Contacts of the helix formed by residues 161 - 175 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 3.3 33.7 - - - +
84A ALA* 5.0 4.0 - - + -
87A TYR* 4.1 17.7 - - + -
91A VAL* 4.2 17.3 - - + -
33C ALA* 4.8 10.1 - - + +
34C ASN* 3.7 17.5 - - - +
157F GLY 3.0 3.2 + - - -
158F PHE 3.8 0.4 - - - -
159F GLU 3.4 1.8 - - - -
160F TYR* 1.3 97.6 - - + +
162F GLY* 1.3 69.5 + - - +
163F CYS 3.3 2.2 - - - -
164F SER* 2.8 29.9 + - - +
165F LEU* 3.2 33.8 + - + +
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 3.6 32.9 - - - -
58F HIS* 3.7 4.9 - - - +
157F GLY 3.1 9.6 + - - -
158F PHE* 3.7 13.9 - - - -
161F MET* 1.3 79.2 - - - +
163F CYS* 1.3 62.2 + - - +
165F LEU* 3.2 5.0 + - - +
166F ALA* 2.9 22.9 + - - +
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Residues in contact with CYS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 3.9 11.4 - - - -
96F GLY* 3.6 5.4 - - - +
97F CYS* 3.2 46.9 - - + -
106F SER* 5.2 2.2 - - - -
158F PHE* 2.8 61.5 + - + +
159F GLU* 5.1 1.8 - - - -
162F GLY* 1.3 70.6 - - - +
164F SER* 1.3 58.6 + - - +
166F ALA* 2.9 3.1 + - - +
167F ILE* 2.8 30.1 + - - +
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Residues in contact with SER 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ARG* 5.5 3.8 - - - -
33C ALA* 4.5 15.6 + - - -
97F CYS* 3.8 16.6 - - - +
99F GLU* 5.4 1.6 - - - +
106F SER* 5.9 3.3 - - - -
158F PHE 4.6 0.2 + - - -
161F MET* 2.8 31.7 + - - +
163F CYS* 1.3 78.3 - - - +
165F LEU* 1.3 60.3 + - - +
167F ILE* 3.3 16.8 - - - +
168F LEU* 3.8 11.3 - - - +
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.1 4.7 - - + -
91A VAL* 3.8 22.4 - - + -
33C ALA* 3.5 27.8 - - + -
58F HIS* 3.7 39.5 - - + +
161F MET* 3.2 29.5 + - + +
162F GLY* 3.6 6.5 - - - +
163F CYS 3.0 0.8 - - - -
164F SER* 1.3 80.4 + - - +
166F ALA* 1.3 67.2 + - - +
168F LEU* 3.3 25.9 + - + +
169F ASP* 3.9 8.0 + - - +
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 4.2 6.1 - - + -
56F SER* 4.5 1.8 - - - +
58F HIS* 3.7 30.3 - - + +
59F THR* 4.4 1.8 - - - +
158F PHE* 4.8 2.5 - - + -
162F GLY 2.9 17.0 + - - +
163F CYS* 3.5 5.8 - - - +
165F LEU* 1.3 73.1 - - - +
167F ILE* 1.3 56.0 + - - +
168F LEU 2.9 2.7 - - - -
169F ASP* 2.7 32.3 + - - +
170F TYR* 3.2 28.3 + - + -
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Residues in contact with ILE 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ILE* 3.8 33.5 - - + +
2F THR* 3.9 5.8 - - - -
3F LEU* 3.8 36.2 - - + +
25F TYR* 4.1 9.1 - - + -
97F CYS* 3.8 25.6 - - - +
98F TYR* 4.5 4.5 - - - -
99F GLU* 4.7 7.9 - - + +
163F CYS 2.8 17.1 + - - +
164F SER* 3.3 21.8 - - - +
166F ALA* 1.3 72.7 - - - +
168F LEU* 1.3 71.8 + - + +
170F TYR* 3.4 5.7 + - - +
171F GLN* 3.1 21.3 + - - +
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 6.3 0.7 - - + -
32C ARG* 3.6 53.8 - - + +
33C ALA* 6.2 0.9 - - + +
1F ILE* 4.9 2.7 - - + -
99F GLU* 4.0 8.5 - - - +
164F SER 3.8 15.9 - - - +
165F LEU* 3.5 16.8 - - + +
166F ALA 2.9 1.0 - - - -
167F ILE* 1.3 85.1 - - + +
