Contacts of the helix formed by residues 132 - 152 (chain A) in PDB entry 1LT8
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 LYS 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A SER* 3.1 28.0 + - - +
128A TYR* 4.4 1.0 + - - +
130A SER* 4.2 26.2 + - - +
131A ALA* 1.3 75.0 - - - +
133A SER* 1.3 72.1 + - - +
136A GLU* 3.1 49.4 - - + +
137A VAL 4.6 0.2 + - - -
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 5.3 0.7 - - - +
128A TYR* 5.3 3.3 - - - -
131A ALA 3.2 8.6 + - - -
132A LYS* 1.3 87.7 + - - +
134A GLU* 1.3 62.0 + - - +
135A THR* 4.5 4.7 - - - -
136A GLU 5.4 0.4 - - - -
137A VAL* 4.3 5.4 + - - +
169A TRP* 3.7 14.4 - - - -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 1.3 77.4 - - - +
135A THR* 1.3 62.1 + - - +
136A GLU 3.4 2.7 - - - -
137A VAL* 3.5 5.6 - - - +
138A LYS* 2.8 51.0 + - + +
169A TRP* 3.3 44.3 + - + -
172A GLU* 4.6 0.7 - - - +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 3.7 3.5 - - - -
134A GLU* 1.3 78.5 - - - +
136A GLU* 1.3 65.6 + - - +
138A LYS* 4.3 6.7 + - - +
139A LYS* 3.2 37.3 + - + +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.8 9.2 - - - +
132A LYS* 3.1 50.0 + - + +
133A SER* 5.4 0.4 - - - -
134A GLU 3.4 0.6 - - - -
135A THR* 1.3 77.9 - - - +
137A VAL* 1.3 61.8 + - - +
139A LYS* 2.9 39.0 + - - +
140A VAL* 3.4 8.7 + - + +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 3.5 28.5 - - + -
127A SER* 4.7 5.3 - - - -
128A TYR* 4.5 7.0 - - + +
132A LYS 4.6 0.8 + - - -
133A SER 4.3 3.4 - - - +
134A GLU 3.5 9.9 - - - +
136A GLU* 1.3 75.4 - - - +
138A LYS* 1.3 65.4 + - + +
140A VAL* 2.6 33.9 + - + +
141A PHE* 2.9 38.4 + - + -
166A GLU* 4.3 6.7 - - + +
169A TRP* 3.1 38.6 - - + -
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 2.8 51.0 + - - +
135A THR* 4.6 6.1 - - - +
136A GLU 3.4 0.6 - - - -
137A VAL* 1.3 86.1 - - + +
139A LYS* 1.3 54.2 + - + +
141A PHE* 3.6 11.0 - - - +
142A LEU* 2.7 36.3 + - - +
169A TRP* 4.0 21.1 - - + +
172A GLU* 3.2 23.2 + - + +
173A THR* 3.8 20.5 - - + +
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.2 32.8 - - + +
136A GLU* 2.9 24.0 + - - +
138A LYS* 1.3 76.0 - - + +
140A VAL* 1.3 54.5 + - + +
142A LEU* 3.6 8.0 - - + +
143A GLN* 2.7 37.9 + - - +
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Residues in contact with VAL 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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79A SER* 3.7 28.7 - - - -
80A GLU 4.1 16.3 + - - +
81A ASP* 5.8 0.9 - - + -
125A THR* 3.9 15.9 - - - +
127A SER* 3.9 21.8 - - - +
136A GLU* 4.0 10.1 - - + +
137A VAL* 2.6 19.3 + - + +
139A LYS* 1.3 70.4 - - + +
141A PHE* 1.3 69.7 + - + +
143A GLN* 3.1 27.8 + - - +
144A GLN* 3.2 10.4 + - - +
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.6 17.9 - - + +
123A SER 3.6 20.9 - - - -
125A THR* 4.5 6.7 - - - -
137A VAL* 2.9 39.5 + - + -
138A LYS* 3.6 13.5 - - - +
140A VAL* 1.3 80.9 - - + +
142A LEU* 1.3 56.9 + - - +
144A GLN* 2.9 11.8 + - - +
145A LEU* 2.8 26.5 + - - +
161A PHE* 3.8 16.2 - + - -
166A GLU* 3.6 21.1 - - + -
169A TRP* 4.3 5.8 - - + -
170A ALA* 3.4 37.7 - - + -
173A THR* 4.0 14.4 - - + -
174A LEU* 4.6 6.4 - - + +
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Residues in contact with LEU 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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138A LYS 2.7 22.2 + - - +
139A LYS* 3.8 8.1 - - + +
141A PHE* 1.3 73.4 - - - +
143A GLN* 1.3 62.6 + - - +
145A LEU* 3.9 25.1 - - + -
146A GLU* 3.0 28.0 + - + +
149A MET* 4.7 9.2 - - + -
173A THR* 3.8 11.1 - - + +
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Residues in contact with GLN 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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80A GLU* 3.4 38.6 - - - +
97A GLN* 4.8 11.0 - - - +
139A LYS* 2.7 21.2 + - - +
140A VAL* 3.1 24.1 + - - +
141A PHE 3.1 0.2 - - - -
142A LEU* 1.3 75.5 - - - +
144A GLN* 1.3 55.9 + - + +
146A GLU* 4.0 19.9 - - - +
147A VAL* 4.6 7.3 + - - +
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.5 22.0 + - - -
78A ALA 3.6 16.1 + - - +
79A SER* 3.2 25.1 + - - -
100A ASN* 2.9 38.0 - - - +
