Contacts of the helix formed by residues 161 - 175 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82H ARG* 3.2 33.9 - - - +
84H ALA* 4.9 4.0 - - + -
87H TYR* 4.1 12.1 - - + -
91H VAL* 4.0 22.4 - - + -
33I ALA* 4.9 9.4 - - + +
34I ASN* 3.7 17.7 - - - +
157L GLY 3.0 3.2 + - - -
158L PHE 4.2 0.2 - - - -
159L GLU 3.4 1.4 - - - -
160L TYR* 1.3 99.5 - - + +
162L GLY* 1.3 71.5 + - - +
163L CYS 3.3 2.0 - - - -
164L SER* 2.8 31.5 + - - +
165L LEU* 3.2 31.4 + - + +
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Residues in contact with GLY 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H TYR* 3.5 34.0 - - - -
58L HIS* 3.8 4.6 - - - +
157L GLY 3.2 9.4 + - - -
158L PHE* 3.7 12.6 - - - -
161L MET* 1.3 78.7 - - - +
163L CYS* 1.3 62.8 + - - +
165L LEU* 3.2 4.6 + - - +
166L ALA* 2.9 22.9 + - - +
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Residues in contact with CYS 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L LEU* 3.9 11.7 - - - -
96L GLY* 3.6 6.1 - - - +
97L CYS* 3.2 46.9 - - + -
106L SER* 5.2 2.0 - - - -
158L PHE* 2.7 62.4 + - + +
159L GLU* 5.1 1.8 - - - -
162L GLY* 1.3 71.0 - - - +
164L SER* 1.3 60.0 + - - +
166L ALA* 2.9 2.8 + - - +
167L ILE* 2.8 29.6 + - - +
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Residues in contact with SER 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I ARG* 5.6 3.6 - - - -
33I ALA* 4.5 16.3 + - - -
97L CYS* 3.9 16.7 - - - +
99L GLU* 5.4 1.4 - - - +
106L SER* 5.9 3.1 - - - -
161L MET* 2.8 32.6 + - - +
163L CYS* 1.3 77.9 - - - +
165L LEU* 1.3 60.2 + - - +
167L ILE* 3.3 17.5 - - - +
168L LEU* 3.8 11.1 - - - +
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Residues in contact with LEU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H TYR* 4.1 4.3 - - + -
91H VAL* 3.7 32.8 - - + -
33I ALA* 3.6 27.1 - - + -
34I ASN* 5.8 0.2 - - - +
58L HIS* 3.7 32.8 - - + +
161L MET* 3.2 27.0 + - + +
162L GLY 3.6 5.6 - - - +
163L CYS 3.0 0.8 - - - -
164L SER* 1.3 80.5 + - - +
166L ALA* 1.3 67.0 + - - +
168L LEU* 3.3 25.9 + - + +
169L ASP* 3.9 7.6 + - - +
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Residues in contact with ALA 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 4.3 6.1 - - + -
5L TYR* 5.2 0.2 - - - +
56L SER* 4.7 0.4 - - - -
58L HIS* 3.7 31.1 - - + +
59L THR* 4.3 2.2 - - - +
158L PHE* 4.8 2.5 - - + -
162L GLY 2.9 16.2 + - - +
163L CYS* 3.5 6.1 - - - +
165L LEU* 1.3 71.8 - - - +
167L ILE* 1.3 57.7 + - - +
168L LEU 2.9 2.5 - - - -
169L ASP* 2.6 33.9 + - - +
170L TYR* 3.2 27.6 + - + -
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Residues in contact with ILE 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L ILE* 3.8 33.4 - - + +
2L THR* 3.9 6.3 - - - -
3L LEU* 3.8 37.3 - - + +
25L TYR* 4.1 9.1 - - + -
97L CYS* 3.8 25.1 - - - +
98L TYR* 4.5 4.0 - - - -
99L GLU* 4.7 7.9 - - + +
163L CYS 2.8 16.3 + - - +
164L SER* 3.3 21.1 - - - +
166L ALA* 1.3 73.1 - - - +
168L LEU* 1.3 72.5 + - + +
170L TYR* 3.4 4.9 + - - +
171L GLN* 3.1 21.3 + - - +
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Residues in contact with LEU 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I PRO* 6.4 0.2 - - + -
32I ARG* 3.7 51.8 - - + +
33I ALA* 6.1 1.6 - - + +
1L ILE* 4.9 2.5 - - + -
