Contacts of the helix formed by residues 117 - 133 (chain A) in PDB entry 2LCP
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 THR 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A TYR* 4.9 5.2 - - + +
116A ILE* 1.3 85.8 - - - +
118A ARG* 1.3 70.8 + - - +
119A ASN* 3.5 11.3 + - - +
120A GLU* 3.1 37.5 + - - +
121A MET* 3.0 17.3 + - - +
163A LYS* 5.2 16.2 - - + +
164A LEU 5.0 0.4 - - - +
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Residues in contact with ARG 118 (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 THR* 1.3 76.9 - - - +
119A ASN* 1.3 67.3 + - - +
121A MET* 2.9 22.6 + - + -
122A LEU* 2.8 35.4 + - + +
150A ASP* 5.8 2.1 + - - +
153A PHE* 4.0 15.0 + - - +
154A ALA* 4.4 8.9 - - - +
157A ASP* 2.6 51.3 + - - +
162A GLY 5.4 0.4 + - - -
163A LYS* 4.2 3.4 - - - +
164A LEU* 3.7 34.9 - - - +
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Residues in contact with ASN 119 (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 THR* 3.2 9.6 + - - +
118A ARG* 1.3 79.2 - - - +
120A GLU* 1.3 59.8 + - + +
122A LEU* 3.9 5.6 - - - +
123A ASP* 2.9 30.3 + - - +
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Residues in contact with GLU 120 (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 TYR 4.4 4.3 - - - +
109A ASP* 2.3 35.5 - - - +
110A LEU* 4.9 8.3 - - + +
111A ASP* 2.6 22.5 - - - +
116A ILE* 4.7 3.1 - - + -
117A THR* 3.1 34.4 + - - +
118A ARG 3.1 0.6 - - - -
119A ASN* 1.3 79.8 - - + +
121A MET* 1.3 62.9 + - - +
123A ASP* 3.6 6.0 - - - +
124A ILE* 2.9 31.2 + - + +
601A CA 2.7 12.6 - - - -
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Residues in contact with MET 121 (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 TYR* 3.3 45.3 + - + +
116A ILE* 4.8 5.3 - - + +
117A THR 3.0 12.1 + - - +
118A ARG* 2.9 25.0 + - + +
120A GLU* 1.3 78.4 - - - +
122A LEU* 1.3 66.0 + - + +
124A ILE* 3.8 1.1 - - - +
125A VAL* 2.9 38.7 + - + +
149A VAL* 3.1 44.4 - - + +
150A ASP* 3.3 19.1 - - - +
153A PHE* 4.3 13.5 - - + -
164A LEU* 5.3 3.4 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 2.8 29.1 + - + +
119A ASN* 3.9 5.8 - - - +
121A MET* 1.3 87.3 - - + +
123A ASP* 1.3 63.8 + - - +
125A VAL* 3.6 3.2 - - + +
126A ASP* 2.9 25.6 + - - +
146A GLU* 3.7 35.6 - - + +
149A VAL* 5.3 0.7 - - + -
150A ASP* 3.3 31.4 - - - +
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Residues in contact with ASP 123 (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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63A LYS* 5.3 7.6 + - - -
67A PHE* 3.7 28.6 - - - -
110A LEU* 5.8 2.4 - - - +
119A ASN 2.9 18.8 + - - +
120A GLU* 3.6 7.9 - - - +
122A LEU* 1.3 79.9 - - - +
124A ILE* 1.3 59.7 + - + +
126A ASP* 3.4 6.9 + - - +
127A ALA* 2.9 24.6 + - - +
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Residues in contact with ILE 124 (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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67A PHE* 3.7 33.0 - - + -
107A LEU* 3.3 31.6 - - + +
108A TYR* 3.1 39.7 - - + +
110A LEU* 4.4 17.3 - - + +
120A GLU* 2.9 17.4 + - - +
121A MET* 4.0 2.9 - - - +
123A ASP* 1.3 74.6 - - + +
125A VAL* 1.3 68.1 + - - +
127A ALA* 2.9 5.8 + - + +
128A ILE* 2.9 37.1 + - + +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 4.2 14.8 - - + +
121A MET* 2.9 42.0 + - + +
122A LEU* 3.6 8.3 - - + +
124A ILE* 1.3 76.8 - - - +
126A ASP* 1.3 58.8 + - - +
128A ILE* 3.2 14.5 - - + +
129A TYR* 2.7 34.1 + - + +
144A THR* 4.2 14.1 - - - +
145A PRO 4.7 9.0 - - - +
146A GLU* 3.6 41.5 - - + +
149A VAL* 5.0 1.3 - - + -