121A GLY 3.8 10.3 + - - -
122A VAL* 3.9 24.8 - - + +
123A SER 5.3 0.9 + - - -
140A VAL 3.2 6.2 + - - +
141A PHE* 2.9 10.1 + - - +
143A GLN* 1.3 75.5 - - + +
145A LEU* 1.3 67.0 + - - +
146A GLU 3.1 2.5 + - - -
147A VAL* 3.2 15.8 + - - +
148A PHE* 3.3 19.7 + - + -
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Residues in contact with LEU 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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122A VAL* 5.3 0.4 - - - +
141A PHE 2.8 14.8 + - - +
142A LEU* 3.2 12.8 + - + +
144A GLN* 1.3 77.0 - - - +
146A GLU* 1.3 63.4 + - - +
148A PHE* 3.2 9.9 + - + +
149A MET* 3.0 61.9 + - + +
156A LEU* 3.6 19.5 - - + -
173A THR* 3.1 35.9 - - + +
174A LEU* 3.5 31.4 - - + +
176A ALA* 4.8 2.5 - - + -
177A SER* 3.9 7.0 - - - +
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Residues in contact with GLU 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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97A GLN* 4.3 17.0 + - - +
142A LEU* 3.0 18.9 + - + +
143A GLN* 4.0 16.2 - - - +
145A LEU* 1.3 78.1 - - - +
147A VAL* 1.3 64.4 + - - +
149A MET* 3.5 10.9 + - - +
150A LYS* 2.7 69.2 + - + +
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Residues in contact with VAL 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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97A GLN* 3.9 32.5 - - + +
100A ASN* 4.1 16.8 - - + +
101A GLU* 3.6 41.1 - - + +
143A GLN 4.7 7.2 - - - +
144A GLN* 3.2 10.1 + - - +
146A GLU* 1.3 78.2 - - + +
148A PHE* 1.3 65.9 + - + +
150A LYS* 3.3 8.2 + - + +
151A LYS* 2.8 46.6 + - + +
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Residues in contact with PHE 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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73A THR* 3.4 23.3 - - + -
75A THR* 3.7 21.3 - - + -
100A ASN* 4.2 14.8 - - + -
104A ALA* 5.0 6.3 - - + -
120A GLY* 3.8 14.4 - - - -
121A GLY 3.6 26.7 - - - -
122A VAL* 4.1 14.8 - - + -
144A GLN* 3.3 23.6 - - + -
145A LEU* 3.2 10.6 + - + +
147A VAL* 1.3 80.9 - - + +
149A MET* 1.3 52.5 + - - +
151A LYS* 3.1 2.9 + - - +
152A ASN 2.6 30.1 + - - -
153A VAL* 3.2 43.4 + - + -
156A LEU* 4.1 12.1 - - + -
174A LEU* 5.3 0.4 - - + -
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Residues in contact with MET 149 (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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142A LEU* 4.7 9.9 - - + -
145A LEU* 3.0 52.1 + - + +
146A GLU* 3.8 7.9 - - - +
148A PHE* 1.3 72.4 - - + +
150A LYS* 1.3 60.2 + - + +
151A LYS 3.0 4.5 - - - -
152A ASN* 2.8 22.1 + - - +
176A ALA* 5.4 2.9 - - + -
177A SER* 3.4 32.3 - - - +
179A LYS* 4.4 11.4 + - - +
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Residues in contact with LYS 150 (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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101A GLU* 5.9 2.7 - - - +
146A GLU* 2.7 53.3 + - + +
147A VAL* 3.8 7.4 - - + +
149A MET* 1.3 76.4 - - + +
151A LYS* 1.3 63.9 + - + +
152A ASN* 5.1 1.1 - - - +
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Residues in contact with LYS 151 (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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101A GLU* 3.7 34.8 + - - +
104A ALA* 3.8 22.0 - - + -
105A ASP* 2.8 37.0 + - - +
108A ARG* 5.3 5.9 + - - +
147A VAL* 2.8 28.6 + - + +
148A PHE* 3.5 7.2 - - - +
149A MET 3.0 0.2 - - - -
150A LYS* 1.3 82.9 - - + +
152A ASN* 1.3 72.2 + - - +
153A VAL* 4.6 4.4 - - + +
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Residues in contact with ASN 152 (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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108A ARG* 3.5 15.6 + - - +
148A PHE 2.6 11.9 + - - -
149A MET 2.8 12.9 + - - +
150A LYS 3.4 1.1 - - - +
151A LYS* 1.3 79.2 - - - +
153A VAL* 1.3 63.5 + - - +
154A ASP* 5.1 0.2 - - - -
179A LYS* 3.6 16.8 + - - +
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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
------------------------------------------------------------
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