Contacts of the helix formed by residues 115 - 133 (chain L) in PDB entry 1JH0
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 TYR 115 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241H LEU* 6.0 2.4 - - - +
105L VAL* 4.4 19.7 - - + -
108L CYS* 3.8 27.8 - - + -
109L ARG* 3.6 35.0 + - + +
113L ILE 4.4 7.6 - - - -
114L GLY* 1.3 69.8 - - - -
116L HIS* 1.3 63.3 + - - +
117L ILE 3.4 2.2 - - - -
118L PRO* 3.5 12.8 - - + +
119L PHE* 3.1 28.3 + - + +
2M GLU* 4.1 28.8 + - - -
4M GLN* 5.0 8.4 + - - +
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Residues in contact with HIS 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L GLY* 3.2 24.6 - - - -
115L TYR* 1.3 72.1 + - - +
117L ILE* 1.3 59.9 + - - +
119L PHE* 3.4 8.9 + - - +
120L ALA* 2.9 30.3 + - - +
234L LEU* 4.9 5.5 - - + +
3M TYR 5.4 0.9 - - - -
4M GLN* 2.9 50.1 + - + -
6M ILE* 4.6 7.4 - - + -
221M ALA* 3.2 30.4 - - + +
224M LEU* 3.3 44.2 + - + +
225M ALA* 3.8 2.9 - - + -
228M ARG* 5.2 4.0 - - - -
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Residues in contact with ILE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L GLU* 3.6 15.3 - - - +
108L CYS* 4.5 2.9 - - - -
113L ILE* 3.9 14.1 - - + -
114L GLY 3.8 9.0 - - - +
116L HIS* 1.3 75.3 - - - +
118L PRO* 1.3 66.3 - - + +
120L ALA* 3.0 6.0 + - - +
121L PHE* 3.0 23.4 + - - +
855L BPH 3.7 10.7 - - + +
218M MET* 5.7 0.7 - - - -
221M ALA* 3.8 14.1 - - + +
222M THR* 4.4 12.8 - - + +
225M ALA* 3.8 28.5 - - + -
251M PHE* 3.7 17.9 - - + -
252M TRP* 3.4 36.6 - - + -
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Residues in contact with PRO 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ALA* 3.9 21.4 - - + +
104L GLU* 3.7 21.1 - - + +
105L VAL* 3.9 33.4 - - + +
108L CYS* 4.4 7.4 - - - -
115L TYR* 3.5 22.7 - - + +
117L ILE* 1.3 99.6 - - + +
119L PHE* 1.3 61.5 + - - +
121L PHE* 3.8 4.8 - - + +
122L ALA* 3.3 19.9 + - - +
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Residues in contact with PHE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L TYR* 3.1 22.2 + - + +
116L HIS* 3.5 8.7 - - - +
117L ILE 3.0 0.6 - - - -
118L PRO* 1.3 79.5 - - - +
120L ALA* 1.3 64.8 + - - +
122L ALA* 3.3 20.8 + - + +
123L PHE* 3.6 34.6 - + - -
234L LEU* 6.1 4.3 - - + -
238L LEU* 4.7 12.1 - - + -
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Residues in contact with ALA 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L HIS 2.9 17.3 + - - +
117L ILE 3.0 4.2 + - - +
119L PHE* 1.3 76.9 - - + +
121L PHE* 1.3 62.6 + - - +
123L PHE* 3.3 17.7 + - - +
124L ALA 4.1 0.9 + - - -
234L LEU* 4.0 16.6 - - + -
238L LEU* 3.6 30.0 - - + +
855L BPH 3.6 21.7 - - + +
217M ALA* 4.6 3.1 - - + -
221M ALA* 4.3 5.2 - - + -
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Residues in contact with PHE 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L PHE* 3.3 25.8 - + + -
100L TRP* 3.8 12.6 - + - -
101L ALA* 3.6 23.3 - - + -
104L GLU* 3.9 8.5 - - - +
117L ILE 3.0 13.6 + - - +
118L PRO 3.9 4.3 - - - +
119L PHE 3.2 0.2 - - - -
120L ALA* 1.3 72.8 - - - +
122L ALA* 1.3 63.9 + - - +
123L PHE 2.9 6.5 + - - -
124L ALA* 3.0 13.3 + - + -
125L ILE* 3.1 34.5 + - + +
851L BCL 4.3 10.5 - - + -
855L BPH 3.3 82.1 - + + +
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Residues in contact with ALA 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ALA* 5.9 2.5 - - + -
118L PRO 3.3 10.9 + - - +
119L PHE* 3.3 17.0 + - + +
120L ALA 3.2 0.4 - - - -
121L PHE* 1.3 79.4 - - - +
123L PHE* 1.3 61.3 + - + +
124L ALA 3.4 0.2 - - - -
125L ILE* 3.5 13.7 - - + +
126L LEU* 3.1 27.4 + - - +
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Residues in contact with PHE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L PHE* 3.6 40.6 - + - -
120L ALA 3.3 11.4 + - - +
121L PHE 2.9 1.2 - - - -
122L ALA* 1.3 81.8 - - + +
124L ALA* 1.3 64.1 + - - +
126L LEU* 3.4 17.1 - - + +
127L ALA 3.2 10.7 + - - -
238L LEU* 3.6 52.0 - - + -
241L VAL* 3.2 21.5 - - + +
242L PHE* 4.6 23.1 - + + -
855L BPH 4.3 5.4 - - + -
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Residues in contact with ALA 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L ALA 4.1 0.8 + - - -
