Contacts of the helix formed by residues 130 - 143 (chain C) in PDB entry 1LUA
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 GLY 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ALA 4.1 4.0 + - - -
128C GLY 3.3 1.2 - - - -
129C THR* 1.3 81.0 + - - +
131C PRO* 1.3 70.0 - - - +
132C VAL 3.3 3.1 - - - -
133C GLY 3.2 1.9 + - - +
134C MET* 2.9 30.5 + - - +
196C ALA 5.6 0.2 - - - -
2456C NAP 3.5 28.2 + - - -
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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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70C MET* 3.8 34.1 - - + +
97C ASN* 5.8 2.0 - - + +
99C SER* 3.6 23.3 - - - +
130C GLY* 1.3 82.9 - - - +
132C VAL* 1.3 61.7 + - - +
134C MET* 4.0 7.6 - - + +
135C ARG* 3.0 32.5 + - + +
2456C NAP 3.3 26.5 - - - +
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Residues in contact with VAL 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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99C SER* 3.9 28.3 - - - +
102C THR* 4.2 8.3 - - + -
103C ALA* 3.8 5.4 - - + +
131C PRO* 1.3 77.4 - - - +
133C GLY* 1.3 58.9 + - - +
136C SER* 2.9 35.1 + - - +
196C ALA* 4.5 0.2 - - + -
221C TYR* 3.7 44.0 - - + -
2456C NAP 3.1 53.5 + - + +
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Residues in contact with GLY 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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125C VAL* 4.0 9.3 - - - +
127C ALA 4.9 0.2 - - - -
128C GLY* 3.3 21.0 - - - +
130C GLY* 3.2 5.2 + - - -
132C VAL* 1.3 80.7 - - - +
134C MET* 1.3 55.3 + - - +
136C SER* 3.4 3.7 + - - -
137C ALA* 3.0 28.6 + - - +
196C ALA* 3.7 24.2 - - - +
2456C NAP 4.2 0.6 + - - -
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Residues in contact with MET 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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128C GLY 3.4 12.8 - - - +
129C THR 3.5 19.5 - - - +
130C GLY 2.9 20.1 + - - +
131C PRO* 4.0 6.5 - - + +
133C GLY* 1.3 77.9 - - - +
135C ARG* 1.3 66.3 + - + +
137C ALA* 3.4 4.1 + - - +
138C ALA* 3.1 22.9 + - - +
149C LEU* 4.4 1.3 - - + -
160C ALA* 3.6 36.6 - - + +
163C SER* 3.7 22.9 - - - +
164C VAL* 3.6 21.0 - - + +
168C PHE* 5.3 0.4 - - - -
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Residues in contact with ARG 135 (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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70C MET* 4.0 23.0 - - + +
74C GLU* 2.9 30.1 + - - +
94C LEU* 4.0 1.4 - - - +
99C SER* 4.5 10.3 - - - +
100C ASN* 2.9 25.2 + - - +
103C ALA* 3.5 19.3 - - + -
131C PRO* 3.0 22.8 + - + +
134C MET* 1.3 76.6 - - + +
136C SER* 1.3 66.9 + - - +
138C ALA* 3.3 3.9 + - - +
139C LEU* 3.1 28.8 + - + +
167C ARG* 5.2 5.2 - - - +
168C PHE* 3.9 31.0 - - - -
276C ASP* 3.0 30.1 + - - -
277C ALA* 3.7 10.2 - - + +
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Residues in contact with SER 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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103C ALA* 3.5 6.4 - - - +
107C VAL* 3.8 14.8 - - - +
125C VAL* 4.9 5.8 - - - -
132C VAL 2.9 23.1 + - - -
133C GLY* 3.6 7.4 - - - -
134C MET 3.3 0.2 - - - -
135C ARG* 1.3 78.3 - - - +
137C ALA* 1.3 61.8 + - - +
139C LEU 3.3 0.2 + - - -
140C LEU* 3.1 35.4 + - - +
194C PHE* 4.9 4.0 - - - -
221C TYR* 2.7 38.0 + - - -
