Contacts of the helix formed by residues 161 - 175 (chain K) in PDB entry 3IT8
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 MET 161 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ARG* 3.0 35.9 - - - +
84G ALA* 4.9 3.6 - - + -
87G TYR* 4.2 14.8 - - + -
91G VAL* 4.2 11.9 - - - -
33H ALA* 4.7 10.3 - - + +
34H ASN* 3.5 25.4 - - - +
157K GLY 3.1 2.8 + - - -
158K PHE 3.8 0.2 - - - -
159K GLU 3.4 2.0 - - - -
160K TYR* 1.3 95.8 - - + +
162K GLY* 1.3 72.0 + - - +
163K CYS 3.2 2.7 - - - -
164K SER* 2.7 30.4 + - - +
165K LEU* 3.1 32.0 + - + +
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Residues in contact with GLY 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G TYR* 3.5 34.0 - - - -
58K HIS* 3.8 5.1 - - - +
157K GLY 3.1 10.0 + - - -
158K PHE* 3.7 12.8 - - - -
161K MET* 1.3 77.2 - - - +
163K CYS* 1.3 62.6 + - - +
165K LEU* 3.2 4.2 + - - +
166K ALA* 2.9 22.3 + - - +
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Residues in contact with CYS 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 3.9 12.3 - - - -
96K GLY* 3.6 9.2 - - - +
97K CYS* 3.1 47.6 - - + -
106K SER* 5.2 1.8 - - - -
158K PHE* 2.7 58.4 + - + +
159K GLU* 5.1 2.0 - - - -
162K GLY* 1.3 72.4 - - - +
164K SER* 1.3 63.5 + - - +
166K ALA* 2.9 3.1 + - - +
167K ILE* 2.8 25.1 + - - +
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Residues in contact with SER 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ARG* 5.6 3.3 - - - -
33H ALA* 4.5 15.2 + - - -
97K CYS* 3.8 16.0 - - - +
99K GLU* 5.4 1.2 - - - +
106K SER* 5.8 3.1 - - - -
158K PHE 4.6 0.2 + - - -
161K MET* 2.7 32.8 + - - +
163K CYS* 1.3 78.3 - - - +
165K LEU* 1.3 59.8 + - - +
167K ILE* 3.2 17.3 - - - +
168K LEU* 3.8 11.3 - - - +
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Residues in contact with LEU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G TYR* 4.1 5.4 - - + -
91G VAL* 3.8 20.6 - - + -
33H ALA* 3.4 28.0 - - + -
58K HIS* 3.7 39.5 - - + +
161K MET* 3.1 30.6 + - + +
162K GLY 3.5 5.8 - - - +
163K CYS 3.0 0.8 - - - -
164K SER* 1.3 79.5 + - - +
166K ALA* 1.3 67.7 + - - +
168K LEU* 3.3 26.0 + - + +
169K ASP* 3.8 7.8 + - - +
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Residues in contact with ALA 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K LEU* 4.2 12.3 - - + -
5K TYR* 5.2 0.2 - - - +
56K SER* 4.5 1.1 - - - +
58K HIS* 3.7 31.1 - - + +
59K THR* 4.3 2.2 - - - +
158K PHE* 4.8 2.5 - - + -
162K GLY 2.9 12.7 + - - +
163K CYS* 2.9 8.6 + - - +
165K LEU* 1.3 73.1 - - - +
167K ILE* 1.3 56.6 + - - +
168K LEU 2.9 2.2 - - - -
169K ASP* 2.6 32.8 + - - +
170K TYR* 3.2 22.2 + - + -
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Residues in contact with ILE 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K ILE* 3.8 34.5 - - + +
2K THR* 3.9 4.3 - - - +
3K LEU* 3.8 36.7 - - + +
25K TYR* 4.0 9.3 - - + -
97K CYS* 3.8 24.2 - - - +
98K TYR* 4.5 4.3 - - - -
99K GLU* 4.7 7.9 - - + +
163K CYS 2.8 17.8 + - - +
164K SER* 3.2 21.1 - - - +
166K ALA* 1.3 72.7 - - - +
168K LEU* 1.3 73.8 + - + +
170K TYR* 3.4 5.1 + - - +
171K GLN* 3.1 21.5 + - - +
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Residues in contact with LEU 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ARG* 3.5 55.2 - - + +
33H ALA* 6.0 1.1 - - + +
1K ILE* 5.0 2.5 - - + -
