Contacts of the helix formed by residues 117 - 138 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 4.5 2.5 - - + -
101C ALA* 4.3 8.7 - - + -
110C ILE* 2.8 18.0 + - + +
112C VAL* 3.5 37.5 - - + -
115C LYS 4.1 3.4 - - - +
116C ASP* 1.3 76.2 + - - +
118C MET* 1.3 63.7 + - - +
119C PRO* 3.2 4.0 - - - -
120C GLU* 3.1 18.3 + - + +
121C VAL* 3.2 17.0 + - + -
268C TRP* 3.1 44.6 - - + +
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Residues in contact with MET 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ALA* 3.2 38.8 - - - +
102C LEU 5.3 0.2 - - - +
104C ASN* 3.4 36.3 - - - +
107C ASN* 3.7 22.4 - - + +
108C THR 3.5 22.2 - - - +
110C ILE* 4.5 4.9 - - - +
116C ASP* 3.0 13.3 + - - +
117C VAL* 1.3 78.6 - - - +
119C PRO* 1.3 67.3 - - + +
121C VAL* 3.5 15.7 - - + +
122C ASN* 2.9 41.0 + - - +
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Residues in contact with PRO 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASP* 3.2 34.3 - - + +
117C VAL 3.2 5.6 - - - -
118C MET* 1.3 91.0 - - + +
120C GLU* 1.3 64.1 + - + +
122C ASN* 3.6 5.3 + - + +
123C LYS* 3.0 27.8 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LYS* 6.0 5.8 - - - -
116C ASP 5.6 2.9 - - - +
117C VAL* 3.1 10.9 + - + +
119C PRO* 1.3 80.1 - - + +
121C VAL* 1.3 66.1 + - - +
123C LYS* 3.1 34.4 + - - +
124C VAL* 3.1 29.6 + - - +
264C GLU* 4.4 11.4 - - - +
266C TRP* 3.7 27.7 + - + +
268C TRP* 6.2 0.2 - - + -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ALA 3.8 25.4 - - - +
102C LEU* 3.8 23.8 - - + +
117C VAL* 3.2 33.3 + - + +
118C MET* 3.2 18.5 + - + +
120C GLU* 1.3 78.4 - - - +
122C ASN* 1.3 58.7 + - - +
124C VAL* 3.3 3.5 + - - +
125C LEU* 3.1 36.4 + - + +
128C MET* 5.3 0.2 - - - +
266C TRP* 3.7 12.5 - - + -
268C TRP* 3.9 13.5 - - + -
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASN 5.4 0.2 - - - +
105C ARG* 5.1 3.3 + - - -
107C ASN* 2.8 35.7 + - - +
118C MET* 2.9 34.9 + - - +
119C PRO* 4.1 4.1 - - + +
121C VAL* 1.3 72.0 - - - +
123C LYS* 1.3 60.8 + - - +
125C LEU* 3.7 20.2 - - - +
126C ASP* 2.8 41.1 + - - +
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PRO 3.0 18.4 + - - +
120C GLU* 3.1 37.5 + - - +
122C ASN* 1.3 78.1 - - - +
124C VAL* 1.3 63.6 + - + +
126C ASP* 3.4 8.6 + - - +
127C LYS* 3.2 29.5 + - - +
264C GLU* 5.5 5.3 + - - +
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU* 3.1 16.2 + - - +
121C VAL 3.8 4.9 - - - +
123C LYS* 1.3 78.0 - - + +
125C LEU* 1.3 59.4 + - - +
127C LYS* 3.1 13.5 + - + +
128C MET* 2.9 55.0 + - + +
263C PHE* 4.2 9.9 - - + -
264C GLU* 3.3 46.7 - - + +
266C TRP* 3.5 15.0 - - + -
278C ALA* 4.1 7.9 - - + +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU 4.2 7.9 - - - +
105C ARG* 3.9 21.3 - - - +
121C VAL* 3.1 31.1 + - + +
122C ASN* 3.7 27.1 - - + +
124C VAL* 1.3 76.9 - - - +
126C ASP* 1.3 58.6 + - - +
128C MET* 3.1 17.4 + - + +
129C LYS 2.8 24.8 + - - -
276C TRP 5.0 3.8 - - - +
289C PHE* 3.3 26.0 - - + -
292C PHE* 3.9 27.4 - - + -
296C LEU* 4.1 9.2 - - + -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ASN* 2.8 28.4 + - - +
123C LYS* 3.7 7.5 - - - +
125C LEU* 1.3 76.9 - - - +
127C LYS* 1.3 63.8 + - - +
129C LYS* 3.2 12.1 + - - +
130C SER* 2.9 24.6 + - - -
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Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LYS* 3.2 19.3 + - - +
124C VAL* 3.1 16.4 + - - +
126C ASP* 1.3 79.0 - - - +
128C MET* 1.3 57.5 + - - +
130C SER* 3.5 6.5 + - - -
131C PHE* 3.0 27.9 + - - +
134C ARG* 4.4 4.1 + - - +
259C PRO 5.3 1.0 + - - -
260C GLN* 3.7 26.4 + - - +
262C MET 3.4 20.6 + - - +
263C PHE* 3.4 27.2 - - + +
264C GLU* 5.4 9.1 + - - +
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Residues in contact with MET 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C VAL* 2.9 46.4 + - + +
125C LEU* 3.1 28.0 + - + +
