Contacts of the helix formed by residues 160 - 179 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P ILE* 3.2 27.4 - - + +
152P GLU* 2.8 26.3 + - - +
153P THR* 3.8 4.0 - - + -
158P SER 3.2 2.0 + - - -
159P THR* 1.3 83.7 - - - +
161P VAL* 1.3 56.0 + - - +
162P GLU* 3.3 2.8 - - - +
163P ALA* 3.6 16.1 - - - +
164P ALA* 2.6 36.0 + - - +
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Residues in contact with VAL 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P LEU* 4.0 22.2 - - + +
30P ARG* 3.5 32.8 - - + -
31P PHE* 3.9 22.9 - - + +
153P THR* 4.6 2.9 - - - -
154P SER 3.7 20.6 - - - +
155P ALA* 4.0 8.7 - - - +
158P SER* 3.2 15.2 + - - +
159P THR 2.9 7.4 + - - +
160P ASN* 1.3 79.4 - - - +
162P GLU* 1.3 66.8 + - + +
164P ALA* 3.4 7.2 + - - +
165P PHE* 3.3 27.8 + - + -
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Residues in contact with GLU 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ARG 6.2 0.2 - - - -
31P PHE* 4.2 7.8 - - - -
34P ASN* 5.6 1.9 - - - +
51P ARG* 2.7 44.3 + - - -
158P SER* 4.4 8.3 + - - +
160P ASN* 5.7 0.7 - - - +
161P VAL* 1.3 81.2 - - + +
163P ALA* 1.3 60.8 + - - +
165P PHE* 3.5 2.1 + - - +
166P GLN* 3.0 37.5 + - + +
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Residues in contact with ALA 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P ILE* 4.0 9.9 - - + -
160P ASN* 3.3 23.8 + - - +
162P GLU* 1.3 80.3 - - - +
164P ALA* 1.3 56.8 + - - +
166P GLN* 3.3 6.6 + - - +
167P THR* 2.8 38.0 + - - +
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Residues in contact with ALA 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P LEU* 6.4 0.4 - - + -
88P LEU* 5.7 1.6 - - + -
120P MET* 2.9 38.3 - - + +
122P VAL* 4.9 2.9 - - + -
151P ILE* 3.7 19.7 - - + +
153P THR* 3.8 10.5 - - + -
160P ASN 2.6 21.5 + - - +
161P VAL* 3.8 5.2 - - - +
162P GLU 3.3 0.2 - - - -
163P ALA* 1.3 73.9 - - - +
165P PHE* 1.3 67.9 + - + +
167P THR* 3.4 1.5 + - - -
168P ILE* 3.2 13.5 + - - +
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Residues in contact with PHE 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P VAL* 5.2 4.5 - - + -
16P LEU* 4.4 9.0 - - + -
27P LEU* 3.7 24.0 - - + -
31P PHE* 3.2 57.4 - + + -
62P ALA* 6.2 0.4 - - + -
64P ILE* 3.1 39.5 - - + -
88P LEU* 3.1 32.8 - - + -
161P VAL* 3.3 21.9 + - + +
163P ALA 3.3 0.2 - - - -
164P ALA* 1.3 79.1 - - + +
166P GLN* 1.3 66.3 + - - +
168P ILE* 3.2 9.9 - - + +
169P LEU* 2.9 37.8 + - + +
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Residues in contact with GLN 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P PHE* 5.4 3.5 - - + -
51P ARG* 5.9 2.2 - - - +
53P ILE* 4.4 30.5 - - + +
54P GLN 4.2 15.0 + - - +
55P VAL* 5.8 0.2 - - - +
162P GLU* 3.0 35.1 + - + +
163P ALA* 3.5 8.3 - - - +
165P PHE* 1.3 76.2 - - + +
167P THR* 1.3 61.1 + - - +
169P LEU* 4.0 7.0 - - - +
170P THR* 3.3 35.7 + - - +
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Residues in contact with THR 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P MET* 4.1 13.5 - - - -
149P SER* 5.0 2.5 - - - -
150P PHE 6.1 1.1 - - - +
151P ILE* 5.2 3.8 - - + +
163P ALA* 2.8 26.9 + - - +
164P ALA* 3.5 7.0 - - - -
165P PHE 3.1 0.2 - - - -
166P GLN* 1.3 75.3 - - - +
168P ILE* 1.3 65.0 + - - +
170P THR* 3.1 14.4 + - - -
171P GLU* 3.1 40.5 - - + +
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Residues in contact with ILE 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P VAL* 4.5 6.7 - - + -
86P GLY* 4.4 3.4 - - - -
87P ALA 3.6 29.8 - - - +
88P LEU* 3.3 31.2 - - + -
118P VAL* 3.8 18.2 - - + +
120P MET* 3.7 20.2 - - + +
164P ALA 3.2 11.5 + - - +
165P PHE* 3.2 20.4 - - + +
167P THR* 1.3 82.5 - - - +
169P LEU* 1.3 74.3 + - + +
171P GLU* 3.7 8.7 + - - +
172P ILE* 3.1 31.7 + - + +
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Residues in contact with LEU 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.9 24.3 - - + -
14P VAL* 4.1 22.0 - - + -
31P PHE* 4.9 4.9 - - + -
53P ILE* 3.7 34.3 - - + -