99K GLU* 4.0 11.7 - - - +
164K SER 3.8 15.7 - - - +
165K LEU* 3.3 17.4 + - + +
166K ALA 2.8 2.0 + - - -
167K ILE* 1.3 84.5 - - + +
169K ASP* 1.3 64.1 + - - +
171K GLN* 3.5 19.5 + - - +
172K LYS* 3.2 28.6 + - - +
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Residues in contact with ASP 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K ARG 3.6 20.8 - - - +
56K SER* 3.7 18.3 + - - +
57K PRO* 3.6 18.8 - - - +
58K HIS* 4.3 9.2 - - - -
165K LEU 4.0 11.1 - - - +
166K ALA* 2.6 18.2 + - - +
168K LEU* 1.3 72.2 - - - +
170K TYR* 1.3 63.1 + - - +
172K LYS* 3.3 17.7 + - - +
173K MET* 3.2 28.6 + - + +
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Residues in contact with TYR 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K LEU* 3.7 28.3 - - + -
5K TYR* 2.7 16.2 + - - -
23K ASP* 2.6 38.5 + - - -
25K TYR* 3.5 31.9 - + + -
30K VAL* 4.0 10.3 - - + -
50K TRP* 3.7 5.3 - + + -
51K PHE* 3.5 36.1 - + - -
56K SER* 3.8 4.7 - - - -
59K THR* 3.3 26.2 + - - +
166K ALA* 3.2 19.6 + - + -
167K ILE* 3.6 3.8 - - - +
169K ASP* 1.3 79.2 - - - +
171K GLN* 1.3 56.9 + - - +
173K MET* 3.2 3.5 + - - -
174K ALA* 2.8 33.0 + - - +
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Residues in contact with GLN 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H GLN* 4.2 31.8 - - - +
32H ARG* 4.7 5.7 + - - -
1K ILE* 3.7 29.0 - - + +
25K TYR* 3.3 22.6 + - - +
99K GLU* 5.7 0.2 - - - +
167K ILE 3.1 9.8 + - - +
168K LEU* 3.6 28.1 - - - +
169K ASP 3.3 0.2 - - - -
170K TYR* 1.3 80.2 - - - +
172K LYS* 1.3 62.3 + - - +
174K ALA* 3.1 0.9 + - - +
175K LYS* 2.9 24.8 + - - +
286K ASP* 5.5 0.8 + - - -
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Residues in contact with LYS 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PRO* 5.7 9.7 - - - +
21H GLN* 5.1 10.3 - - - +
145H ALA* 4.5 15.2 + - - +
55K ARG* 5.5 8.5 - - - +
168K LEU* 3.2 16.1 + - - +
169K ASP* 3.6 20.0 + - - +
170K TYR 3.2 0.2 - - - -
171K GLN* 1.3 82.1 - - + +
173K MET* 1.3 64.3 + - + +
174K ALA 3.3 0.3 + - - -
175K LYS* 3.5 18.0 + - - +
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Residues in contact with MET 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K TRP* 3.4 36.0 - - + +
51K PHE* 3.8 22.2 - - + -
52K ASN* 3.3 42.2 - - - +
55K ARG* 3.4 62.8 - - + +
56K SER* 4.0 1.6 - - - -
169K ASP* 3.2 22.1 + - + +
170K TYR 3.2 4.5 + - - +
172K LYS* 1.3 76.0 - - + +
174K ALA* 1.3 60.3 + - - +
176K GLY 5.2 0.7 + - - -
177K LYS* 4.9 3.5 - - - +
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Residues in contact with ALA 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 3.7 24.2 - - + -
50K TRP* 3.5 24.7 - - + -
170K TYR 2.8 16.4 + - - +
171K GLN 3.1 2.7 + - - +
173K MET* 1.3 78.5 - - - +
175K LYS* 1.3 68.7 + - - +
176K GLY 3.3 2.0 - - - -
177K LYS* 2.8 16.6 + - - +
178K ILE* 3.6 20.8 + - + +
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Residues in contact with LYS 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLN* 3.8 28.4 - - - +
23H GLU* 4.5 14.3 + - - -
171K GLN 2.9 11.9 + - - +
172K LYS* 3.5 16.1 + - - +
173K MET 3.5 0.2 - - - -
174K ALA* 1.3 76.4 - - - +
176K GLY* 1.3 61.1 + - - +
178K ILE* 4.5 9.9 + - - +
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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