Contacts of the helix formed by residues 117 - 137 (chain D) in PDB entry 1JLH
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 117 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.5 2.7 - - + -
101D ALA* 4.1 13.7 - - + -
110D ILE* 2.9 15.7 + - + +
112D VAL* 3.5 33.2 - - + -
115D LYS 3.2 2.8 + - - +
116D ASP* 1.3 71.8 - - - +
118D MET* 1.3 67.8 + - - +
119D PRO* 3.3 1.6 - - - -
120D GLU* 3.2 18.5 + - - +
121D VAL* 3.3 15.3 + - + -
268D TRP* 3.2 48.5 - - + +
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Residues in contact with MET 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA* 3.3 40.2 - - - +
102D LEU 5.5 0.2 - - - +
104D ASN* 3.4 45.8 - - - +
107D ASN* 3.6 20.4 - - + +
108D THR 3.7 9.0 - - - +
110D ILE* 4.4 5.2 - - - +
116D ASP* 3.6 14.6 - - - +
117D VAL* 1.3 78.4 - - - +
119D PRO* 1.3 69.3 - - + +
121D VAL* 3.1 16.6 + - + +
122D ASN* 2.9 39.5 + - - +
125D LEU* 6.2 0.2 - - + -
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Residues in contact with PRO 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ASP* 3.3 34.1 - - + +
117D VAL 3.4 4.5 - - - -
118D MET* 1.3 88.9 - - + +
120D GLU* 1.3 65.3 + - + +
122D ASN* 3.4 6.0 + - + +
123D LYS* 2.9 28.3 + - - +
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D LYS* 5.7 9.6 - - - -
116D ASP 5.7 2.2 - - - +
117D VAL* 3.2 10.4 + - + +
118D MET 3.2 0.6 - - - -
119D PRO* 1.3 79.8 - - + +
121D VAL* 1.3 66.7 + - - +
123D LYS* 2.9 35.4 + - - +
124D VAL* 3.0 19.1 + - - +
266D TRP* 3.7 30.4 + - + +
268D TRP* 6.1 0.2 - - + -
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA 3.9 16.8 - - - +
102D LEU* 3.8 23.3 - - + +
117D VAL* 3.3 32.3 + - + +
118D MET* 3.1 18.2 + - + +
120D GLU* 1.3 77.0 - - - +
122D ASN* 1.3 58.8 + - - +
124D VAL* 3.3 4.3 + - - +
125D LEU* 3.0 44.1 + - + +
266D TRP* 3.7 14.8 - - + -
268D TRP* 3.8 14.8 - - + -
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Residues in contact with ASN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 5.3 2.3 + - - -
107D ASN* 2.9 34.3 + - - +
118D MET* 2.9 32.5 + - - +
119D PRO* 3.9 4.6 - - + +
121D VAL* 1.3 74.2 - - - +
123D LYS* 1.3 60.0 + - - +
125D LEU* 3.7 22.0 - - - +
126D ASP* 2.8 40.3 + - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D PRO 2.9 15.1 + - - +
120D GLU* 2.9 31.9 + - - +
122D ASN* 1.3 76.3 - - - +
124D VAL* 1.3 65.3 + - + +
126D ASP* 3.2 11.2 + - + +
127D LYS* 3.1 26.7 + - - +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D GLU* 3.0 17.9 + - - +
121D VAL 3.7 6.5 - - - +
123D LYS* 1.3 76.4 - - + +
125D LEU* 1.3 59.6 + - + +
127D LYS* 3.1 9.4 + - + +
128D MET* 2.9 45.2 + - + +
263D PHE* 4.8 4.0 - - + -
264D GLU* 3.5 41.1 - - + +
266D TRP* 3.7 18.2 - - + -
278D ALA* 4.0 12.6 - - + +
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Residues in contact with LEU 125 (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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102D LEU 4.2 9.4 - - - +
105D ARG* 4.3 17.7 - - - +
121D VAL* 3.0 35.0 + - + +
122D ASN* 3.7 24.0 - - - +
123D LYS 3.3 0.2 - - - -
124D VAL* 1.3 76.9 - - + +
126D ASP* 1.3 58.8 + - - +
128D MET* 3.6 13.1 - - - +
129D LYS* 2.9 30.0 + - - +
276D TRP 4.9 4.9 - - - +
277D SER* 5.9 1.1 - - - -
289D PHE* 3.4 19.5 - - + -
292D PHE* 4.0 26.9 - - + -
296D LEU* 4.1 9.0 - - + -
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Residues in contact with ASP 126 (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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122D ASN* 2.8 26.4 + - - +
123D LYS* 3.4 11.9 - - - +
124D VAL 3.2 0.2 - - - -
125D LEU* 1.3 78.2 - - - +
127D LYS* 1.3 57.5 + - - +
129D LYS* 3.3 12.0 + - - +
130D SER* 3.0 30.9 + - - -
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LYS* 3.1 17.9 + - - +
124D VAL* 3.1 12.8 + - + +
126D ASP* 1.3 76.0 - - - +
128D MET* 1.3 58.2 + - - +
130D SER* 3.5 5.6 + - - -
131D PHE* 3.0 28.5 + - + +
134D ARG* 4.5 4.5 + - - +
259D PRO 4.8 1.8 + - - -
260D GLN* 3.4 33.0 + - - +
262D MET 4.0 18.0 + - - +
263D PHE* 3.5 27.8 - - + -
264D GLU* 5.5 3.6 + - - -