121L PHE* 3.0 13.1 + - + +
123L PHE* 1.3 73.1 - - - +
125L ILE* 1.3 67.3 + - - +
126L LEU 3.0 1.3 - - - -
127L ALA* 2.9 19.0 + - - +
128L TYR 3.1 11.1 + - - -
241L VAL* 4.5 1.8 - - - -
851L BCL 3.7 28.4 - - + +
855L BPH 3.7 42.3 - - + +
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Residues in contact with ILE 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L THR* 6.2 1.1 - - + -
97L PHE* 3.2 39.3 - - + +
98L VAL* 4.8 15.3 - - + -
101L ALA* 5.3 2.9 - - + -
121L PHE* 3.1 45.9 + - + +
122L ALA* 3.5 15.5 - - - +
124L ALA* 1.3 77.9 - - - +
126L LEU* 1.3 59.3 + - + +
128L TYR* 3.9 3.2 - - - +
129L LEU* 3.1 39.2 + - + +
851L BCL 3.7 9.9 - - + -
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L ALA 3.1 14.6 + - - +
123L PHE* 3.4 22.2 - - + +
124L ALA 3.0 0.2 - - - -
125L ILE* 1.3 76.6 - - - +
127L ALA* 1.3 66.7 + - - +
129L LEU* 3.2 8.4 + - + +
130L THR* 2.9 31.0 + - - +
134L PHE* 4.5 18.6 - - + -
242L PHE* 5.3 15.7 - - + -
245L ALA* 5.1 10.5 - - + -
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Residues in contact with ALA 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L PHE 3.2 2.8 + - - -
124L ALA 2.9 9.1 + - - +
126L LEU* 1.3 77.8 - - - +
128L TYR* 1.3 65.4 + - - +
130L THR* 3.0 18.7 + - - -
131L LEU* 3.2 10.4 + - - +
241L VAL* 3.9 16.8 - - + +
245L ALA* 4.3 16.6 - - + +
851L BCL 3.4 43.2 - - + +
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Residues in contact with TYR 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L THR* 3.9 6.2 + - - -
93L ALA* 3.3 17.7 - - + +
94L THR* 3.6 20.6 - - - -
97L PHE* 3.7 26.2 - + - -
124L ALA 3.1 11.0 + - - +
125L ILE* 3.9 3.6 - - + +
127L ALA* 1.3 78.1 - - - +
129L LEU* 1.3 75.8 + - + +
131L LEU* 2.9 22.5 + - - +
132L VAL* 2.9 43.7 + - + +
146L PHE* 4.1 4.0 - + - -
148L TYR* 3.1 21.1 + - - -
851L BCL 3.5 25.0 - - + +
853L BCL 3.2 35.4 - - + -
855L BPH 4.4 4.5 - - + -
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Residues in contact with LEU 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L THR* 6.1 0.7 - - + -
94L THR* 3.4 35.9 - - + +
98L VAL* 5.9 1.8 - - + -
125L ILE* 3.1 33.1 + - + +
126L LEU* 3.8 7.9 - - + +
128L TYR* 1.3 88.3 - - + +
130L THR* 1.3 58.3 + - - +
132L VAL* 4.3 4.7 - - + -
133L LEU* 3.0 37.8 + - + +
134L PHE* 2.9 44.7 + - + -
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Residues in contact with THR 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L LEU* 2.9 18.5 + - - +
127L ALA 3.0 10.3 + - - -
129L LEU* 1.3 77.7 - - - +
131L LEU* 1.3 77.2 + - + +
134L PHE* 3.5 16.2 + - - -
135L ARG* 3.0 31.4 + - + +
245L ALA* 3.7 37.9 - - - +
248L MET* 4.6 1.1 - - + -
249L ILE* 4.4 25.5 - - + +
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Residues in contact with LEU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L ALA 3.6 10.5 - - - +
128L TYR 2.9 5.1 + - - +
130L THR* 1.3 79.1 - - + +
132L VAL* 1.3 58.6 + - - +
135L ARG* 4.4 7.2 + - - +
136L PRO* 3.2 22.3 - - - +
144L TYR 5.1 0.2 - - - +
145L ALA* 3.8 9.2 - - - +
146L PHE* 3.5 20.0 - - + -
156L TRP* 4.5 9.3 - - + -
248L MET* 4.1 19.1 - - + -
851L BCL 3.7 55.9 - - + +
853L BCL 3.4 36.1 - - + -
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Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L TRP* 3.9 31.0 - - + -
90L THR* 4.1 13.5 - - + +
128L TYR* 2.9 53.6 + - + +
129L LEU* 4.3 8.7 - - + -
131L LEU* 1.3 72.0 - - - +
133L LEU* 1.3 59.2 + - + +
136L PRO* 4.0 6.6 - - - +
142L TRP* 4.0 11.6 - - - -
145L ALA* 4.1 6.3 - - + -
146L PHE* 3.1 37.5 - - + -
148L TYR* 4.1 7.6 - - + +
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Residues in contact with LEU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L THR* 6.2 3.6 - - + -
129L LEU* 3.0 39.9 + - + +
131L LEU 3.4 2.0 - - - -
132L VAL* 1.3 81.8 - - + +
134L PHE* 1.3 88.9 + - + +
135L ARG 3.5 1.3 - - - -
136L PRO* 3.5 2.3 - - - +
137L VAL* 3.1 35.7 + - + +
142L TRP* 4.0 25.1 - - + -
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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