Contacts of the helix formed by residues 161 - 175 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 4.9 9.2 - - + +
34A ASN* 3.7 17.0 - - - +
82B ARG* 3.2 34.5 - - - +
84B ALA* 4.9 4.3 - - + -
87B TYR* 4.1 12.6 - - + -
91B VAL* 4.0 26.7 - - + -
157D GLY 3.0 3.2 + - - -
158D PHE 3.8 0.2 - - - -
159D GLU 3.4 1.8 - - - -
160D TYR* 1.3 98.7 - - + +
162D GLY* 1.3 70.2 + - - +
163D CYS 3.3 2.7 - - - -
164D SER* 2.7 30.0 + - - +
165D LEU* 3.1 28.7 + - + +
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.5 34.6 - - - -
58D HIS* 3.7 4.6 - - - +
157D GLY 3.2 9.0 + - - -
158D PHE* 3.7 13.0 - - - -
161D MET* 1.3 77.9 - - - +
163D CYS* 1.3 62.7 + - - +
165D LEU* 3.2 4.6 + - - +
166D ALA* 2.9 23.0 + - - +
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Residues in contact with CYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.9 12.6 - - - -
96D GLY* 3.6 4.9 - - - +
97D CYS* 3.2 47.1 - - + -
106D SER* 5.2 2.2 - - - -
158D PHE* 2.8 60.9 + - + +
159D GLU* 5.2 2.5 - - - -
162D GLY* 1.3 71.1 - - - +
164D SER* 1.3 65.3 + - - +
166D ALA* 3.0 2.7 + - - -
167D ILE* 2.9 24.8 + - - +
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 5.6 2.6 - - - -
33A ALA* 4.5 16.4 + - - -
97D CYS* 3.8 17.7 - - - +
99D GLU* 5.4 1.4 - - - +
106D SER* 5.9 3.1 - - - -
158D PHE 4.6 0.2 + - - -
161D MET* 2.7 31.9 + - - +
163D CYS* 1.3 77.3 - - - +
165D LEU* 1.3 61.0 + - - +
167D ILE* 3.2 17.4 - - - +
168D LEU* 3.8 11.1 - - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.6 27.6 - - + -
34A ASN* 5.7 0.2 - - - +
147A SER* 6.0 2.0 - - - +
87B TYR* 4.2 4.3 - - + -
91B VAL* 3.6 32.8 - - + -
58D HIS* 3.7 32.4 - - + +
161D MET* 3.1 26.2 + - + +
162D GLY 3.5 5.6 - - - +
163D CYS 3.0 1.0 - - - -
164D SER* 1.3 81.7 + - - +
166D ALA* 1.3 65.9 + - - +
168D LEU* 3.3 26.4 + - + +
169D ASP* 3.9 7.1 + - - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.2 6.1 - - + -
5D TYR* 5.2 0.2 - - - +
56D SER* 4.5 1.8 - - - +
58D HIS* 3.7 30.9 - - + +
59D THR* 4.3 2.0 - - - +
158D PHE* 4.8 2.2 - - + -
162D GLY 2.9 16.8 + - - +
163D CYS* 3.0 6.0 + - - +
165D LEU* 1.3 75.7 - - - +
167D ILE* 1.3 56.4 + - - +
169D ASP* 2.6 33.3 + - - +
170D TYR* 3.2 27.1 + - + -
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ILE* 3.8 33.7 - - + +
2D THR* 3.9 6.1 - - - -
3D LEU* 3.8 35.5 - - + +
25D TYR* 4.1 8.7 - - + -
97D CYS* 3.8 25.8 - - - +
98D TYR* 4.5 4.3 - - - -
99D GLU* 4.7 8.1 - - + +
163D CYS 2.9 17.1 + - - +
164D SER* 3.2 20.6 - - - +
166D ALA* 1.3 72.5 - - - +
168D LEU* 1.3 69.9 + - + +
170D TYR* 3.4 5.1 + - - +
171D GLN* 3.1 26.0 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.5 54.5 - - + +
1D ILE* 5.0 2.7 - - + -
99D GLU* 4.0 8.7 - - - +
164D SER 3.8 16.6 - - - +
165D LEU* 3.5 16.4 - - + +