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Residues in contact with MET 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D VAL* 2.9 28.5 + - + +
125D LEU* 3.6 20.9 - - - +
126D ASP 3.2 0.2 - - - -
127D LYS* 1.3 75.0 - - - +
129D LYS* 1.3 60.2 + - - +
131D PHE* 3.3 1.0 + - - +
132D CYS* 2.9 37.3 + - - -
263D PHE* 3.8 23.8 - - + -
277D SER 3.6 20.9 - - - +
278D ALA* 3.7 19.3 - - - +
280D GLY 4.2 0.2 - - - -
281D LEU* 3.7 36.6 - - + +
284D ALA* 4.9 2.5 - - + -
289D PHE* 4.0 7.6 - - + -
292D PHE* 3.9 19.3 - - + -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU 2.9 17.4 + - - +
126D ASP* 3.3 13.4 + - - +
128D MET* 1.3 75.2 - - - +
130D SER* 1.3 63.8 - - - +
132D CYS* 3.5 1.9 + - - +
133D GLN* 3.1 24.5 + - + +
289D PHE* 3.5 44.8 - - + +
290D ASP* 5.2 7.4 + - - -
293D GLU* 4.8 10.7 + - - +
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP 3.0 17.3 + - - -
127D LYS* 3.7 6.5 - - - -
129D LYS* 1.3 78.9 - - - +
131D PHE* 1.3 61.4 + - - +
133D GLN* 3.4 12.9 + - - +
134D ARG* 3.1 45.8 + - - +
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Residues in contact with PHE 131 (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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127D LYS 3.0 17.9 + - - +
128D MET 3.7 2.7 - - - +
130D SER* 1.3 77.2 - - - +
132D CYS* 1.3 65.6 + - - +
134D ARG* 3.3 24.0 + - - +
135D VAL* 3.0 47.6 + - + +
140D TRP* 3.6 37.0 - + - -
204D LEU* 3.7 19.7 - - + -
243D VAL* 3.6 26.2 - - + -
261D ASN* 4.4 5.2 - - - -
263D PHE* 3.6 24.7 - + + -
281D LEU* 4.1 21.8 - - + -
285D LEU* 4.1 11.9 - - + -
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Residues in contact with CYS 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 MET 2.9 24.6 + - - +
129D LYS 3.8 3.8 - - - +
131D PHE* 1.3 75.3 - - - +
133D GLN* 1.3 59.7 + - - +
135D VAL 3.2 0.3 + - - -
136D ARG* 2.6 38.6 + - + +
281D LEU* 3.9 9.0 - - - -
284D ALA* 3.4 40.6 - - - +
285D LEU* 3.7 30.7 - - + -
289D PHE* 4.6 12.1 - - + +
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Residues in contact with GLN 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 LYS* 3.1 15.4 + - + +
130D SER* 3.4 18.8 + - - +
132D CYS* 1.3 76.2 - - - +
134D ARG* 1.3 74.3 + - - +
136D ARG* 3.9 3.6 - - - +
137D SER* 2.9 34.4 + - - +
139D ASP* 5.1 5.4 - - - +
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Residues in contact with ARG 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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127D LYS* 4.5 5.5 + - - +
130D SER* 3.1 28.5 + - - +
131D PHE* 3.3 42.5 + - - +
133D GLN* 1.3 90.0 - - - +
135D VAL* 1.3 60.5 + - - +
137D SER* 3.2 7.5 + - - -
139D ASP* 2.9 47.0 + - + +
140D TRP* 2.9 33.5 + - + +
260D GLN* 5.2 6.7 + - - -
261D ASN* 5.0 6.1 + - - -
263D PHE* 5.8 0.2 - - - -
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Residues in contact with VAL 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 PHE* 3.0 52.2 + - + +
134D ARG* 1.3 77.1 - - - +
136D ARG* 1.3 63.0 + - - +
138D GLY* 3.3 11.6 + - - -
140D TRP* 3.8 20.8 - - + +
147D THR* 5.8 0.2 - - - -
148D ILE* 4.1 37.9 + - + +
151D VAL* 5.0 0.9 - - + -
178D PRO* 4.8 10.7 - - + +
204D LEU* 4.3 8.3 - - + -
285D LEU* 3.8 18.8 - - + -
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D CYS* 2.6 33.9 + - - +
133D GLN* 4.1 3.1 - - - +
135D VAL* 1.3 75.5 - - + +
137D SER* 1.3 59.5 + - - +
138D GLY* 3.2 0.9 + - - -
173D TYR 5.5 0.4 + - - -
175D SER 4.0 15.4 + - - -
176D GLY* 3.8 25.7 + - - +
177D GLY* 3.2 11.3 - - - +
178D PRO* 4.6 8.3 - - + -
284D ALA 4.0 6.5 - - - -
285D LEU* 3.0 27.9 + - + +
286D HIS 2.9 27.5 + - - -
287D VAL 3.7 4.0 + - - -
288D GLY* 3.2 26.8 - - - +
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Residues in contact with SER 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 GLN* 2.9 26.5 + - - -
134D ARG 3.2 1.9 + - - -
136D ARG* 1.3 75.6 - - - +
138D GLY* 1.3 58.9 + - - +
139D ASP* 2.8 36.1 + - - +
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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