99L GLU* 4.0 9.4 - - - +
164L SER 3.8 16.8 - - - +
165L LEU* 3.3 17.0 + - + +
166L ALA 2.8 2.4 + - - -
167L ILE* 1.3 80.6 - - + +
169L ASP* 1.3 63.9 + - - +
171L GLN* 3.5 19.5 + - - +
172L LYS* 3.2 28.9 + - - +
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Residues in contact with ASP 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ARG 3.6 23.2 - - - +
56L SER* 3.7 18.3 + - - +
57L PRO* 3.6 18.4 - - - +
58L HIS* 4.3 8.5 - - - -
165L LEU 4.0 11.0 - - - +
166L ALA* 2.6 18.1 + - - +
168L LEU* 1.3 72.7 - - - +
170L TYR* 1.3 63.3 + - - +
172L LYS* 3.3 18.1 + - - +
173L MET* 3.2 28.0 + - + +
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Residues in contact with TYR 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L LEU* 3.7 26.7 - - + -
5L TYR* 2.7 16.0 + - - -
23L ASP* 2.6 38.4 + - - -
25L TYR* 3.5 32.1 - + + -
30L VAL* 4.0 11.0 - - + -
50L TRP* 3.7 5.8 - + + -
51L PHE* 3.5 36.4 - + - -
56L SER* 3.8 4.7 - - - -
59L THR* 3.3 25.4 + - - +
166L ALA* 3.2 20.5 + - + -
167L ILE 3.6 4.0 - - - +
168L LEU 3.3 0.2 - - - -
169L ASP* 1.3 78.9 - - - +
171L GLN* 1.3 56.6 + - - +
173L MET* 3.2 3.3 + - - -
174L ALA* 2.8 32.6 + - - +
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Residues in contact with GLN 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I GLN* 3.7 38.5 + - - +
32I ARG* 4.8 5.6 + - - +
1L ILE* 3.7 30.9 - - + +
25L TYR* 3.3 21.3 + - - +
167L ILE 3.1 9.8 + - - +
168L LEU* 3.6 27.0 - - - +
170L TYR* 1.3 80.7 - - - +
172L LYS* 1.3 63.4 + - + +
174L ALA* 3.1 0.9 + - - +
175L LYS* 2.9 24.7 + - - +
286L ASP* 5.5 0.6 + - - -
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Residues in contact with LYS 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I PRO* 6.1 4.7 - - - -
21I GLN* 5.9 3.4 - - - +
145I ALA* 4.0 21.3 + - - +
55L ARG* 5.5 8.7 - - - +
168L LEU* 3.2 15.4 + - - +
169L ASP* 3.5 18.9 + - - +
170L TYR 3.2 0.4 - - - -
171L GLN* 1.3 81.0 - - + +
173L MET* 1.3 64.1 + - + +
174L ALA 3.3 0.2 + - - -
175L LYS* 3.5 18.0 + - - +
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Residues in contact with MET 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L TRP* 3.4 36.0 - - + +
51L PHE* 3.8 21.8 - - + -
52L ASN* 3.4 42.8 - - - +
55L ARG* 3.4 64.4 - - + +
56L SER* 4.0 1.3 - - - -
169L ASP 3.2 21.9 + - - +
170L TYR 3.2 5.1 + - - +
172L LYS* 1.3 76.8 - - + +
174L ALA* 1.3 59.4 + - - +
176L GLY 5.2 0.6 + - - -
177L LYS* 4.9 3.6 + - - +
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Residues in contact with ALA 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L TYR* 3.7 24.2 - - + -
50L TRP* 3.5 24.7 - - + -
170L TYR 2.8 16.4 + - - +
171L GLN 3.1 2.7 + - - +
173L MET* 1.3 78.6 - - - +
175L LYS* 1.3 68.9 + - - +
176L GLY 3.3 2.0 - - - -
177L LYS 2.8 16.4 + - - +
178L ILE* 3.6 21.0 + - + +
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Residues in contact with LYS 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I GLN* 4.3 24.4 - - - +
23I GLU* 4.4 15.2 + - - -
171L GLN* 2.9 12.1 + - - +
172L LYS* 3.6 15.9 - - - +
173L MET 3.5 0.6 - - - -
174L ALA* 1.3 74.9 - - - +
176L GLY* 1.3 61.3 + - - +
178L ILE* 4.5 9.8 + - - +
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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