Contacts of the helix formed by residues 161 - 175 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ALA* 4.9 10.5 - - + +
34G ASN* 3.5 24.9 - - - +
82I ARG* 3.0 34.8 - - - +
84I ALA* 5.0 4.3 - - + -
87I TYR* 4.3 14.8 - - + -
91I VAL* 4.2 11.0 - - - -
157J GLY 3.0 3.2 + - - -
158J PHE 3.8 0.2 - - - -
159J GLU 3.4 1.6 - - - -
160J TYR* 1.3 98.4 - - + +
162J GLY* 1.3 72.0 + - - +
163J CYS 3.3 2.5 - - - -
164J SER* 2.7 30.7 + - - +
165J LEU* 3.1 30.0 + - + +
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Residues in contact with GLY 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I TYR* 3.5 36.0 - - - -
58J HIS* 3.8 4.3 - - - +
157J GLY 3.2 10.0 + - - -
158J PHE* 3.7 13.2 - - - -
161J MET* 1.3 77.7 - - - +
163J CYS* 1.3 63.2 + - - +
165J LEU* 3.1 4.1 + - - +
166J ALA* 2.9 22.7 + - - +
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Residues in contact with CYS 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.9 11.2 - - - -
96J GLY* 3.5 9.6 - - - +
97J CYS* 3.1 48.7 - - + -
106J SER* 5.2 2.0 - - - -
158J PHE* 2.7 58.2 + - + +
159J GLU* 5.1 1.8 - - - -
162J GLY* 1.3 72.2 - - - -
164J SER* 1.3 58.8 + - - +
166J ALA* 2.9 2.8 + - - +
167J ILE* 2.8 30.0 + - - +
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Residues in contact with SER 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ARG* 5.6 2.7 - - - -
33G ALA* 4.4 16.8 + - - -
97J CYS* 3.9 16.2 - - - +
99J GLU* 5.4 1.6 - - - +
106J SER* 5.9 2.9 - - - -
158J PHE 4.6 0.2 + - - -
161J MET* 2.7 32.9 + - - +
163J CYS* 1.3 78.4 - - - +
165J LEU* 1.3 61.7 + - - +
167J ILE* 3.2 15.4 - - - +
168J LEU* 3.8 11.3 - - - +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ALA* 3.3 31.2 - - + -
87I TYR* 4.0 6.7 - - + -
91I VAL* 3.6 33.7 - - + -
58J HIS* 3.7 29.7 - - + +
161J MET* 3.1 26.6 + - + +
162J GLY 3.5 5.6 - - - +
163J CYS 3.0 0.8 - - - -
164J SER* 1.3 79.9 + - - +
166J ALA* 1.3 68.5 + - - +
168J LEU* 3.2 26.0 + - + +
169J ASP* 3.8 6.8 + - - +
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Residues in contact with ALA 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 4.2 5.6 - - + -
5J TYR* 5.2 0.2 - - - +
56J SER* 4.5 0.9 - - - +
58J HIS* 3.7 30.7 - - + +
59J THR* 4.3 2.7 - - - +
158J PHE* 4.8 2.7 - - + -
162J GLY 2.9 16.8 + - - +
163J CYS* 3.5 6.1 - - - +
165J LEU* 1.3 74.2 - - - +
167J ILE* 1.3 58.8 + - - +
169J ASP* 2.7 32.4 + - - +
170J TYR* 3.3 27.6 + - + -
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Residues in contact with ILE 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J ILE* 3.8 34.1 - - + +
2J THR* 3.9 6.5 - - - +
3J LEU* 3.8 36.4 - - + +
25J TYR* 4.1 8.7 - - + -
97J CYS* 3.8 26.0 - - - +
98J TYR* 4.5 3.8 - - - -
99J GLU* 4.7 7.6 - - + +
163J CYS 2.8 15.8 + - - +
164J SER* 3.2 21.3 - - - +
166J ALA* 1.3 72.7 - - - +
168J LEU* 1.3 73.2 + - + +
170J TYR* 3.4 5.2 + - - +
171J GLN* 3.1 21.7 + - - +
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Residues in contact with LEU 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ARG* 3.7 54.3 - - + +
33G ALA* 5.9 2.5 - - + +
1J ILE* 4.9 3.1 - - + -
99J GLU* 4.0 9.2 - - - +
164J SER 3.8 15.3 - - - +
