Contacts of the helix formed by residues 121 - 139 (chain P) in PDB entry 3J7Y
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 VAL 121 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640B A 3.8 16.8 - - - +
1641B G 3.2 31.3 + - - +
84P ARG* 5.4 0.4 - - - +
120P ASN* 1.3 72.9 - - - +
122P VAL* 1.3 65.5 + - + +
124P CYS* 3.2 8.0 + - - +
125P GLU* 2.9 27.7 + - - +
155P ASP* 4.6 7.6 - - + -
156P SER* 4.0 23.6 - - - +
159P ARG* 3.6 40.0 - - + +
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Residues in contact with VAL 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236 ALA* 4.5 12.6 - - + +
1276 THR* 3.1 33.4 - - + +
1286 ALA* 3.2 34.3 - - + +
1306 VAL* 6.0 2.2 - - + -
1641B G 5.8 0.9 - - - +
120P ASN* 3.6 15.9 - - - +
121P VAL* 1.3 80.4 - - + +
123P ALA* 1.3 59.2 + - - +
125P GLU* 3.2 11.1 + - + +
126P SER* 2.9 28.4 + - - -
159P ARG* 5.9 2.7 - - - +
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Residues in contact with ALA 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P VAL* 6.1 2.0 - - + -
106P THR* 4.7 16.8 - - + -
120P ASN* 3.4 26.2 + - + +
121P VAL 3.2 0.2 - - - -
122P VAL* 1.3 79.3 - - - +
124P CYS* 1.3 58.2 + - - +
126P SER* 2.5 26.8 + - - +
127P ILE* 2.9 20.5 + - + +
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Residues in contact with CYS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ARG* 3.8 22.0 - - - -
89P VAL* 3.7 36.6 - - + -
120P ASN 3.1 22.7 + - - -
121P VAL 3.2 9.4 + - - +
123P ALA* 1.3 76.7 - - - +
125P GLU* 1.3 55.7 - - - +
127P ILE* 3.2 12.1 + - - +
128P GLY* 2.9 25.8 + - - -
156P SER* 3.9 20.0 - - - +
157P MET* 4.7 5.4 - - + -
160P LEU* 4.5 9.3 - - + +
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Residues in contact with GLU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286 ALA 5.3 0.3 - - - +
1296 SER* 4.1 16.5 + - - +
121P VAL 2.9 13.0 + - - +
122P VAL* 3.3 12.9 - - - +
124P CYS* 1.3 76.1 - - - +
126P SER* 1.3 61.7 + - - +
128P GLY* 3.2 2.6 + - - -
129P ARG* 2.9 48.1 + - - +
159P ARG* 3.9 41.4 - - + +
160P LEU 4.6 5.2 - - - +
162P SER* 4.6 3.5 + - - +
163P ALA* 3.3 24.4 + - - +
166P GLU* 4.3 4.9 - - - +
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Residues in contact with SER 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296 SER 4.5 5.6 - - - -
1306 VAL* 4.4 21.1 - - - -
1326 LEU* 4.7 0.6 - - - +
106P THR* 5.4 0.7 - - - +
111P ILE* 3.9 25.4 - - - +
122P VAL* 2.9 14.5 + - - -
123P ALA* 2.5 24.8 + - - +
125P GLU* 1.3 81.3 + - - +
127P ILE* 1.3 59.3 + - - +
129P ARG* 3.2 7.9 + - - +
130P VAL* 2.9 34.8 + - - +
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Residues in contact with ILE 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89P VAL* 3.1 40.8 - - + +
90P GLU 5.0 0.2 - - - -
91P ALA* 3.9 14.6 - - + -
104P ALA* 3.2 34.3 - - + +
105P SER 4.6 2.0 - - - +
106P THR* 3.5 34.8 - - + +
111P ILE* 4.8 6.1 - - + -
123P ALA* 2.9 21.2 + - + +
124P CYS* 3.4 8.3 - - - +
126P SER* 1.3 84.9 + - - +
128P GLY* 1.3 56.8 + - - +
130P VAL* 3.2 9.6 + - - +
131P LEU* 2.9 27.2 + - - +
160P LEU* 5.9 0.2 - - + -
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Residues in contact with GLY 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P CYS 2.9 10.7 + - - -
125P GLU 3.2 4.2 + - - -
127P ILE* 1.3 77.0 - - - +
129P ARG* 1.3 57.5 + - - +
131P LEU* 3.2 8.0 + - - +
132P ALA* 2.9 25.3 + - - +
160P LEU* 3.3 31.6 - - - -
163P ALA* 3.9 8.3 - - - -
164P MET* 3.4 7.8 - - - +
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Residues in contact with ARG 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1296 SER* 2.8 34.7 + - - -
1306 VAL 4.0 4.0 + - - -
1326 LEU* 3.6 46.6 - - + +
125P GLU* 2.9 36.9 + - - +
126P SER 3.3 9.9 - - - +
128P GLY* 1.3 76.7 - - - +
130P VAL* 1.3 61.5 + - - +
132P ALA* 3.2 8.7 + - - +
133P GLN* 3.1 21.8 + - - +
163P ALA* 3.5 16.2 - - + +
166P GLU* 3.8 21.7 + - + +
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Residues in contact with VAL 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326 LEU* 4.2 16.8 - - + +
1356 VAL* 4.0 29.4 - - + -
104P ALA* 4.2 3.1 - - + -
111P ILE* 4.4 16.8 - - + -
126P SER 2.9 19.8 + - - +
