Contacts of the helix formed by residues 118 - 138 (chain D) in PDB entry 1JIQ
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 118 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 4.6 1.3 - - + -
102D ALA* 3.9 28.5 - - + -
111D ILE* 2.9 25.9 + - + +
113D VAL* 3.5 33.2 - - + -
116D LYS 4.0 3.6 - - - +
117D ASP* 1.3 75.8 + - - +
119D MET* 1.3 70.2 + - - +
120D PRO* 3.3 2.2 - - - -
121D GLU* 3.1 11.9 + - + +
122D VAL* 3.1 20.2 + - + +
269D TRP* 3.7 29.6 - - + +
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Residues in contact with MET 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ALA* 3.3 41.1 - - - +
105D ASN* 3.5 34.3 - - - +
108D ASN* 3.7 20.9 - - + +
109D THR 3.6 19.5 - - - +
111D ILE* 4.4 3.6 - - - +
117D ASP* 3.0 17.5 + - - +
118D VAL* 1.3 81.6 - - + +
120D PRO* 1.3 61.9 - - + +
122D VAL* 3.6 17.0 - - + +
123D ASN* 2.8 45.0 + - - +
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Residues in contact with PRO 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP* 3.4 31.0 - - + +
118D VAL 3.3 4.3 - - - -
119D MET* 1.3 94.8 - - + +
121D GLU* 1.3 62.2 + - - +
123D ASN* 3.8 4.9 - - + +
124D LYS* 2.9 29.1 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP 5.2 0.6 + - - +
118D VAL* 3.1 11.9 + - + +
120D PRO* 1.3 82.4 - - - +
122D VAL* 1.3 66.8 + - - +
124D LYS* 3.3 31.7 + - - +
125D VAL* 3.1 29.0 + - + +
265D GLU* 5.2 6.2 - - - +
267D TRP* 3.8 28.3 - - + +
269D TRP* 6.2 0.7 - - + -
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ALA 3.8 26.5 - - - +
103D LEU* 3.8 22.4 - - + +
118D VAL* 3.1 18.6 + - + +
119D MET* 3.6 19.1 - - + +
121D GLU* 1.3 76.2 - - - +
123D ASN* 1.3 59.0 + - - +
125D VAL* 3.4 3.5 + - - +
126D LEU* 3.0 37.2 + - + +
267D TRP* 3.6 13.8 - - + -
269D TRP* 3.8 27.4 - - + -
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Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ARG* 5.0 3.8 + - - -
108D ASN* 2.9 36.6 + - - +
119D MET* 2.8 27.3 + - - +
120D PRO* 4.0 4.9 - - + +
122D VAL* 1.3 76.5 - - - +
124D LYS* 1.3 59.8 + - - +
126D LEU* 3.7 20.2 - - - +
127D ASP* 2.9 40.5 + - - +
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Residues in contact with LYS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D PRO 2.9 18.9 + - - +
121D GLU* 3.3 31.1 + - - +
123D ASN* 1.3 75.3 - - - +
125D VAL* 1.3 65.3 + - + +
127D ASP* 3.3 9.1 + - - +
128D LYS* 3.1 23.5 + - + +
265D GLU* 5.5 6.1 - - - -
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLU* 3.1 15.1 + - + +
122D VAL 3.8 6.3 - - - +
124D LYS* 1.3 78.4 - - + +
126D LEU* 1.3 66.1 + - - +
128D LYS* 3.1 10.4 + - + +
129D MET* 2.8 45.5 + - + +
264D PHE* 4.5 5.2 - - + -
265D GLU* 3.5 48.0 - - + +
267D TRP* 3.9 13.5 - - + -
279D ALA* 4.1 12.1 - - + +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LEU 4.1 9.6 - - - +
106D ARG* 3.9 21.8 - - - +
122D VAL* 3.0 30.1 + - + +
123D ASN* 3.7 24.0 - - - +
125D VAL* 1.3 76.2 - - + +
127D ASP* 1.3 61.0 + - - +
129D MET* 3.2 14.6 + - - -
130D LYS 2.8 25.1 + - - -
277D TRP 4.9 5.8 - - - +
278D SER* 5.9 0.9 - - - -
290D PHE* 3.4 26.4 - - + -
293D PHE* 3.9 28.0 - - + -
297D LEU* 3.9 9.2 - - + -
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN* 2.9 26.5 + - - +
124D LYS* 3.6 7.8 - - - +
125D VAL 3.2 0.2 - - - -
126D LEU* 1.3 79.4 - - - +
128D LYS* 1.3 58.1 + - - +
130D LYS* 3.3 12.2 + - - +
131D SER* 3.0 28.1 + - - -
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Residues in contact with LYS 128 (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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124D LYS* 3.1 12.6 + - + +
125D VAL* 3.1 13.4 + - + +
127D ASP* 1.3 77.0 - - - +
129D MET* 1.3 59.2 + - - +
131D SER* 3.2 7.3 + - - -
132D PHE* 2.9 31.0 + - - +
260D PRO 4.0 4.2 + - - -
261D GLN* 2.8 33.9 + - - +
263D MET 2.6 35.1 + - - +
264D PHE* 3.7 22.7 - - + +
265D GLU* 5.9 0.6 + - - -
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Residues in contact with MET 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D VAL* 2.8 26.8 + - + +
126D LEU* 3.4 23.6 - - - +
128D LYS* 1.3 75.9 - - - +
130D LYS* 1.3 57.4 + - - +
132D PHE* 3.2 1.4 + - - +
