Contacts of the strand formed by residues 178 - 187 (chain A) in PDB entry 3IU3
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 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 4.0 19.1 - - + +
146A ASP 3.1 10.0 + - - -
147A TYR* 2.6 62.2 + - + +
148A PHE* 3.9 23.1 - + - -
149A PRO 4.3 1.3 - - - -
150A GLU* 4.0 39.7 - - + -
170A ALA* 4.2 8.7 - - + -
171A VAL 3.5 4.7 - - - -
172A LEU* 3.7 50.0 - - + +
173A GLN* 4.7 0.2 - - - -
177A LEU* 1.3 75.4 - - - +
179A SER* 1.3 60.4 + - - +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.1 8.7 - - - +
144A VAL 3.2 16.0 + - - -
145A LYS* 3.4 20.5 + - - +
147A TYR* 3.9 2.7 - - - -
169A PRO 4.4 0.3 - - - +
170A ALA* 3.4 1.0 - - - -
171A VAL* 2.9 40.5 + - - +
173A GLN* 3.3 26.1 + - - -
178A TYR* 1.3 78.4 - - - +
180A LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.7 6.2 - - - +
144A VAL* 2.9 51.9 + - + +
147A TYR* 3.4 22.2 - - - +
150A GLU* 4.8 2.2 - - - +
152A VAL* 3.9 17.9 - - + -
154A VAL* 4.6 4.0 - - + -
167A THR* 4.1 13.5 - - - +
168A PHE* 3.4 24.7 - - - +
169A PRO 4.0 2.9 - - - +
170A ALA* 3.9 13.0 - - + +
171A VAL* 5.7 0.2 - - - -
179A SER* 1.3 76.5 + - - +
181A SER* 1.3 75.1 + - - +
182A SER 4.3 0.7 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.9 20.3 - - - +
142A CYS 3.3 6.4 + - - -
143A LEU* 3.7 21.0 - - - +
167A THR* 3.8 0.3 - - - -
168A PHE* 3.0 45.5 + - - +
180A LEU* 1.3 76.6 - - - +
182A SER* 1.3 61.1 + - - +
183A VAL* 4.8 4.7 - - - -
130B VAL* 4.4 12.3 - - - +
173B SER* 5.0 7.8 + - - -
175B THR* 5.1 3.6 + - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY* 3.0 2.8 - - - -
142A CYS* 2.7 41.5 + - - +
144A VAL* 5.4 0.2 - - - -
154A VAL* 3.4 29.6 + - - +
156A TRP* 2.9 27.8 + - - -
165A VAL* 4.4 2.9 - - - +
166A HIS 3.6 4.2 + - - -
167A THR* 4.0 17.9 - - - +
180A LEU* 4.3 1.0 - - - +
181A SER* 1.3 73.7 - - - +
183A VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 4.3 19.3 - - + -
139A ALA* 5.0 2.2 - - + -
140A LEU 3.4 11.7 - - - +
141A GLY* 4.1 0.4 - - - -
156A TRP* 4.8 1.8 - - - -
164A GLY 3.5 0.8 - - - +
165A VAL* 3.4 2.6 - - - +
166A HIS* 2.6 48.7 + - + +
168A PHE* 4.2 16.2 - - + -
181A SER* 4.8 3.4 - - - -
182A SER* 1.3 80.4 + - - +
184A VAL* 1.3 68.4 + - - +
185A THR* 5.0 2.5 - - + +
115B PHE* 4.9 4.9 - - + -
130B VAL* 5.8 2.2 - - + -
132B LEU* 3.2 41.3 - - + -
134B ASN* 4.6 6.1 - - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA 4.1 0.5 - - - +
139A ALA* 3.6 0.9 - - - -
140A LEU* 2.8 65.4 + - + +
156A TRP* 4.1 20.2 - - + +
161A LEU* 4.0 19.1 - - + -
163A SER 3.8 10.8 - - - +
164A GLY 3.2 18.2 - - - +
165A VAL* 3.9 14.8 - - + -
183A VAL* 1.3 78.3 - - - +
185A THR* 1.3 75.6 + - - +
186A VAL* 4.1 5.5 + - + +
196A TYR* 5.1 0.4 - - + -
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 3.6 20.6 - - + -
138A ALA 3.4 3.1 - - - -
139A ALA* 4.0 19.5 - - + -
163A SER 4.6 1.7 - - - +
164A GLY* 3.3 23.0 + - - +
183A VAL* 5.2 2.9 - - + -
184A VAL* 1.3 81.0 - - - +
186A VAL* 1.3 66.0 + - - +
113B PHE* 4.4 6.5 - - + -
134B ASN* 3.5 32.8 + - - +
135B ASN* 5.0 3.3 + - - -
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 3.4 8.2 - - - +
138A ALA* 2.8 41.7 + - + +
140A LEU* 4.2 12.3 - - + -
161A LEU* 4.7 6.1 - - + -
184A VAL* 4.3 15.3 - - + -
185A THR* 1.3 79.9 - - - +
187A PRO* 1.4 81.3 - - + +
191A LEU* 4.0 21.5 - - + -
196A TYR* 3.3 38.6 - - + +
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY 3.6 9.4 - - - +
137A THR* 4.7 0.2 - - - -
185A THR 5.0 0.2 - - - +
186A VAL* 1.4 96.7 - - + +
188A SER* 1.3 65.3 + - - +
189A SER* 3.2 14.8 - - - +
190A SER* 2.8 33.5 + - - +
191A LEU* 3.7 2.9 + - - +
196A TYR* 5.4 0.2 - - - +
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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