127C LYS* 1.3 74.3 - - - +
129C LYS* 1.3 66.0 + - - +
131C PHE* 3.3 1.2 + - - +
132C CYS* 2.9 29.9 + - - -
263C PHE* 3.8 22.4 - - + -
277C SER* 3.9 9.4 - - - +
278C ALA* 3.4 31.6 - - - +
281C LEU* 4.1 20.0 - - + -
284C ALA* 5.5 0.9 - - + -
289C PHE* 3.7 11.0 - - + -
292C PHE* 4.5 9.6 - - - -
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Residues in contact with LYS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU 2.8 8.0 + - - +
126C ASP* 3.5 16.6 - - - +
128C MET* 1.3 77.0 - - - +
130C SER* 1.3 62.4 + - - +
132C CYS* 3.5 1.9 + - - +
133C GLN* 3.1 24.9 + - + +
289C PHE* 3.5 49.7 - - + +
290C ASP* 5.2 7.8 + - - -
293C GLU* 5.3 6.5 + - - +
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP 2.9 16.4 + - - -
127C LYS* 3.7 7.2 - - - -
129C LYS* 1.3 78.4 - - - +
131C PHE* 1.3 61.1 + - - +
133C GLN* 3.5 9.5 + - - +
134C ARG* 2.9 49.4 + - - +
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Residues in contact with PHE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LYS 3.0 17.5 + - - +
128C MET* 3.7 3.8 - - - +
130C SER* 1.3 78.0 - - - +
132C CYS* 1.3 62.9 + - - +
134C ARG* 3.2 18.8 + - - +
135C VAL* 3.0 44.0 + - + +
140C TRP* 3.4 42.8 - + - -
204C LEU* 3.7 22.4 - - + -
243C VAL* 3.5 28.9 - - + -
261C ASN* 4.2 8.3 - - - -
263C PHE* 3.7 20.9 - + + -
281C LEU* 4.1 20.6 - - + -
285C LEU* 4.1 9.0 - - + -
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Residues in contact with CYS 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C MET 2.9 21.9 + - - +
129C LYS 3.9 3.8 - - - +
131C PHE* 1.3 75.9 - - - +
133C GLN* 1.3 56.7 + - - +
136C ARG* 2.6 41.7 + - + +
281C LEU* 3.9 9.0 - - - -
284C ALA* 3.5 38.8 - - - +
285C LEU* 3.7 31.9 - - + -
289C PHE* 4.6 11.9 - - + +
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Residues in contact with GLN 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LYS* 3.1 18.8 + - + +
130C SER* 3.7 8.6 - - - +
131C PHE 3.2 0.2 - - - -
132C CYS* 1.3 77.6 - - - +
134C ARG* 1.3 59.1 + - - +
136C ARG* 4.2 2.6 - - - +
137C SER* 2.7 45.8 + - - -
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Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 4.4 5.7 + - - +
130C SER* 2.9 37.5 + - - +
131C PHE* 3.2 36.8 + - - +
133C GLN* 1.3 84.5 - - - +
135C VAL* 1.3 60.4 + - - +
137C SER* 3.0 8.6 + - - -
139C ASP* 2.9 45.1 + - + +
140C TRP* 3.0 31.0 + - + +
260C GLN* 5.9 2.0 + - - -
261C ASN* 5.2 4.6 + - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PHE* 3.0 53.4 + - + +
134C ARG* 1.3 76.4 - - - +
136C ARG* 1.3 62.9 + - - +
138C GLY* 3.3 12.3 + - - -
140C TRP* 3.8 21.0 - - + +
147C THR* 5.6 0.3 - - - -
148C ILE* 3.9 39.9 + - + +
151C VAL* 5.3 0.4 - - + -
178C PRO* 5.1 10.0 - - + +
204C LEU* 4.3 6.7 - - + -
285C LEU* 3.9 17.9 - - + -
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Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C CYS* 2.6 34.1 + - + +
133C GLN* 4.2 2.2 - - - +
135C VAL* 1.3 73.7 - - - +
137C SER* 1.3 64.2 + - - +
138C GLY* 3.4 0.5 + - - -
173C TYR 5.6 0.4 + - - -
175C SER 4.2 13.5 + - - -
176C GLY* 4.2 18.9 - - - +
177C GLY* 3.3 20.0 - - - +
178C PRO* 4.5 6.7 - - + -
284C ALA 4.2 3.6 - - - -
285C LEU* 2.8 28.0 + - + +
286C HIS 3.0 26.7 + - - -
287C VAL* 3.6 4.6 + - - +
288C GLY* 3.2 29.2 - - - +
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLN* 2.7 33.4 + - - +
134C ARG* 3.0 8.3 + - - -
136C ARG* 1.3 73.4 - - - +
138C GLY* 1.3 61.1 + - - +
139C ASP* 3.1 27.4 + - - +
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ARG 3.1 4.5 + - - -
135C VAL 3.3 8.0 + - - -
136C ARG 3.2 3.6 - - - -
137C SER* 1.3 80.1 + - - +
139C ASP* 1.3 59.2 + - - +
140C TRP 3.2 8.7 - - - +
141C LYS* 2.6 31.7 + - - -
147C THR* 3.6 23.6 - - - +
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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