133D CYS* 2.8 34.9 + - - -
264D PHE* 3.8 25.5 - - + -
278D SER 3.6 18.8 - - - +
279D ALA* 3.7 20.4 - - - +
281D GLY 4.1 0.4 - - - +
282D LEU* 3.7 36.6 - - + +
285D ALA* 4.7 2.5 - - + -
290D PHE* 3.9 9.0 - - + -
293D PHE* 4.0 17.9 - - + -
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Residues in contact with LYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LEU 2.8 13.4 + - - +
127D ASP* 3.5 16.2 - - - +
128D LYS 3.2 0.2 - - - -
129D MET* 1.3 77.9 - - - +
131D SER* 1.3 61.6 + - - +
133D CYS* 3.4 2.1 + - - +
134D GLN* 3.1 24.1 + - + +
290D PHE* 3.5 43.9 - - + +
291D ASP* 5.0 9.8 + - - -
294D GLU* 5.1 7.7 + - - +
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASP 3.0 13.5 + - - -
128D LYS* 3.6 10.1 - - - -
130D LYS* 1.3 76.2 - - - +
132D PHE* 1.3 64.4 + - - +
134D GLN* 3.3 6.8 + - - +
135D ARG* 3.1 38.3 + - - +
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Residues in contact with PHE 132 (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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128D LYS* 2.9 16.4 + - + +
129D MET 3.7 3.1 - - - +
131D SER* 1.3 78.2 - - - +
133D CYS* 1.3 63.4 + - - +
135D ARG* 3.3 11.3 + - - +
136D VAL* 3.1 42.1 + - + +
141D TRP* 3.5 41.1 - + - -
205D LEU* 3.9 18.2 - - + -
244D VAL* 3.7 25.1 - - + -
262D ASN* 4.4 7.0 - - - -
264D PHE* 3.7 25.4 - + + -
282D LEU* 4.1 20.2 - - + -
286D LEU* 3.9 16.4 - - + -
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Residues in contact with CYS 133 (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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129D MET 2.8 26.1 + - - +
130D LYS 3.9 3.1 - - - +
132D PHE* 1.3 71.6 - - - +
134D GLN* 1.3 62.6 + - - +
137D ARG* 2.9 38.8 + - - +
282D LEU* 4.0 10.1 - - - -
285D ALA* 3.4 47.8 - - - +
286D LEU* 3.7 19.7 - - + -
290D PHE* 4.5 12.6 - - + +
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Residues in contact with GLN 134 (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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130D LYS* 3.1 19.3 + - + +
131D SER* 3.6 6.9 - - - +
133D CYS* 1.3 78.6 - - - +
135D ARG* 1.3 72.8 + - - +
137D ARG* 4.9 2.7 - - - +
138D SER* 2.8 50.5 + - - -
140D ASP* 4.3 9.7 + - - +
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Residues in contact with ARG 135 (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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131D SER* 3.1 28.5 + - - +
132D PHE* 3.3 11.9 + - - +
134D GLN* 1.3 87.4 - - - +
136D VAL* 1.3 59.3 + - - +
138D SER* 3.1 5.9 + - - -
140D ASP* 3.0 36.7 + - + +
141D TRP* 3.0 51.8 + - + +
262D ASN* 4.9 6.3 - - - +
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Residues in contact with VAL 136 (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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132D PHE* 3.1 48.6 + - + +
135D ARG* 1.3 77.1 - - - +
137D ARG* 1.3 66.1 + - - +
139D GLY* 3.2 13.0 + - - -
141D TRP* 3.9 20.9 - - + +
148D THR* 5.5 0.3 - - - -
149D ILE* 4.0 39.1 + - + +
179D PRO* 4.8 11.0 - - + -
205D LEU* 4.4 7.6 - - + -
286D LEU* 3.8 17.3 - - + -
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Residues in contact with ARG 137 (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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133D CYS* 2.9 25.9 + - - +
134D GLN* 4.4 2.0 - - - +
136D VAL* 1.3 79.5 - - + +
138D SER* 1.3 65.0 + - - +
139D GLY* 3.3 0.7 + - - -
174D TYR 5.5 1.0 + - - -
176D SER 4.3 13.5 + - - -
177D GLY 4.6 12.0 - - - +
178D GLY* 3.4 15.4 - - - +
179D PRO* 4.2 12.3 - - + -
285D ALA 4.1 3.8 - - - -
286D LEU* 3.0 34.1 + - + +
287D HIS 3.3 17.4 + - - -
288D VAL 4.1 4.6 + - - -
289D GLY* 3.3 32.0 - - - +
290D PHE 5.0 0.4 - - - +
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Residues in contact with SER 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D GLN* 2.8 37.9 + - - -
135D ARG 3.1 7.4 + - - -
137D ARG* 1.3 78.2 - - - +
139D GLY* 1.3 59.9 + - - +
140D ASP* 3.1 25.3 + - - +
148D THR* 5.4 0.2 - - - +
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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