Contacts of the strand formed by residues 185 - 195 (chain B) in PDB entry 4DQ0
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 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 4.0 28.0 - - + -
145B VAL* 5.5 4.3 - - + -
174B GLU* 3.4 9.2 - - - +
175B LEU* 2.7 60.5 + - + +
176B HIS 4.7 1.6 - - - +
177B ARG* 3.9 18.1 - - + +
183B ASN 3.7 9.9 - - - +
184B ARG* 1.3 77.1 - - - +
186B LYS* 1.3 67.6 + - - +
187B LEU* 5.5 1.1 - - + -
201B NHE 3.7 34.1 - - + +
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Residues in contact with LYS 186 (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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141B TYR* 3.8 35.1 + - + +
142B PRO 5.4 1.6 - - - +
172B VAL* 3.7 23.9 + - + +
173B GLY 3.6 8.7 - - - +
174B GLU* 5.5 0.9 - - + -
184B ARG* 4.0 34.2 + - + +
185B ILE* 1.3 79.2 - - - +
187B LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 187 (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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135B ALA* 4.0 27.1 - - + -
136B MET 3.4 22.0 - - - +
141B TYR* 3.8 20.3 - - + +
142B PRO 4.3 5.8 - - - +
143B CYS* 4.3 14.4 - - + -
147B PHE* 4.3 5.8 - - + -
172B VAL* 4.4 2.2 - - - +
173B GLY* 2.7 39.2 + - - +
175B LEU* 4.1 36.6 - - + -
185B ILE* 3.9 1.3 + - + -
186B LYS* 1.3 78.7 - - - +
188B ARG* 1.3 67.4 + - - +
189B PHE* 3.5 12.8 - - + -
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Residues in contact with ARG 188 (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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135B ALA* 4.1 0.7 - - - -
136B MET* 3.0 39.6 + - + +
138B THR* 3.7 25.6 - - - +
140B ASP* 2.7 36.2 + - - -
141B TYR* 3.8 20.5 - - + +
153B GLU* 5.9 1.7 + - - -
170B GLU* 3.0 32.7 + - - +
171B ASP* 3.4 6.9 + - - +
172B VAL* 3.7 24.3 - - + +
187B LEU* 1.3 81.1 - - - +
189B PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 189 (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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103B VAL* 4.5 12.3 - - + -
106B MET* 4.4 10.8 - - + -
133B VAL* 4.8 7.4 - - + -
134B ALA 3.4 15.9 - - - +
135B ALA* 3.8 20.4 - - + -
136B MET* 3.6 4.5 - - - -
169B ASN* 3.4 4.5 - - - +
170B GLU* 3.2 20.3 - - - -
171B ASP 3.0 10.4 + - - +
173B GLY* 4.0 10.8 - - - -
174B GLU 3.6 31.4 - - - -
175B LEU* 3.9 21.5 - - + -
187B LEU* 3.5 25.6 - - + -
188B ARG* 1.3 73.0 - - - +
190B ALA* 1.3 65.7 + - - +
191B THR* 3.6 7.9 + - - +
202B NHE 5.4 2.2 - - + -
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Residues in contact with ALA 190 (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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132B ILE 3.6 1.4 - - - +
133B VAL* 3.2 6.6 - - - +
134B ALA 2.9 38.2 + - - +
136B MET* 3.3 22.2 - - + +
151B PHE* 4.2 13.5 - - + -
156B LEU* 3.8 27.8 - - + +
168B TYR* 4.8 2.0 - - + +
169B ASN 3.7 5.2 - - - -
170B GLU* 4.5 4.7 - - + +
189B PHE* 1.3 69.7 - - - +
191B THR* 1.3 59.7 + - - +
192B MET 4.3 0.4 - - - -
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Residues in contact with THR 191 (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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21B GLU* 3.6 40.1 + - + +
131B LEU* 5.3 1.8 - - + -
132B ILE 3.5 3.1 - - - -
133B VAL* 4.0 16.6 - - + +
156B LEU* 4.8 0.2 - - - +
167B LYS* 3.7 13.6 - - + +
168B TYR* 3.3 7.4 + - - -
169B ASN* 3.0 48.0 + - - +
189B PHE* 3.6 8.3 + - - +
190B ALA* 1.3 75.2 + - - +
192B MET* 1.3 64.5 + - - +
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Residues in contact with MET 192 (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 ASN* 3.5 7.6 - - + +
131B LEU* 3.2 9.8 - - - +
132B ILE* 2.8 53.8 + - + +
156B LEU* 3.7 23.1 - - + +
160B TYR* 3.5 59.0 - - + -
165B MET* 3.9 11.4 - - - +
167B LYS 3.2 5.2 - - - +
168B TYR* 3.6 19.1 - - + -
191B THR* 1.3 77.7 - - - +
193B LEU* 1.3 61.1 + - - +
194B ALA* 3.7 21.1 - - + -
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Residues in contact with LEU 193 (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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25B ALA* 4.3 20.6 - - + -
28B VAL* 4.0 26.9 - - + -
29B VAL* 4.3 7.6 - - + -
98B PHE* 4.5 0.7 - - + -
129B TYR* 4.0 29.4 - - + -
130B ASN 3.4 10.3 - - - +
131B LEU* 4.1 21.1 - - + -
165B MET* 3.8 0.7 - - - -
166B VAL* 2.8 40.3 + - + +
167B LYS* 2.9 28.6 + - + +
192B MET* 1.3 73.2 - - - +
194B ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 194 (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 TYR* 3.3 8.7 - - - +
130B ASN 2.8 32.8 + - - +
160B TYR* 4.0 2.0 - - + -
163B TRP* 3.7 19.0 - - + -
164B GLU 3.1 4.3 - - - +
165B MET* 3.5 27.8 - - + -
166B VAL* 4.5 0.2 - - - -
192B MET* 3.7 19.9 - - + -
193B LEU* 1.3 75.7 - - - +
195B ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 195 (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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127B GLY* 2.9 33.7 + - - +
128B GLY 3.4 11.7 - - - +
129B TYR* 3.2 39.2 + - + -
163B TRP* 3.4 6.9 - - - -
164B GLU* 2.8 65.2 + - + +
166B VAL* 3.9 11.4 - - + +
194B ALA* 1.3 74.3 - - - +
196B LYS* 1.3 68.2 + - - +
197B LYS 3.7 0.5 + - - -
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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