Contacts of the helix formed by residues 130 - 148 (chain C) in PDB entry 5LSW
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 ARG 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 6.1 1.8 - - - -
128C LYS 3.7 1.4 + - - -
129C THR* 1.3 72.2 - - - +
131C PRO* 1.3 71.2 - - + +
133C GLU* 4.0 6.7 - - - +
134C TYR* 2.9 24.8 + - + +
793D ILE* 3.8 45.0 + - + -
798D MET* 5.4 10.9 - - + +
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Residues in contact with PRO 131 (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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82C LEU* 3.6 28.2 - - + +
83C THR* 3.7 13.0 - - - +
84C ALA* 3.6 26.5 - - + +
87C SER* 2.7 30.3 + - - +
129C THR* 3.5 15.3 - - - +
130C ARG* 1.3 94.8 - - + +
132C PHE* 1.3 56.4 + - - +
135C LEU* 3.1 15.1 + - - +
793D ILE* 4.0 4.7 - - + -
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C SER 3.8 4.5 - - - -
77C ILE* 4.1 18.8 - - + -
80C PRO* 3.5 37.5 - - + -
81C THR 4.8 0.2 - - - -
82C LEU* 3.7 38.1 - - + -
125C THR* 3.7 40.4 + - + -
127C SER* 3.6 28.0 - - - +
129C THR* 3.1 26.4 + - + +
131C PRO* 1.3 78.2 - - + +
133C GLU* 1.3 62.2 + - - +
135C LEU* 3.3 7.8 + - + +
136C ARG* 2.8 37.3 + - - +
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Residues in contact with GLU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LYS* 4.8 6.1 - - - +
129C THR 3.0 15.5 + - - +
130C ARG* 4.0 6.5 - - - +
132C PHE* 1.3 76.4 - - - +
134C TYR* 1.3 57.2 + - - +
136C ARG* 3.0 29.9 + - - +
137C LEU* 2.9 61.4 + - + +
175C SER* 2.8 36.9 + - - -
178C SER* 3.5 5.1 + - - -
798D MET* 4.2 11.7 - - + -
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 3.6 12.3 - - - -
88C ASN* 4.4 4.3 + - - -
91C CYS* 3.5 39.9 - - + +
92C ASN* 5.4 3.3 + - - -
130C ARG 2.9 19.5 + - - +
131C PRO 3.9 1.1 - - - +
133C GLU* 1.3 77.5 - - - +
135C LEU* 1.3 58.4 + - - +
138C THR* 2.7 36.5 + - - -
793D ILE* 3.6 24.2 - - + -
797D MET* 3.5 55.3 + - + +
798D MET* 3.9 19.2 - - - +
801D LEU* 3.7 31.0 - - + +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 4.1 0.7 - - + -
77C ILE* 4.0 11.4 - - + -
82C LEU* 3.8 20.9 - - + -
87C SER* 3.7 5.5 + - - +
90C VAL* 3.7 22.4 - - + -
91C CYS* 3.7 7.4 - - - -
94C LEU* 3.7 15.7 - - + -
122C PHE* 3.5 53.6 - - + +
125C THR* 5.6 0.2 - - - +
131C PRO 3.1 18.8 + - - +
132C PHE* 3.3 11.4 + - + +
134C TYR* 1.3 74.7 - - - +
136C ARG* 1.3 57.3 + - - +
138C THR* 3.4 1.4 + - - -
139C SER* 2.7 37.4 + - - -
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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
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122C PHE 3.7 15.7 + - - +
123C LEU* 4.0 15.0 - - + +
125C THR* 3.0 49.5 + - - -
126C VAL* 3.7 4.9 + - - +
127C SER 2.9 30.5 + - - +
128C LYS* 4.4 5.3 - - - +
132C PHE* 2.8 22.5 + - - +
133C GLU* 3.0 35.0 + - - +
135C LEU* 1.3 74.2 - - - +
137C LEU* 1.3 57.6 + - - +
139C SER* 3.3 5.0 + - - -
140C LEU* 2.9 40.7 + - + +
169C ARG* 4.6 8.0 - - - +
170C ILE* 4.8 7.2 - - + -