165J LEU* 3.2 16.1 + - + +
166J ALA 2.8 5.1 + - - -
167J ILE* 1.3 82.4 - - + +
169J ASP* 1.3 64.9 + - - +
171J GLN* 3.5 19.8 + - - +
172J LYS* 3.2 28.4 + - - +
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Residues in contact with ASP 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ARG 3.6 22.7 - - - +
56J SER* 3.7 18.7 + - - +
57J PRO* 3.6 18.4 - - - +
58J HIS* 4.3 8.7 - - - -
165J LEU 4.0 11.3 - - - +
166J ALA* 2.7 18.6 + - - +
168J LEU* 1.3 71.5 - - - +
170J TYR* 1.3 64.0 + - - +
172J LYS* 3.3 17.2 + - - +
173J MET* 3.2 29.0 + - + +
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Residues in contact with TYR 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.7 25.6 - - + -
5J TYR* 2.7 16.6 + - - -
23J ASP* 2.6 39.5 + - - -
25J TYR* 3.5 31.6 - + + -
30J VAL* 4.0 9.9 - - + -
50J TRP* 3.8 5.8 - + + -
51J PHE* 3.5 35.8 - + - -
56J SER* 3.8 4.5 - - - -
59J THR* 3.3 25.3 + - - +
166J ALA* 3.3 20.0 + - + -
167J ILE 3.6 3.8 - - - +
169J ASP* 1.3 79.1 - - - +
171J GLN* 1.3 63.4 + - - +
173J MET* 3.1 3.9 + - - -
174J ALA* 2.8 26.5 + - - +
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Residues in contact with GLN 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G GLN* 4.0 34.8 + - - +
32G ARG* 4.8 5.9 + - - -
1J ILE* 3.7 30.5 - - + +
25J TYR* 3.3 22.6 + - - +
167J ILE 3.1 10.2 + - - +
168J LEU* 3.5 27.9 - - - +
170J TYR* 1.3 79.7 - - - +
172J LYS* 1.3 63.6 + - + +
174J ALA* 3.1 2.0 + - - +
175J LYS* 3.0 24.7 + - - +
286J ASP* 5.5 0.8 + - - -
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Residues in contact with LYS 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G PRO* 6.2 3.8 - - - -
21G GLN* 6.0 1.8 - - - +
145G ALA* 3.9 21.1 + - - +
55J ARG* 5.5 9.2 - - - +
168J LEU* 3.2 17.2 + - - +
169J ASP* 3.5 19.3 + - - +
170J TYR 3.2 0.2 - - - -
171J GLN* 1.3 80.8 - - - +
173J MET* 1.3 63.9 + - + +
174J ALA 3.3 0.2 + - - -
175J LYS* 3.5 18.5 + - - +
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Residues in contact with MET 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J TRP* 3.4 36.4 - - + +
51J PHE* 3.8 22.2 - - + -
52J ASN* 3.4 43.5 - - - +
55J ARG* 3.4 61.9 - - + +
56J SER* 4.0 1.8 - - - -
169J ASP 3.2 22.1 + - - +
170J TYR 3.1 5.1 + - - +
172J LYS* 1.3 76.6 - - + +
174J ALA* 1.3 58.9 + - - +
176J GLY 5.2 0.5 + - - -
177J LYS* 4.9 3.6 - - - +
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Residues in contact with ALA 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J TYR* 3.7 24.9 - - + -
50J TRP* 3.6 22.7 - - + -
170J TYR 2.8 16.4 + - - +
171J GLN 3.8 2.5 - - - +
173J MET* 1.3 78.2 - - - +
175J LYS* 1.3 69.2 + - - +
176J GLY 3.3 2.2 - - - -
177J LYS* 2.8 16.7 + - - +
178J ILE* 3.6 21.5 + - + +
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Residues in contact with LYS 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G GLN* 4.3 22.6 - - - +
23G GLU* 4.8 10.9 + - - -
171J GLN 3.0 12.8 + - - +
172J LYS* 3.5 16.5 + - - +
174J ALA* 1.3 74.8 - - - +
176J GLY* 1.3 61.7 + - - +
178J ILE* 4.5 9.6 + - - +
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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