Contacts of the strand formed by residues 143 - 155 (chain B) in PDB entry 3AIH
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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118B TRP* 4.2 18.8 - - + -
129B GLN* 3.2 7.6 - - - +
130B GLN* 2.8 64.1 + - + +
141B GLU* 3.6 35.9 + - - +
142B VAL* 1.3 75.6 - - - +
144B TYR* 1.3 65.0 + - - +
179B SER* 3.6 23.8 - - - +
180B LYS 5.7 0.2 - - - +
188B ARG* 3.9 15.9 - - - +
3D MAN 3.5 13.5 - - - +
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Residues in contact with TYR 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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127B HIS* 3.9 18.1 + + + -
128B ILE 3.5 6.5 - - - +
129B GLN* 2.9 38.7 + - + -
142B VAL* 4.1 20.0 - - + +
143B LEU* 1.3 73.3 - - - +
145B LEU* 1.3 60.8 + - - +
146B GLY 4.1 3.8 - - - +
147B TYR* 3.3 52.7 - + + +
178B GLY* 3.2 1.6 - - - -
179B SER* 2.7 45.4 + - - +
188B ARG* 3.6 8.4 - - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.5 32.5 - - + -
128B ILE* 2.9 36.6 + - + +
129B GLN 4.6 0.2 - - - +
130B GLN* 3.4 38.4 - - + +
143B LEU 5.2 0.2 - - - -
144B TYR* 1.3 73.9 - - - +
146B GLY* 1.3 56.4 + - - +
178B GLY* 3.9 1.1 - - - -
188B ARG* 3.3 31.6 - - - -
189B GLU* 3.3 11.0 + - - -
190B ALA* 3.9 8.2 + - + -
218B TYR* 3.7 40.8 - - + -
220B LEU* 4.5 5.2 - - + -
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Residues in contact with GLY 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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127B HIS* 3.3 5.5 - - - +
128B ILE* 3.1 26.2 + - - +
144B TYR* 3.2 3.9 - - - -
145B LEU* 1.3 81.7 - - - +
147B TYR* 1.3 65.6 + - - -
175B TYR* 3.9 8.9 - - - +
176B GLY 3.3 19.3 - - - -
178B GLY* 3.7 8.5 - - - -
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Residues in contact with TYR 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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126B ARG 3.5 6.3 - - - +
127B HIS* 4.0 13.7 - - + -
144B TYR* 3.3 56.1 - + + +
146B GLY* 1.3 73.6 - - - -
148B TYR* 1.3 70.4 + - - +
149B GLN* 3.3 1.6 + - - +
175B TYR* 3.3 3.4 - - - -
176B GLY 2.8 27.8 + - - +
177B ASN* 3.4 28.0 - - + -
178B GLY* 4.6 1.1 - - - -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY* 3.2 39.3 - - - +
126B ARG 2.9 10.8 + - - +
147B TYR* 1.3 75.4 - - - +
149B GLN* 1.3 71.9 + - - +
150B SER* 3.3 24.6 - - - -
151B ALA* 3.3 29.9 + - + +
173B GLN* 4.4 7.9 - - - -
174B THR 4.2 0.4 - - - -
175B TYR* 3.4 31.0 - + + -
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Residues in contact with GLN 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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183A LEU 4.9 2.0 - - - +
184A ASN* 3.6 29.9 + - - +
186A ARG* 6.4 0.4 - - - +
147B TYR 3.9 5.6 - - - +
148B TYR* 1.3 86.9 - - - +
150B SER* 1.3 66.6 + - - +
174B THR* 2.9 28.9 + - - +
175B TYR 5.1 0.2 - - - -
176B GLY* 3.7 24.8 - - - +
177B ASN* 4.7 7.9 + - - +
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Residues in contact with SER 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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148B TYR* 3.3 16.9 - - - -
149B GLN* 1.3 85.9 + - - +
151B ALA* 1.3 63.6 + - - +
173B GLN* 3.3 3.1 - - - -
174B THR* 2.7 50.9 + - - +
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Residues in contact with ALA 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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148B TYR* 3.3 18.5 + - + +
150B SER* 1.3 81.9 - - - +
152B PHE* 1.3 61.1 + - - +
153B ASP 4.2 0.6 + - - -
171B HIS* 4.2 11.2 - - + +
172B SER 3.2 6.1 - - - +
173B GLN* 3.7 20.0 - - + +
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Residues in contact with PHE 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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151B ALA* 1.3 75.9 - - - +
153B ASP* 1.3 71.3 + - - +
154B TRP* 4.1 32.5 - + + -
170B TYR* 3.6 31.4 - + - -
171B HIS* 3.2 7.4 - - - -
172B SER* 2.8 41.3 + - - +
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Residues in contact with ASP 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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151B ALA 4.2 0.8 + - - -
152B PHE* 1.3 87.3 - - - +
154B TRP* 1.3 72.4 + - - +
155B ASP* 4.3 10.0 - - - +
169B ARG* 5.1 11.0 + - - +
170B TYR 3.6 6.9 - - - +
171B HIS* 2.9 31.8 + - + +
227B LEU* 5.9 1.2 - - - +
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Residues in contact with TRP 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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152B PHE* 4.1 29.2 - + + -
153B ASP* 1.3 77.4 - - - +
155B ASP* 1.3 64.4 + - - +
156B ASP* 2.4 35.6 + - - -
168B LYS* 3.6 28.5 - - + +
169B ARG* 3.3 7.9 + - - +
170B TYR* 2.8 46.9 + - + +
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Residues in contact with ASP 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 ASP* 4.3 10.9 + - - +
154B TRP* 1.3 78.5 - - - +
156B ASP* 1.3 75.1 + - - +
168B LYS 3.8 3.0 - - - +
169B ARG* 3.5 41.8 + - - +
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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