178C SER* 4.9 7.7 + - - +
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Residues in contact with LEU 137 (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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133C GLU* 2.9 38.5 + - - +
136C ARG* 1.3 77.3 - - - +
138C THR* 1.3 58.5 + - - +
140C LEU* 3.4 7.4 + - + +
141C GLY 3.0 23.0 + - - -
177C LEU* 3.8 20.0 - - + -
178C SER* 3.3 38.1 - - - +
181C VAL* 5.4 0.2 - - + -
798D MET* 3.8 26.7 - - + -
801D LEU* 3.5 20.0 - - + -
805D LEU* 3.7 28.7 - - + +
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Residues in contact with THR 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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91C CYS* 3.4 31.5 - - + +
94C LEU* 3.7 27.6 - - + -
95C ALA* 4.6 5.4 - - + +
98C GLN* 4.9 3.0 - - - +
134C TYR* 2.7 27.8 + - - -
135C LEU 3.8 1.1 - - - -
137C LEU* 1.3 76.0 - - - +
139C SER* 1.3 62.3 + - - +
141C GLY* 3.1 10.0 + - - -
142C VAL* 3.2 15.7 + - + +
801D LEU* 3.6 21.7 - - + +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 3.7 6.5 - - - +
119C LEU* 3.6 25.6 - - - +
122C PHE* 3.5 27.0 - - - +
123C LEU* 4.0 14.8 - - - -
135C LEU 2.7 22.1 + - - -
136C ARG 3.7 4.3 - - - -
138C THR* 1.3 75.2 - - - +
140C LEU* 1.3 65.5 + - - +
142C VAL* 3.1 14.0 + - - +
143C ILE* 3.2 17.7 + - - +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 3.7 21.8 - - + -
136C ARG* 2.9 25.4 + - + +
137C LEU* 3.7 7.2 - - + +
139C SER* 1.3 75.5 - - - +
141C GLY* 1.3 52.5 + - - +
143C ILE* 3.4 5.0 + - - +
144C GLY* 2.7 32.4 + - - -
167C CYS* 5.4 3.4 - - - -
170C ILE* 4.1 20.6 - - + -
178C SER* 3.7 40.6 - - - +
181C VAL* 3.6 19.7 - - + +
182C ALA* 4.4 13.2 - - + +
185C ILE* 4.0 20.9 - - + +
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Residues in contact with GLY 141 (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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98C GLN* 3.7 10.4 - - - +
137C LEU 3.0 11.1 + - - -
138C THR* 3.1 5.6 + - - -
139C SER 3.1 0.8 - - - -
140C LEU* 1.3 74.1 - - - +
142C VAL* 1.3 58.9 + - - +
144C GLY* 4.9 0.4 - - - -
145C ALA* 2.9 31.9 + - - +
181C VAL* 5.0 0.4 - - - -
804D ASN* 5.0 1.1 - - - -
805D LEU* 3.5 25.5 - - - +
808D ILE* 3.5 8.8 - - - +
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Residues in contact with VAL 142 (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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94C LEU* 3.5 32.5 - - + +
97C LEU* 4.4 3.8 - - + -
98C GLN* 3.7 28.0 - - + +
101C ALA* 4.3 3.8 - - + +
110C PHE* 4.3 22.4 - - + -
116C PRO* 6.1 0.4 - - + -
119C LEU* 3.5 24.5 - - + -
138C THR* 3.2 14.3 + - + +
139C SER 3.1 8.1 + - - +
141C GLY* 1.3 77.6 - - - +
143C ILE* 1.3 66.5 + - + +
145C ALA* 3.5 2.4 + - - +
146C LEU* 3.1 21.7 + - + +
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Residues in contact with ILE 143 (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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116C PRO* 3.9 31.4 - - + -
