Contacts of the helix formed by residues 132 - 148 (chain A) in PDB entry 1LTQ
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 PRO 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA 4.4 3.1 - - - +
131A VAL* 1.3 94.3 - - + +
133A ILE* 1.3 67.3 + - - +
134A ASP* 3.6 16.6 - - - +
135A VAL* 3.1 28.7 + - + +
136A LEU 3.1 18.0 + - - -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TRP* 4.8 13.5 - - + -
120A VAL* 5.7 9.0 - - + -
123A ASN* 5.2 2.0 + - - -
131A VAL 3.5 2.3 + - - -
132A PRO* 1.3 71.8 - - - +
134A ASP* 1.3 65.9 + - + +
136A LEU* 3.2 11.6 + - + +
137A ARG* 2.9 54.1 + - - +
280A THR* 6.4 2.2 - - + -
284A GLU* 4.9 4.7 - - - +
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO* 3.6 16.5 - - - +
133A ILE* 1.3 84.5 + - + +
135A VAL* 1.3 73.4 + - - +
137A ARG* 3.6 21.2 + - - +
138A SER* 3.1 21.5 + - - -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL* 3.0 42.0 - - + -
132A PRO* 3.1 24.5 + - + +
134A ASP* 1.3 86.3 - - - +
136A LEU* 1.3 58.9 + - - +
138A SER* 3.2 8.5 + - - -
139A MSE 2.8 38.1 + - + +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A CYS* 4.7 4.7 - - + -
11A PRO* 4.0 36.6 - - + +
116A TRP* 4.0 20.4 - - + -
119A LEU* 4.3 11.0 - - + -
120A VAL* 4.2 29.8 - - + +
123A ASN* 4.2 20.6 - - + +
131A VAL* 3.7 11.4 - - + -
132A PRO 3.1 9.2 + - - +
133A ILE* 3.5 13.9 - - + +
135A VAL* 1.3 82.8 - - - +
137A ARG* 1.3 56.9 + - - +
139A MSE 3.1 6.7 + - - +
140A TYR* 2.9 28.6 + - - +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TRP* 3.4 20.3 - - + -
133A ILE* 2.9 40.8 + - - +
134A ASP* 3.9 24.1 - - - +
135A VAL 3.3 0.2 - - - -
136A LEU* 1.3 75.5 - - - +
138A SER* 1.3 59.2 - - - +
140A TYR* 3.5 3.1 + - - +
141A LYS* 3.1 26.8 + - + +
284A GLU* 2.6 40.9 + - + -
287A ARG* 6.5 0.7 - - - -
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP 3.1 15.2 + - - -
135A VAL* 3.3 12.8 - - - -
136A LEU 3.1 0.4 - - - -
137A ARG* 1.3 78.0 - - - +
139A MSE 1.3 67.6 + - - +
141A LYS* 3.3 12.0 + - - +
142A SER* 3.2 25.6 + - - -
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Residues in contact with MSE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A CYS* 3.5 19.1 - - + -
11A PRO* 3.8 14.1 - - + -
86A THR* 3.9 25.6 - - - +
88A LEU* 3.3 44.3 - - + +
135A VAL* 2.8 25.5 + - + +
136A LEU* 3.1 8.9 + - - +
138A SER* 1.3 81.0 - - - +
140A TYR* 1.3 58.5 + - - +
142A SER* 3.2 7.7 + - - +
143A MSE 2.9 23.4 + - - -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A CYS* 3.5 10.9 - - - -
113A ASP* 5.0 7.4 + - - -
114A VAL 4.0 17.7 + - - -
115A PRO* 5.0 2.1 - - - +
116A TRP* 3.6 40.6 + + + +
119A LEU* 3.7 19.1 - - + -
136A LEU 2.9 15.4 + - - +
137A ARG 3.8 2.9 - - - +
138A SER 3.3 0.2 - - - -
139A MSE 1.3 78.4 - - - +
