Contacts of the helix formed by residues 160 - 179 (chain J) in PDB entry 4UJ3
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 ASN 160 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151J ILE* 3.4 23.8 - - + +
152J GLU* 3.1 26.9 + - - +
153J THR* 3.8 2.0 - - + -
158J SER 3.2 2.2 + - - -
159J THR* 1.3 83.6 - - - +
161J VAL* 1.3 57.5 + - - +
162J GLU* 3.3 2.7 - - - +
163J ALA* 3.8 13.7 - - - +
164J ALA* 2.9 31.0 + - - +
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Residues in contact with VAL 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J LEU* 4.0 17.3 - - + +
30J ARG* 3.6 28.9 - - + -
31J PHE* 4.2 6.5 - - + +
153J THR* 4.2 7.2 - - - -
154J SER 3.5 33.0 - - - +
155J ALA* 3.8 11.0 - - - +
158J SER 3.4 9.3 + - - +
159J THR 2.9 6.1 + - - +
160J ASN* 1.3 76.7 - - - +
162J GLU* 1.3 65.3 + - - +
164J ALA* 3.2 11.6 + - - +
165J PHE* 3.4 34.8 + - + -
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Residues in contact with GLU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J PHE* 3.6 14.3 - - - -
51J ARG* 2.6 46.8 + - - -
158J SER 4.6 2.7 + - - +
160J ASN* 5.8 0.4 - - - +
161J VAL* 1.3 81.2 - - - +
163J ALA* 1.3 62.6 + - - +
164J ALA 3.2 0.2 + - - -
165J PHE* 3.3 2.9 + - - +
166J GLN* 3.0 43.8 + - + +
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Residues in contact with ALA 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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151J ILE* 4.1 12.3 - - + -
160J ASN* 3.4 19.6 + - + +
161J VAL 3.3 0.2 - - - -
162J GLU* 1.3 79.8 - - - +
164J ALA* 1.3 58.2 + - - +
166J GLN* 3.3 7.9 + - - +
167J THR* 2.9 38.0 + - - +
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Residues in contact with ALA 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J LEU* 6.4 0.7 - - + -
88J LEU* 5.3 2.0 - - + -
120J MET* 3.2 39.4 - - + +
122J VAL* 5.2 2.0 - - + -
151J ILE* 3.9 15.5 - - + -
153J THR* 3.9 9.6 - - + -
160J ASN 2.9 18.4 + - - +
161J VAL* 3.4 6.5 - - - +
162J GLU 3.1 0.2 - - - -
163J ALA* 1.3 77.3 - - - +
165J PHE* 1.3 65.7 + - + +
167J THR* 3.3 1.3 + - - -
168J ILE* 3.2 15.4 + - - +
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Residues in contact with PHE 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LEU* 4.9 1.6 - - + -
27J LEU* 3.6 26.9 - - + -
28J LEU* 4.7 1.8 - - - -
31J PHE* 3.2 63.7 - + + -
64J ILE* 3.8 42.0 - - + -
88J LEU* 3.1 33.2 - - + -
161J VAL* 3.4 21.9 + - + -
162J GLU 3.3 2.1 + - - +
164J ALA* 1.3 77.8 - - + +
166J GLN* 1.3 67.6 + - - +
168J ILE* 3.4 8.5 - - + +
169J LEU* 2.9 34.8 + - + +
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Residues in contact with GLN 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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31J PHE* 5.2 2.7 - - + -
51J ARG* 5.2 2.0 - - - +
53J ILE* 3.9 35.9 - - + +
54J GLN 4.6 8.1 + - - +
162J GLU* 3.0 44.8 + - + +
163J ALA* 3.5 7.9 - - - +
165J PHE* 1.3 77.5 - - - +
167J THR* 1.3 58.0 + - - +
169J LEU* 3.9 0.5 - - - +
170J THR* 3.0 41.0 + - + +
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Residues in contact with THR 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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120J MET* 4.5 12.3 - - - -
149J SER* 5.0 1.8 - - - -
151J ILE* 5.8 1.4 - - - +
163J ALA* 2.9 22.6 + - - +
164J ALA* 3.7 5.2 - - - -
165J PHE 3.1 0.2 - - - -
166J GLN* 1.3 74.9 - - - +
168J ILE* 1.3 61.7 + - - +
170J THR* 3.0 8.4 + - - +
171J GLU* 2.9 60.2 + - + +
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Residues in contact with ILE 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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14J VAL* 4.2 10.5 - - + -
86J GLY* 4.1 4.0 - - - -
87J ALA 3.4 41.5 - - - +
88J LEU* 3.7 24.7 - - + -
118J VAL* 3.7 21.5 - - + +
120J MET* 4.2 13.4 - - + +
164J ALA 3.2 10.7 + - - +
165J PHE* 3.4 16.6 - - + +
167J THR* 1.3 80.0 - - - +
169J LEU* 1.3 69.1 + - + +
171J GLU* 4.1 7.1 - - - +
172J ILE* 3.0 38.7 + - + +
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Residues in contact with LEU 169 (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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12J PHE* 3.8 24.7 - - + -
14J VAL* 4.2 22.7 - - + -
31J PHE* 4.5 12.1 - - + -
53J ILE* 3.5 33.9 - - + -
55J VAL* 5.0 2.5 - - + -
60J ILE* 4.5 7.6 - - + +
62J ALA* 3.7 33.7 - - + -