119C LEU* 4.4 14.4 - - + -
120C TYR* 4.4 10.3 - - + +
123C LEU* 4.7 15.9 - - + -
139C SER 3.2 13.8 + - - +
140C LEU* 3.9 2.2 - - - +
142C VAL* 1.3 79.5 - - + +
144C GLY* 1.3 62.7 + - - +
146C LEU* 3.2 10.0 + - + +
147C VAL* 3.1 22.7 + - - +
158C LEU* 4.6 14.8 - - + -
163C ILE* 4.2 12.8 - - + -
185C ILE* 3.7 35.4 - - + -
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Residues in contact with GLY 144 (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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140C LEU 2.7 21.2 + - - -
141C GLY 3.8 1.3 - - - -
143C ILE* 1.3 74.7 - - - +
145C ALA* 1.3 60.6 + - - +
147C VAL* 3.3 11.8 - - - +
148C LYS* 3.1 24.1 + - - +
181C VAL* 4.8 2.9 - - - -
184C PHE* 3.6 7.2 - - - -
185C ILE* 4.1 9.8 - - - +
808D ILE* 3.7 15.7 - - - -
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Residues in contact with ALA 145 (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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98C GLN* 3.6 26.9 - - + +
101C ALA* 5.5 0.2 - - + -
102C SER* 4.3 18.6 - - - -
141C GLY 2.9 18.0 + - - +
142C VAL 3.9 1.8 - - - +
144C GLY* 1.3 75.5 - - - +
146C LEU* 1.3 61.2 + - - +
148C LYS* 3.5 13.4 + - - +
149C THR* 3.4 18.4 - - - +
808D ILE* 4.0 16.2 - - + +
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Residues in contact with LEU 146 (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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101C ALA* 3.6 34.3 - - + +
107C ARG* 4.2 11.9 - - + -
110C PHE* 4.1 13.5 - - + -
111C LEU* 4.0 17.5 - - + -
116C PRO* 3.7 31.0 - - + -
142C VAL* 3.1 14.7 + - + +
143C ILE* 3.4 16.2 - - + +
144C GLY 3.2 0.4 - - - -
145C ALA* 1.3 77.6 - - - +
147C VAL* 1.3 57.2 + - - +
149C THR* 3.1 23.4 + - - +
154C VAL* 3.7 22.3 - - + +
158C LEU* 4.8 10.3 - - + -
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Residues in contact with VAL 147 (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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143C ILE* 3.1 12.5 + - + +
144C GLY* 3.3 19.7 - - - +
146C LEU* 1.3 72.9 - - + +
148C LYS* 1.3 64.0 + - - +
149C THR 3.2 2.8 + - - -
150C ASP* 3.3 11.1 + - - +
151C GLU 5.1 0.2 + - - -
154C VAL* 3.9 12.6 - - + -
155C ILE* 4.3 11.5 - - + +
158C LEU* 3.5 32.5 - - + -
184C PHE* 3.9 4.9 - - + -
185C ILE* 4.3 17.9 - - + +
188C LYS* 3.4 43.3 - - + +
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Residues in contact with LYS 148 (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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234A ARG* 5.1 14.4 - - - +
278A GLN* 6.0 0.4 - - - +
144C GLY 3.1 17.6 + - - +
145C ALA* 3.8 9.2 - - - +
146C LEU 3.3 0.8 - - - -
147C VAL* 1.3 77.7 - - - +
149C THR* 1.3 57.5 + - - +
150C ASP* 2.8 23.4 - - - +
184C PHE* 4.2 14.4 - - + -
188C LYS* 4.6 3.9 + - - +
807D ASP 2.9 26.6 + - - -
808D ILE* 3.3 31.4 + - + +
810D ASP 4.8 5.2 + - - -
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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