55P VAL* 5.7 0.9 - - - -
60P ILE* 5.2 3.1 - - + +
62P ALA* 3.6 35.2 - - + -
165P PHE* 2.9 37.1 + - + +
166P GLN* 4.0 5.2 - - - +
168P ILE* 1.3 80.0 - - + +
170P THR* 1.3 61.1 + - + +
172P ILE* 3.2 7.3 + - + +
173P TYR* 2.9 25.1 + - - +
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Residues in contact with THR 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ILE* 5.9 0.7 - - + -
55P VAL* 3.6 28.3 - - + -
166P GLN* 3.3 20.2 + - - +
167P THR* 3.1 15.2 + - - -
169P LEU* 1.3 74.1 - - + +
171P GLU* 1.3 65.3 + - - +
173P TYR* 3.1 9.1 + - - +
174P ARG* 3.1 47.4 + - - +
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Residues in contact with GLU 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P VAL* 3.8 17.5 - - + +
149P SER* 2.9 30.4 + - - -
167P THR* 3.1 36.5 - - + +
168P ILE* 3.9 8.1 - - - +
169P LEU 3.3 0.4 - - - -
170P THR* 1.3 79.7 + - - +
172P ILE* 1.3 61.6 + - - +
174P ARG* 3.6 7.4 + - - +
175P ILE* 3.3 28.6 + - + +
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Residues in contact with ILE 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.5 31.6 - - + -
14P VAL* 4.2 12.3 - - + -
85P VAL* 3.3 33.0 - - + +
86P GLY* 3.5 17.5 - - - +
118P VAL* 3.3 26.9 - - + -
168P ILE* 3.1 19.5 - - + +
169P LEU* 3.2 12.9 + - + +
170P THR 3.1 0.4 - - - -
171P GLU* 1.3 75.8 - - - +
173P TYR* 1.3 64.6 + - - +
175P ILE* 3.4 2.6 + - - +
176P VAL* 3.2 27.2 + - + +
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Residues in contact with TYR 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P TYR* 4.1 32.6 + + - -
12P PHE* 3.9 12.3 - + + -
55P VAL* 3.3 23.1 - - + -
56P ASP* 3.3 45.1 + - + +
58P LYS* 4.5 13.0 - - + +
60P ILE* 5.2 8.5 - - + -
169P LEU 2.9 13.2 + - - +
170P THR* 3.1 11.4 + - - +
172P ILE* 1.3 78.6 - - - +
174P ARG* 1.3 72.6 + - - +
176P VAL* 3.8 0.9 - - - +
177P SER* 3.0 43.3 + - - -
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Residues in contact with ARG 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P ASP* 4.2 27.0 + - - +
170P THR* 3.1 31.5 + - - +
171P GLU* 3.8 8.1 - - - +
172P ILE 3.3 0.4 - - - -
173P TYR* 1.3 92.5 - - - +
175P ILE* 1.3 62.3 + - + +
177P SER* 3.1 19.9 + - - -
178P GLN* 3.5 13.7 + - - +
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Residues in contact with ILE 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P ASN* 4.7 15.0 - - + +
118P VAL* 3.9 24.5 - - + -
171P GLU* 3.3 16.0 + - + +
172P ILE* 3.4 5.1 + - - +
173P TYR 3.3 0.2 - - - -
174P ARG* 1.3 78.8 - - + +
176P VAL* 1.3 64.3 + - + +
178P GLN* 4.0 2.4 + - - +
179P LYS* 3.8 20.4 + - - +
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Residues in contact with VAL 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P TYR* 3.9 22.4 - - + -
12P PHE* 3.9 20.4 - - + -
85P VAL* 5.6 7.6 - - + -
172P ILE* 3.2 23.4 + - + +
173P TYR 3.9 2.0 - - - +
175P ILE* 1.3 81.7 - - + +
177P SER* 1.3 63.5 + - - +
179P LYS* 3.9 14.8 + - - +
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Residues in contact with SER 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P TYR* 4.3 13.0 - - - -
173P TYR* 3.0 33.3 + - - -
174P ARG* 3.1 18.5 + - - -
176P VAL* 1.3 76.5 - - - +
178P GLN* 1.3 67.7 + - - +
179P LYS 4.4 2.1 - - - -
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Residues in contact with GLN 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P ARG 3.5 12.4 + - - +
175P ILE* 4.4 3.8 - - - +
176P VAL 3.4 0.2 - - - -
177P SER* 1.3 85.0 + - - +
179P LYS* 1.3 64.6 + - - +
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Residues in contact with LYS 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175P ILE 3.8 14.2 + - - +
176P VAL* 3.9 12.5 + - - +
177P SER 3.5 2.8 - - - +
178P GLN* 1.3 85.1 - - - +
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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
------------------------------------------------------------
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