169F ASP* 1.3 64.5 + - - +
171F GLN* 3.5 20.3 + - - +
172F LYS* 3.2 28.3 + - - +
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Residues in contact with ASP 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ARG 3.6 21.6 - - - +
56F SER* 3.7 18.5 + - - +
57F PRO* 3.6 17.9 - - - +
58F HIS* 4.3 9.2 - - - -
165F LEU 4.0 10.7 - - - +
166F ALA* 2.7 18.4 + - - +
168F LEU* 1.3 71.3 - - - +
170F TYR* 1.3 64.0 + - - +
172F LYS* 3.3 17.9 + - - +
173F MET* 3.2 28.4 + - + +
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Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 3.7 26.9 - - + -
5F TYR* 2.7 16.2 + - - -
23F ASP* 2.7 38.9 + - - -
25F TYR* 3.6 32.1 - + + -
30F VAL* 4.0 11.4 - - + -
50F TRP* 3.7 5.2 - + + -
51F PHE* 3.5 35.4 - + - -
56F SER* 3.8 4.7 - - - -
59F THR* 3.3 24.8 + - - +
166F ALA* 3.2 27.4 + - + -
167F ILE 3.6 4.3 - - - +
169F ASP* 1.3 79.4 - - - +
171F GLN* 1.3 63.9 + - - +
173F MET* 3.2 3.8 + - - -
174F ALA* 2.8 26.9 + - - +
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Residues in contact with GLN 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 3.6 40.2 + - - +
32C ARG* 4.7 4.9 + - - -
1F ILE* 3.7 28.4 - - + +
25F TYR* 3.3 21.5 + - - +
167F ILE 3.1 10.4 + - - +
168F LEU* 3.6 26.9 - - - +
170F TYR* 1.3 79.3 - - - +
172F LYS* 1.3 63.1 + - + +
174F ALA* 3.2 1.5 + - - +
175F LYS* 2.9 24.5 + - - +
286F ASP* 5.5 0.8 + - - -
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Residues in contact with LYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 5.9 7.4 - - - -
21C GLN* 5.6 5.6 - - - +
145C ALA* 3.9 23.0 + - - +
55F ARG* 5.5 8.5 - - - +
168F LEU* 3.2 13.8 + - - +
169F ASP* 3.5 20.0 + - - +
170F TYR 3.2 0.6 - - - -
171F GLN* 1.3 81.2 - - + +
173F MET* 1.3 64.4 + - + +
174F ALA 3.3 0.2 + - - -
175F LYS* 3.5 18.2 + - - +
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Residues in contact with MET 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F TRP* 3.4 36.4 - - + +
51F PHE* 3.8 21.8 - - + -
52F ASN* 3.4 43.1 - - - +
55F ARG* 3.4 63.5 - - + +
56F SER* 4.0 1.8 - - - -
169F ASP 3.2 22.6 + - - +
170F TYR 3.2 4.7 + - - +
172F LYS* 1.3 77.5 - - + +
174F ALA* 1.3 60.2 + - - +
176F GLY 5.2 0.3 + - - -
177F LYS* 4.9 3.6 + - - +
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Residues in contact with ALA 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F TYR* 3.7 25.1 - - + +
50F TRP* 3.5 23.3 - - + -
170F TYR 2.8 17.2 + - - +
171F GLN 3.8 2.0 - - - +
173F MET* 1.3 78.3 - - - +
175F LYS* 1.3 69.7 + - - +
176F GLY 3.3 1.8 - - - -
177F LYS* 2.8 16.6 + - - +
178F ILE* 3.6 21.5 + - + +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 4.2 24.4 - - - +
23C GLU* 4.0 18.3 + - - -
171F GLN 2.9 13.1 + - - +
172F LYS* 3.5 16.7 + - - +
173F MET 3.5 0.2 - - - -
174F ALA* 1.3 74.5 - - - +
176F GLY* 1.3 61.2 + - - +
178F ILE* 4.5 10.5 + - - +
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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