -
169B VAL* 3.3 9.2 + - - +
170B GLN* 2.7 54.6 + - + +
172B VAL* 5.3 0.7 - - + -
183B LEU* 3.7 35.2 - - + -
186B LEU* 3.9 13.7 - - + -
192B TYR* 3.6 25.6 - - + -
193B THR 3.8 2.0 - - - -
194B PHE* 3.5 25.1 - - + -
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Residues in contact with SER 161 (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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159B ASP* 3.6 13.2 + - - -
160B VAL* 1.3 73.2 - - - +
162B ALA* 1.3 67.5 + - - +
167B GLY* 2.5 28.8 + - - -
168B SER* 4.6 0.2 - - - +
192B TYR* 3.4 9.2 - - - -
193B THR* 2.9 47.9 + - - -
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Residues in contact with ALA 162 (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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160B VAL 4.1 1.8 + - - -
161B SER* 1.3 80.0 + - - +
163B GLY* 1.3 66.4 + - - +
164B GLN 3.5 10.0 - - - +
165B GLY 4.2 1.2 - - - +
166B ALA 4.7 2.0 - - - +
167B GLY* 3.3 32.0 + - - -
168B SER 4.2 0.2 - - - +
169B VAL* 4.2 20.3 - - + +
190B THR* 5.2 6.5 - - + -
191B ARG 4.2 2.0 - - - -
192B TYR* 4.4 11.0 - - + -
193B THR* 5.5 0.4 - - - -
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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