127P ILE* 3.4 9.2 - - - +
129P ARG* 1.3 76.2 - - - +
131P LEU* 1.3 59.2 + - - +
133P GLN* 3.2 12.8 + - - +
134P ARG* 2.9 63.2 + - - +
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Residues in contact with LEU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 4.5 10.5 - - + -
91P ALA* 3.3 38.1 - - + +
92P LEU 4.2 7.0 - - - +
93P VAL* 3.4 18.6 - - + -
102P VAL* 3.8 9.0 - - + -
103P SER 4.7 0.7 - - - -
104P ALA* 4.1 14.3 - - + +
127P ILE 2.9 12.5 + - - +
128P GLY 3.2 9.4 + - - +
130P VAL* 1.3 77.9 - - - +
132P ALA* 1.3 51.5 + - - +
134P ARG* 3.0 8.2 + - - +
135P CYS* 2.6 53.7 + - - -
160P LEU* 4.8 4.7 - - + -
164P MET* 4.0 14.8 - - + -
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Residues in contact with ALA 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P GLY 2.9 12.3 + - - +
129P ARG* 3.3 10.3 - - - +
131P LEU* 1.3 75.4 - - - +
133P GLN* 1.3 56.6 + - - +
135P CYS* 3.2 8.4 + - - +
136P LEU* 2.9 36.0 + - - +
163P ALA 4.0 3.6 - - - +
164P MET* 3.8 26.2 - - - +
167P GLY* 3.7 26.7 - - - -
169P VAL* 4.3 2.7 - - + -
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Residues in contact with GLN 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326 LEU* 5.5 11.7 - - + +
1366 ARG* 3.4 53.6 + - - +
1396 TRP* 5.8 0.2 - - - -
1886 TYR* 5.0 8.3 + - - -
129P ARG 3.1 12.0 + - - +
130P VAL* 3.2 12.9 + - - +
132P ALA* 1.3 75.6 - - - +
134P ARG* 1.3 80.4 + - - +
136P LEU* 3.2 13.7 + - + +
137P GLU* 3.0 29.4 + - - +
167P GLY* 5.3 0.6 - - - -
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Residues in contact with ARG 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396 TRP* 2.9 47.6 - - + +
1476 HIS* 3.3 16.3 + - - +
102P VAL* 3.5 23.2 - - + +
103P SER 2.9 20.1 + - - +
104P ALA* 3.4 12.1 - - - +
105P SER 4.8 1.0 - - - +
108P GLU* 4.3 6.7 + - - +
111P ILE* 5.9 2.6 - - - +
130P VAL* 2.9 45.8 + - - +
131P LEU* 3.3 9.0 - - - +
133P GLN* 1.3 90.4 - - - +
135P CYS* 1.3 56.3 + - - +
137P GLU* 2.9 40.2 - - - +
138P ALA* 2.9 15.9 + - - +
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Residues in contact with CYS 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P VAL* 4.1 4.3 - - - -
102P VAL* 4.6 3.4 - - - -
131P LEU* 2.6 37.1 + - - -
132P ALA 3.3 8.5 - - - +
134P ARG* 1.3 72.5 - - - +
136P LEU* 1.3 52.3 - - - +
138P ALA* 3.2 5.8 + - - -
139P GLY 2.6 32.2 + - - -
140P ILE* 2.9 31.2 + - - +
143P MET* 3.3 35.0 - - - -
164P MET* 3.9 7.4 - - - -
169P VAL* 3.6 8.5 - - + -
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Residues in contact with LEU 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1886 TYR* 5.7 0.4 - - - -
1916 ASN* 4.3 13.2 + - - +
132P ALA 2.9 22.7 + - - +
133P GLN* 3.4 11.4 - - + +
135P CYS* 1.3 74.9 - - - +
137P GLU* 1.3 64.8 + - - +
139P GLY* 3.2 13.0 + - - -
140P ILE 5.6 0.2 - - - +
141P ASN* 5.7 5.4 - - + -
167P GLY* 3.2 25.1 - - - +
168P GLY* 3.5 25.1 - - - +
169P VAL* 3.9 8.1 - - + -
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Residues in contact with GLU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366 ARG* 4.5 5.9 + - - +
1396 TRP* 3.2 31.6 - - - -
1516 LEU* 4.3 7.9 - - - +
1886 TYR* 3.6 33.8 - - + +
1896 CYS* 3.2 51.3 + - - +
1916 ASN* 3.3 18.6 + - - +
133P GLN* 3.0 17.8 + - - +
134P ARG* 2.9 40.8 - - - +
136P LEU* 1.3 79.6 - - - +
138P ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516 LEU* 4.2 16.4 - - + -
1556 TYR* 3.4 15.1 + - + +
1896 CYS 3.8 9.9 - - - -
1906 GLY* 2.8 25.6 - - - +
101P VAL* 5.2 0.2 - - + -
102P VAL* 3.8 23.3 - - + -
134P ARG 2.9 16.1 + - - +
135P CYS 3.6 3.6 - - - +
137P GLU* 1.3 79.6 - - + +
139P GLY* 1.3 55.2 + - - +
140P ILE* 4.1 12.3 - - + -
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Residues in contact with GLY 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1906 GLY 4.2 3.1 - - - -
1916 ASN* 5.2 0.9 - - - -
1926 GLU* 3.4 23.1 - - - +
3206 GLN* 5.1 2.1 + - - -
53P ARG* 3.0 23.2 + - - -
57P LEU* 5.0 1.7 - - - +
135P CYS 2.6 13.1 + - - -
136P LEU* 3.2 11.0 + - - -
138P ALA* 1.3 75.7 - - - +
140P ILE* 1.3 56.0 + - - -
141P ASN* 3.0 16.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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