64J ILE* 5.3 1.1 - - + -
165J PHE* 2.9 30.0 + - + +
166J GLN 3.9 3.4 - - - +
168J ILE* 1.3 80.7 - - + +
170J THR* 1.3 58.1 + - - +
172J ILE* 3.3 5.9 + - + +
173J TYR* 3.0 25.3 + - - +
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Residues in contact with THR 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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55J VAL* 3.2 37.2 - - + -
166J GLN* 3.0 27.9 + - + +
167J THR* 3.0 15.9 + - - +
169J LEU* 1.3 74.1 - - - +
171J GLU* 1.3 62.5 + - - +
173J TYR* 3.3 8.6 + - - +
174J ARG* 3.0 42.1 + - - +
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Residues in contact with GLU 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J VAL* 3.7 18.3 - - + +
149J SER* 3.4 30.6 + - - -
167J THR* 2.9 48.4 + - + +
168J ILE* 4.1 5.4 - - - +
170J THR* 1.3 79.4 + - - +
172J ILE* 1.3 59.6 + - - +
174J ARG* 3.6 6.8 + - - +
175J ILE* 3.0 35.5 + - + +
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Residues in contact with ILE 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J PHE* 3.6 20.9 - - + -
14J VAL* 4.2 10.3 - - + -
85J VAL* 3.1 45.8 - - + +
86J GLY* 3.4 18.6 - - - +
118J VAL* 3.3 26.7 - - + -
168J ILE* 3.0 27.2 + - + +
169J LEU* 3.6 6.7 - - - +
170J THR 3.2 0.2 - - - -
171J GLU* 1.3 73.8 - - - +
173J TYR* 1.3 62.0 + - - +
175J ILE* 3.5 3.6 + - - +
176J VAL* 2.9 37.0 + - + +
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Residues in contact with TYR 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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10J TYR* 4.1 31.6 - + - -
12J PHE* 3.7 12.5 - - + -
55J VAL* 3.0 32.1 - - + -
56J ASP* 3.2 39.7 + - + -
58J LYS* 3.5 26.6 - - + +
60J ILE* 4.7 9.2 - - + -
169J LEU 3.0 14.1 + - - +
170J THR* 3.3 10.3 - - - +
172J ILE* 1.3 77.3 - - - +
174J ARG* 1.3 65.5 + - - +
176J VAL* 3.0 3.1 + - - -
177J SER* 2.8 55.8 + - - -
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Residues in contact with ARG 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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55J VAL* 3.9 12.7 - - - +
56J ASP* 3.5 41.6 + - - +
170J THR* 3.0 25.1 + - - +
171J GLU* 3.9 7.4 - - - +
172J ILE 3.4 0.4 - - - -
173J TYR* 1.3 87.3 - - - +
175J ILE* 1.3 63.3 + - + +
177J SER* 3.4 6.6 + - - -
178J GLN* 3.2 24.4 + - - +
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Residues in contact with ILE 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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116J ASN* 5.2 11.9 - - + +
118J VAL* 4.0 21.5 - - + -
171J GLU* 3.0 21.5 + - + +
172J ILE* 3.8 6.1 - - - +
173J TYR 3.2 0.2 - - - -
174J ARG* 1.3 78.3 - - + +
176J VAL* 1.3 63.6 + - + +
178J GLN* 3.8 5.0 + - - +
179J LYS* 3.5 23.4 + - + +
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Residues in contact with VAL 176 (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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10J TYR* 3.6 29.7 + - + -
12J PHE* 4.0 20.6 - - + -
85J VAL* 5.9 4.3 - - + -
172J ILE* 2.9 28.0 - - + +
173J TYR 3.0 5.2 + - - +
175J ILE* 1.3 80.5 - - + +
177J SER* 1.3 64.7 + - - +
178J GLN 3.3 0.2 - - - -
179J LYS* 3.8 16.1 + - - +
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Residues in contact with SER 177 (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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10J TYR* 4.5 7.6 + - - -
173J TYR* 2.8 53.1 + - - -
174J ARG* 3.8 8.4 + - - -
176J VAL* 1.3 73.8 - - - +
178J GLN* 1.3 64.8 + - - +
179J LYS 3.5 5.4 - - - +
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Residues in contact with GLN 178 (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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174J ARG 3.2 14.3 + - - +
175J ILE* 4.0 5.4 - - - +
176J VAL 3.3 0.2 - - - -
177J SER* 1.3 77.2 - - - +
179J LYS* 1.3 68.3 + - - +
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Residues in contact with LYS 179 (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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175J ILE* 3.5 16.4 + - + +
176J VAL* 3.8 11.9 + - - +
177J SER 3.5 7.8 - - - +
178J GLN* 1.3 88.4 - - - +
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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
------------------------------------------------------------
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