Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 1LL9
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.4 0.3 - - - +
126A LYS* 1.3 85.9 + - - +
128A SER* 1.3 64.5 + - - +
129A SER* 3.2 10.6 + - - -
130A ASP* 2.7 47.3 + - - +
131A LEU* 3.2 12.6 + - - +
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Residues in contact with SER 128 (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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93A TRP* 4.8 6.2 - - - -
127A SER* 1.3 74.7 - - - +
129A SER* 1.3 57.7 + - - +
130A ASP 3.3 0.2 - - - -
131A LEU* 3.4 11.0 + - - +
132A LEU* 3.1 24.4 + - - +
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Residues in contact with SER 129 (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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127A SER* 3.2 13.0 + - - -
128A SER* 1.3 77.0 - - - +
130A ASP* 1.3 70.7 + - - +
131A LEU 3.2 0.4 - - - -
132A LEU* 3.5 10.4 + - - +
133A ARG* 3.1 37.9 + - - +
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Residues in contact with ASP 130 (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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124A GLU 3.5 10.5 - - - +
125A VAL* 3.8 13.7 - - + +
126A LYS* 3.4 26.6 + - - +
127A SER* 2.7 32.7 + - - +
129A SER* 1.3 79.9 + - - +
131A LEU* 1.3 57.7 + - - +
133A ARG* 3.0 28.9 + - - +
134A PHE* 3.0 27.0 + - - +
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Residues in contact with LEU 131 (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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93A TRP* 4.2 11.4 - - + -
121A VAL* 4.1 16.2 - - + -
125A VAL* 3.7 19.7 - - + +
127A SER 3.2 9.2 + - - +
128A SER* 3.6 13.0 - - - +
129A SER 3.2 0.2 - - - -
130A ASP* 1.3 78.6 - - - +
132A LEU* 1.3 65.6 + - - +
134A PHE* 3.2 4.8 + - + +
135A TYR* 3.1 53.5 + - + -
157A LEU* 5.5 1.6 - - + -
215A ALA* 4.2 10.3 - - + -
216A LEU* 4.0 31.4 - - + -
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Residues in contact with LEU 132 (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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93A TRP* 3.8 30.0 - - + +
95A GLU* 3.8 47.8 - - + +
96A LEU* 4.3 6.1 - - + +
128A SER 3.1 17.1 + - - +
129A SER* 3.8 9.6 - - - +
131A LEU* 1.3 76.4 - - - +
133A ARG* 1.3 57.9 + - - +
135A TYR* 3.5 0.9 + - - +
136A GLN* 2.9 45.6 + - + +
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Residues in contact with ARG 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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129A SER* 3.1 33.8 + - - +
130A ASP* 3.0 38.9 + - - +
131A LEU 3.2 0.2 - - - -
132A LEU* 1.3 74.9 - - - +
134A PHE* 1.3 65.7 + - - +
136A GLN* 3.2 5.7 + - - +
137A ASN* 2.9 50.0 + - - +
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Residues in contact with PHE 134 (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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117A LEU* 5.3 0.4 - - + -
118A PRO* 3.3 35.7 - - + -
121A VAL* 4.4 11.4 - - + -
122A PRO* 3.3 38.1 - - + -
125A VAL* 4.3 9.9 - - + -
130A ASP 3.0 14.9 + - - +
131A LEU* 3.4 10.8 - - + +
133A ARG* 1.3 75.7 - - - +
135A TYR* 1.3 100.6 + + - +
137A ASN* 3.9 3.1 - - - +
138A TRP* 3.1 28.4 + + + +
153A SER* 4.0 10.5 - - - -
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Residues in contact with TYR 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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93A TRP* 3.6 15.0 - + + -
96A LEU* 3.7 19.3 - - + -
100A GLN* 3.7 0.5 + - - -
101A TRP* 2.9 45.2 + + + -
117A LEU* 4.0 17.0 - - + -
121A VAL* 4.4 0.9 - - - +
131A LEU* 3.1 45.6 + - + +
132A LEU 4.1 1.1 - - - +
134A PHE* 1.3 97.7 - + - +
136A GLN* 1.3 65.2 + - - +
138A TRP* 3.5 11.2 + - - +
153A SER* 2.6 34.9 + - - -
157A LEU* 3.7 25.2 - - + +
216A LEU* 3.3 20.1 - - + +
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Residues in contact with GLN 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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95A GLU 3.3 14.1 + - - -
96A LEU* 3.4 10.7 - - + +
97A THR* 3.1 29.5 + - - -
98A ALA* 2.9 41.2 + - + +
100A GLN* 2.7 21.7 + - - -
132A LEU* 2.9 39.6 + - + +
133A ARG* 3.7 6.7 - - - +
135A TYR* 1.3 77.6 - - - +
137A ASN* 1.3 64.7 + - - +
139A GLN* 4.5 1.9 + - - -
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Residues in contact with ASN 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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133A ARG* 2.9 38.2 + - - +
134A PHE* 4.3 2.9 - - - +
136A GLN* 1.3 83.3 + - - +
138A TRP* 1.3 64.3 + - - +
139A GLN* 3.4 17.4 + - - +
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Residues in contact with TRP 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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100A GLN* 2.8 32.3 + - + -
101A TRP* 3.7 27.8 - + - -
104A ILE* 3.7 20.9 - - + -
114A ALA* 3.8 17.5 - - + -
115A GLY 3.6 5.2 - - - -
116A GLY 3.2 17.6 + - - -
117A LEU* 3.4 40.4 - - + +
118A PRO* 4.0 15.5 - - + -
134A PHE* 3.1 23.2 + + + +
135A TYR* 3.7 8.1 - - + +
136A GLN 3.4 0.8 - - - -
137A ASN* 1.3 76.5 - - - +
139A GLN* 1.3 72.4 + - - +
140A PRO* 3.5 40.5 - - + +
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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