166D ALA 2.8 1.2 + - - -
167D ILE* 1.3 85.8 - - + +
169D ASP* 1.3 65.2 + - - +
171D GLN* 3.5 19.1 + - - +
172D LYS* 3.2 28.6 + - - +
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Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ARG 3.6 21.0 - - - +
56D SER* 3.7 18.7 + - - +
57D PRO* 3.6 18.3 - - - +
58D HIS* 4.3 8.7 - - - -
165D LEU 4.1 11.1 - - - +
166D ALA* 2.6 18.2 + - - +
168D LEU* 1.3 73.1 - - - +
170D TYR* 1.3 64.8 + - - +
172D LYS* 3.3 17.5 + - - +
173D MET* 3.2 28.7 + - + +
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Residues in contact with TYR 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.7 27.4 - - + -
5D TYR* 2.8 16.2 + - - -
23D ASP* 2.7 39.2 + - - -
25D TYR* 3.5 31.9 - + + -
30D VAL* 4.0 11.2 - - + -
50D TRP* 3.7 5.0 - + + -
51D PHE* 3.5 34.1 - + - -
56D SER* 3.8 5.4 - - - -
59D THR* 3.3 25.8 + - - +
166D ALA* 3.2 19.2 + - + -
167D ILE 3.6 4.3 - - - +
169D ASP* 1.3 78.5 - - - +
171D GLN* 1.3 57.5 + - - +
173D MET* 3.1 3.2 + - - -
174D ALA* 2.8 33.2 + - - +
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.6 39.8 + - - +
32A ARG* 4.6 5.9 + - - -
1D ILE* 3.8 30.0 - - + +
25D TYR* 3.4 22.6 + - + +
167D ILE 3.1 9.6 + - - +
168D LEU* 3.6 27.4 - - - +
170D TYR* 1.3 79.2 - - - +
172D LYS* 1.3 63.1 + - + +
174D ALA* 3.1 1.1 + - - +
175D LYS* 3.0 24.1 + - - +
286D ASP* 5.5 0.2 + - - -
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 5.7 10.1 - - - -
21A GLN* 5.5 6.5 - - - +
145A ALA* 3.7 26.0 + - - +
55D ARG* 5.5 8.1 - - - +
168D LEU* 3.2 15.7 + - - +
169D ASP* 3.5 19.1 + - - +
170D TYR 3.2 0.8 - - - -
171D GLN* 1.3 82.6 - - + +
173D MET* 1.3 65.0 + - + +
174D ALA 3.3 0.2 + - - -
175D LYS* 3.5 17.9 + - - +
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Residues in contact with MET 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D TRP* 3.4 37.7 - - + +
51D PHE* 3.8 21.8 - - + -
52D ASN* 3.4 40.4 - - - +
55D ARG* 3.4 64.2 - - + +
56D SER* 4.0 1.6 - - - -
169D ASP* 3.2 21.3 + - + +
170D TYR 3.1 4.6 + - - +
172D LYS* 1.3 78.1 - - + +
174D ALA* 1.3 59.5 + - - +
176D GLY 5.2 0.3 + - - -
177D LYS* 4.9 3.5 - - - +
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 3.7 24.0 - - + -
50D TRP* 3.5 24.5 - - + -
170D TYR 2.8 15.7 + - - +
171D GLN 3.1 2.7 + - - +
173D MET* 1.3 77.2 - - - +
175D LYS* 1.3 69.1 + - - +
176D GLY 3.3 1.8 - - - -
177D LYS 2.8 16.5 + - - +
178D ILE* 3.5 22.4 + - + +
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Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 4.0 26.2 - - - +
23A GLU* 3.9 20.6 + - - +
171D GLN 3.0 12.1 + - - +
172D LYS* 3.5 17.0 + - - +
173D MET 3.5 0.2 - - - -
174D ALA* 1.3 74.9 - - - +
176D GLY* 1.3 62.2 + - - +
178D 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