Contacts of the helix formed by residues 160 - 171 (chain B) in PDB entry 2I91
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 ASP 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LYS* 2.8 26.8 + - - +
158B THR 4.0 0.3 - - - +
159B LYS* 1.3 80.2 - - - +
161B ALA* 1.3 58.0 + - - +
162B LEU* 3.1 4.0 - - + +
163B ASN* 2.6 57.2 + - - +
164B LEU* 2.9 9.4 + - - -
192B ASN* 6.2 0.4 - - - +
221B GLU* 6.2 0.4 - - - +
14D A 3.5 34.8 + - + +
15D A 4.7 3.5 - - - +
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Residues in contact with ALA 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 LYS 4.0 2.8 + - - -
160B ASP* 1.3 69.1 - - - +
162B LEU* 1.3 58.9 + - - +
164B LEU* 3.2 7.8 + - - +
165B ALA* 2.9 30.0 + - - +
192B ASN* 4.9 8.5 - - - +
194B GLY* 3.5 34.8 - - - +
195B LEU* 4.0 10.1 - - - +
198B VAL* 3.8 4.4 - - - +
221B GLU* 5.6 2.7 - - - +
225B VAL* 3.4 22.7 - - + -
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Residues in contact with LEU 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 ASP* 2.9 4.1 + - + +
161B ALA* 1.3 77.6 - - - +
163B ASN* 1.3 63.3 + - - +
165B ALA* 3.6 3.5 - - + +
166B MET* 3.0 33.5 + - - +
221B GLU* 4.6 13.5 + - - +
224B LYS* 3.9 44.6 - - + +
225B VAL* 3.5 15.7 - - + +
228B TYR* 4.1 23.3 - - + -
14D A 6.2 1.8 - - - +
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Residues in contact with ASN 163 (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 LYS* 4.9 7.4 - - + +
160B ASP* 2.6 45.9 + - - +
162B LEU* 1.3 74.5 - - - +
164B LEU* 1.3 66.0 + - - +
165B ALA 3.1 1.6 - - - -
166B MET* 3.0 28.3 + - - +
167B ALA* 3.0 20.5 + - - +
14D A 4.3 11.4 + - - -
14F A 5.1 6.3 + - - +
15F A 4.0 22.4 + - - -
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Residues in contact with LEU 164 (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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155B TRP* 3.8 28.9 - - + -
156B TYR* 3.6 25.4 - - + +
159B LYS* 4.2 25.0 - - + +
160B ASP 2.9 9.5 + - - +
161B ALA* 3.6 11.0 - - - +
163B ASN* 1.3 76.7 - - - +
165B ALA* 1.3 57.8 + - - +
167B ALA* 3.2 7.8 + - + +
168B VAL* 2.8 46.1 + - + +
183B LEU* 6.4 0.9 - - + -
195B LEU* 4.3 14.6 - - + +
198B VAL* 3.3 29.8 - - + -
199B ALA* 6.2 0.2 - - - -
202B VAL* 6.1 0.2 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA 2.9 16.4 + - - +
162B LEU* 3.6 11.2 - - + +
163B ASN 3.1 0.2 - - - -
164B LEU* 1.3 76.5 - - - +
166B MET* 1.3 53.4 + - - +
168B VAL* 3.2 12.4 - - - +
169B THR* 2.6 35.8 + - - +
198B VAL* 4.2 15.0 - - + +
225B VAL* 4.5 7.9 - - + -
228B TYR* 3.7 21.5 - - + -
229B LEU* 4.6 8.1 - - + -
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Residues in contact with MET 166 (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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162B LEU* 3.0 26.5 - - - +
163B ASN* 3.5 28.5 - - - +
165B ALA* 1.3 71.0 - - - +
167B ALA* 1.3 59.5 + - - +
169B THR* 2.9 2.0 + - - -
170B LYS* 2.7 40.3 + - + +
228B TYR* 3.1 36.4 + - + +
251B TYR 5.6 2.0 - - - +
252B ARG* 5.9 5.2 - - - +
257B HIS* 5.4 0.9 - - - +
14F A 3.7 32.3 - - + +
15F A 5.0 5.8 - - - +
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Residues in contact with ALA 167 (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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122B PRO* 3.7 22.6 - - + +
159B LYS* 4.6 9.6 - - - +
163B ASN 3.0 11.9 + - - +
164B LEU* 3.5 21.3 - - + +
166B MET* 1.3 76.4 - - - +
168B VAL* 1.3 57.3 + - + +
170B LYS* 4.6 0.7 - - - -
171B TYR* 3.0 43.3 + - + +
15F A 5.4 7.0 - - - +
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Residues in contact with VAL 168 (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* 4.5 1.3 - - + -
164B LEU* 2.8 48.6 + - + +
165B ALA* 3.2 18.2 - - - +
167B ALA* 1.3 72.9 - - - +
169B THR* 1.3 63.5 + - + +
171B TYR 4.1 0.7 - - - -
172B LYS* 3.5 26.7 - - - +
179B HIS* 3.6 37.1 + - + +
198B VAL* 4.0 11.2 - - + -
201B TYR* 4.9 7.6 - - + -
202B VAL* 4.1 19.5 - - + -
229B LEU* 5.4 0.7 - - + -
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Residues in contact with THR 169 (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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165B ALA 2.6 23.4 + - - +
166B MET* 2.9 12.3 + - - -
168B VAL* 1.3 80.0 - - + +
170B LYS* 1.3 65.2 + - - +
171B TYR 3.4 0.4 - - - -
172B LYS* 3.9 17.7 - - - +
201B TYR* 4.0 28.0 - - + +
228B TYR* 3.6 3.4 + - + -
229B LEU* 4.3 5.8 - - + -
232B THR* 4.0 22.4 - - + +
256B GLU 4.6 6.8 - - - +
257B HIS* 3.0 31.8 + - - -
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Residues in contact with LYS 170 (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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166B MET* 2.7 23.9 + - + +
167B ALA* 5.8 0.2 - - - -
169B THR* 1.3 76.4 + - - +
171B TYR* 1.3 86.2 + - + +
172B LYS* 3.7 1.4 + - - +
174B ARG* 3.7 6.1 + - - -
254B VAL* 3.8 25.7 - - + +
256B GLU* 3.2 47.6 - - - +
257B HIS* 4.1 11.0 - - - +
277B PRO* 4.3 12.7 - - - +
5E A 6.0 1.4 - - - +
13F C 2.5 30.3 + - - -
14F A 2.7 27.6 + - - +
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Residues in contact with TYR 171 (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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121B ILE* 4.0 12.3 - - + -
122B PRO* 3.7 29.5 - - + +
123B THR* 3.4 21.3 - - - +
126B PHE* 4.3 0.7 - - - -
167B ALA* 3.0 20.4 + - - +
168B VAL 3.8 2.9 - - - -
170B LYS* 1.3 104.3 - - + +
172B LYS* 1.3 60.6 + - - +
173B GLN 3.3 2.2 + - - -
174B ARG* 3.1 33.4 - - + +
179B HIS* 2.7 25.5 - - - -
256B GLU* 5.1 0.9 - - - -
12F U 3.5 21.5 - - - -
13F C 2.8 19.1 - - - -
14F A 2.4 29.4 + - - -
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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