141A LYS* 1.3 57.3 + - - +
143A MSE 3.3 10.6 + - + +
144A ARG* 2.9 52.4 + - + +
147A LEU* 6.4 0.7 - - + -
149A LEU* 5.2 4.9 - - + +
288A ARG* 3.4 39.6 + - + -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.1 15.4 + - + +
138A SER* 3.5 14.1 - - - +
139A MSE 3.2 0.4 - - - -
140A TYR* 1.3 76.9 - - - +
142A SER* 1.3 62.0 + - - +
144A ARG* 3.3 14.1 + - - +
145A GLU* 3.0 52.1 + - + +
288A ARG* 5.9 3.6 - - + +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.7 34.2 + - - +
90A PRO* 5.7 1.5 - - - +
93A ARG* 5.4 0.3 + - - -
138A SER* 3.2 12.6 + - - -
139A MSE 3.2 13.5 + - - +
141A LYS* 1.3 76.5 - - - +
143A MSE 1.3 60.4 + - - +
145A GLU* 3.1 19.4 + - - +
146A TYR* 2.9 27.5 + - - +
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Residues in contact with MSE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.3 40.6 - - - +
9A GLY* 3.4 9.6 - - - -
10A CYS* 3.9 17.3 - - - +
88A LEU* 3.7 10.5 - - + +
111A VAL* 4.0 5.2 - - + -
112A PHE 3.1 33.7 - - - +
113A ASP* 3.7 13.5 - - - +
114A VAL 5.0 0.9 - - - +
139A MSE 2.9 13.2 + - - +
140A TYR* 3.5 16.4 - - + +
142A SER* 1.3 77.3 - - - +
144A ARG* 1.3 61.2 + - - +
146A TYR* 3.0 13.4 + - - +
147A LEU* 3.0 37.0 + - + +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 2.9 38.8 + - + +
141A LYS* 3.6 12.6 + - - +
142A SER 3.2 0.2 - - - -
143A MSE 1.3 78.1 - - + +
145A GLU* 1.3 58.1 + - + +
147A LEU* 3.4 2.4 + - + -
148A GLY 3.0 6.8 + - - -
149A LEU* 3.0 70.0 + - + +
150A PRO 2.9 27.9 + - - -
151A VAL* 3.7 17.4 - - + +
259A GLU* 4.9 7.5 + - - -
288A ARG* 3.2 50.7 + - - +
289A ILE* 4.1 10.4 - - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PRO* 6.0 1.7 - - - +
141A LYS* 3.0 41.3 + - + +
142A SER* 3.1 21.5 + - - +
144A ARG* 1.3 74.1 - - + +
146A TYR* 1.3 66.6 + - - +
148A GLY* 3.1 13.6 + - - +
149A LEU 5.5 1.6 - - - -
151A VAL* 6.1 5.4 - - + -
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.8 24.0 - - + -
88A LEU* 4.8 0.9 - - + -
93A ARG* 3.8 36.1 - - - +
109A HIS* 2.7 42.9 + + - +
111A VAL* 3.5 32.6 - - + +
142A SER 2.9 12.7 + - - +
143A MSE 3.2 15.7 - - - +
145A GLU* 1.3 78.7 - - - +
147A LEU* 1.3 74.2 + - + +
148A GLY* 3.1 1.4 + - - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.5 16.6 - - + -
113A ASP* 3.3 35.7 - - + +
140A TYR* 6.4 0.4 - - + -
143A MSE 3.0 27.8 + - + +
144A ARG* 3.4 5.1 + - + +
146A TYR* 1.3 91.9 - - + +
148A GLY* 1.3 62.6 + - - +
149A LEU* 3.5 29.6 + - + +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG 3.0 4.0 + - - -
145A GLU* 3.1 15.0 + - - -
146A TYR 3.1 1.5 + - - -
147A LEU* 1.3 79.9 - - - +
149A LEU* 1.3 66.5 + - - +
150A PRO* 3.8 2.4 - - - +
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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