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Residues in contact with ASP 126 (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 LEU 2.9 16.3 + - - +
123A ASP* 3.7 7.6 - - - +
125A VAL* 1.3 78.7 - - - +
127A ALA* 1.3 63.2 + - - +
129A TYR* 3.9 8.9 - - - +
130A GLN* 2.9 52.3 + - - +
146A GLU* 5.8 2.9 + - - +
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Residues in contact with ALA 127 (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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63A LYS* 5.1 3.8 - - + -
64A PHE* 3.3 37.3 - - + +
67A PHE* 4.6 13.7 - - + -
123A ASP* 2.9 14.4 + - - +
124A ILE* 2.9 16.3 + - + +
126A ASP* 1.3 78.0 - - - +
128A ILE* 1.3 64.3 + - + +
130A GLN* 3.5 8.9 + - - +
131A MET 3.1 17.0 + - - -
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Residues in contact with ILE 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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64A PHE* 4.9 2.5 - - + -
107A LEU* 4.2 25.1 - - + -
108A TYR* 5.8 5.6 - - + -
124A ILE* 2.9 19.8 + - + +
125A VAL* 3.2 21.5 - - + +
127A ALA* 1.3 76.6 - - + +
129A TYR* 1.3 62.3 + - + +
131A MET* 4.2 15.3 - - + -
132A VAL* 2.6 45.9 + - + +
144A THR* 4.8 7.9 - - - +
183A LEU* 3.5 44.4 - - + -
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Residues in contact with TYR 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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125A VAL* 2.7 24.5 + - + +
126A ASP* 3.6 12.3 - - - +
127A ALA 3.2 0.2 - - - -
128A ILE* 1.3 77.5 - - - +
130A GLN* 1.3 53.4 + - + +
132A VAL* 3.1 5.9 + - + -
133A GLY* 2.5 44.9 + - - -
142A GLU* 2.5 42.4 + - + +
144A THR* 3.3 32.5 - - + -
146A GLU* 4.4 17.7 - - + -
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Residues in contact with GLN 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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58A PHE 4.5 2.8 - - - +
59A GLY* 4.5 9.8 - - - -
61A PRO* 3.0 38.3 - - + +
63A LYS* 5.1 6.4 - - - +
64A PHE* 5.3 1.0 - - + -
126A ASP* 2.9 46.3 + - - +
127A ALA* 3.9 6.8 - - - +
129A TYR* 1.3 76.9 - - + +
131A MET* 1.3 64.0 + - - +
133A GLY* 3.0 15.1 + - - +
134A ASN* 4.7 1.4 - - - +
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Residues in contact with MET 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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52A TYR* 3.3 23.1 - - + +
56A PHE* 3.3 48.8 - - + +
58A PHE* 4.9 1.7 - - - +
59A GLY* 4.6 9.3 + - - -
64A PHE* 2.9 55.1 - - + -
127A ALA 3.1 12.7 + - - +
128A ILE* 3.7 13.7 - - + +
130A GLN* 1.3 80.4 - - - +
132A VAL* 1.3 74.7 + - + +
133A GLY 3.4 1.9 + - - +
136A VAL* 3.7 14.7 - - - +
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Residues in contact with VAL 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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56A PHE* 5.1 4.0 - - + -
128A ILE* 2.6 35.6 + - + +
129A TYR* 3.2 6.5 - - + +
131A MET* 1.3 88.0 - - + +
133A GLY* 1.3 70.6 + - - +
134A ASN 4.3 0.2 - - - +
136A VAL* 3.9 11.2 - - + +
137A GLU 4.7 1.1 - - - +
138A LEU* 3.1 47.6 - - + +
139A PRO* 4.1 9.4 - - + -
144A THR* 6.2 5.8 - - + -
183A LEU* 5.6 11.2 - - + -
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Residues in contact with GLY 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 TYR* 2.5 27.9 + - - -
130A GLN* 3.0 12.8 + - - -
131A MET 3.1 2.1 - - - +
132A VAL* 1.3 90.5 - - - +
134A ASN* 1.3 77.0 + - - +
135A THR 2.9 3.3 + - - -
136A VAL* 3.7 4.5 + - - +
138A LEU* 5.6 1.3 - - - -
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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