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Residues in contact with ALA 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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125C VAL* 4.4 9.4 - - + +
133C GLY 3.0 16.3 + - - +
134C MET 3.7 5.6 - - - +
135C ARG 3.3 0.2 - - - -
136C SER* 1.3 76.6 - - - +
138C ALA* 1.3 56.8 + - - +
140C LEU* 3.5 2.7 + - - +
141C ALA* 2.9 30.8 + - - +
147C VAL* 3.9 27.6 - - + +
149C LEU* 4.1 21.8 - - + -
164C VAL* 4.9 1.6 - - + -
172C VAL* 4.0 10.0 - - + +
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Residues in contact with ALA 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 MET 3.1 13.7 + - - +
135C ARG 3.6 8.3 - - - +
136C SER 3.2 0.4 - - - -
137C ALA* 1.3 77.4 - - - +
139C LEU* 1.3 59.0 + - + +
141C ALA* 3.5 4.9 + - - +
142C GLY* 3.0 23.2 + - - -
164C VAL* 3.7 12.0 - - + +
168C PHE* 3.4 48.0 - - + +
170C VAL* 4.5 5.8 - - - +
277C ALA* 6.2 0.2 - - + -
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Residues in contact with LEU 139 (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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100C ASN 5.4 0.4 - - - +
103C ALA* 4.0 9.0 - - + +
104C ALA* 3.7 35.4 - - + +
107C VAL* 4.1 14.8 - - + -
135C ARG* 3.1 17.7 + - + +
136C SER 3.3 3.1 + - - +
138C ALA* 1.3 77.0 - - + +
140C LEU* 1.3 65.0 + - - +
142C GLY* 3.2 3.8 + - - -
143C GLU* 3.1 26.0 + - - +
168C PHE* 5.8 2.0 - - + -
277C ALA* 4.0 26.2 - - + +
278C GLU* 4.6 8.7 - - + -
281C TYR* 3.7 40.2 - - + -
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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
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107C VAL* 4.0 21.1 - - + -
110C VAL* 5.6 2.5 - - + -
111C VAL* 5.1 4.0 - - + -
118C VAL* 5.0 12.1 - - + -
123C ALA* 4.2 17.7 - - + -
125C VAL* 4.1 15.9 - - + -
136C SER 3.1 25.9 + - - +
137C ALA* 3.7 3.8 - - - +
139C LEU* 1.3 75.2 - - - +
141C ALA* 1.3 64.5 + - - +
143C GLU* 3.0 17.2 + - - +
145C ALA* 3.2 22.9 + - + +
147C VAL* 3.9 13.0 - - + -
192C PHE* 5.8 2.2 - - + -
194C PHE* 3.6 41.5 - - + -
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Residues in contact with ALA 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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137C ALA 2.9 18.3 + - - +
138C ALA 3.9 2.5 - - - +
140C LEU* 1.3 75.9 - - - +
142C GLY* 1.3 57.9 + - - +
144C GLY* 2.9 20.8 + - - -
145C ALA 4.0 6.8 - - - +
147C VAL* 3.6 11.1 - - + +
170C VAL* 3.7 30.1 - - + +
171C ASN 4.9 2.5 - - - +
172C VAL* 3.8 16.2 - - + +
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Residues in contact with GLY 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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138C ALA 3.0 15.4 + - - -
139C LEU* 3.2 6.5 + - - -
140C LEU 3.2 0.4 - - - -
141C ALA* 1.3 75.8 - - - +
143C GLU* 1.3 59.4 + - - +
144C GLY 3.2 1.2 + - - -
170C VAL* 4.2 10.0 - - - +
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Residues in contact with GLU 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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111C VAL* 4.1 18.2 - - + +
116C GLY 4.8 4.5 - - - +
117C SER* 5.3 0.5 - - - -
118C VAL* 3.5 18.0 + - + +
119C LYS* 3.7 20.1 + - - +
139C LEU 3.1 15.4 + - - +
140C LEU* 3.0 12.6 + - - +
142C GLY* 1.3 78.2 - - - +
144C GLY* 1.3 60.2 + - - +
145C ALA 3.4 0.2 - - - -
281C TYR* 2.7 35.1 + - + +
285C LYS* 2.8 29.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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