Contacts of the helix formed by residues 124 - 139 (chain A) in PDB entry 4LT6
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 GLU 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LYS* 6.0 1.8 - - - +
122A HIS 4.0 1.2 + - - +
123A VAL* 1.3 77.9 - - - +
125A ARG* 1.3 61.6 + - + +
126A SER* 2.9 27.6 - - - +
127A ASP* 2.7 39.7 + - - +
128A PHE 3.6 2.9 + - - -
169A PHE* 4.4 3.1 - - - -
171A ARG* 2.7 33.5 + - - +
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Residues in contact with ARG 125 (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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123A VAL 4.1 0.6 + - - -
124A GLU* 1.3 77.0 - - + +
126A SER* 1.3 60.3 + - - +
127A ASP 3.5 0.2 + - - -
128A PHE* 3.7 5.1 + - - +
129A PHE* 3.3 35.1 - - - -
154A PRO* 3.6 34.6 + - - +
169A PHE* 3.3 48.4 + - + +
171A ARG* 4.7 5.8 - - + -
193A ASP* 4.5 3.4 - - - -
195A ARG* 3.7 57.9 + - - +
196A CYS* 3.4 35.6 - - - +
199A SER* 3.5 12.9 + - - -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 3.1 25.5 - - - +
125A ARG* 1.3 79.4 - - - +
127A ASP* 1.3 69.6 + - - -
129A PHE* 3.6 5.9 + - - +
130A GLN* 3.2 25.6 + - - +
195A ARG* 5.7 1.3 - - - +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 4.1 6.3 - - + -
78A VAL* 3.7 26.5 - - + +
82A LYS* 3.8 13.9 + - - -
123A VAL* 4.1 8.7 - - + -
124A GLU* 2.7 34.8 + - - +
126A SER* 1.3 80.1 + - - +
128A PHE* 1.3 66.0 + - - +
130A GLN* 3.2 14.9 + - - +
131A SER* 2.9 34.3 + - - +
132A PHE 3.5 0.7 + - - -
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Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.8 12.2 - + + -
117A CYS* 4.6 4.7 - - + -
124A GLU 3.6 2.0 + - - -
125A ARG 4.0 6.3 - - - +
126A SER 3.5 0.2 - - - -
127A ASP* 1.3 78.5 - - - +
129A PHE* 1.3 81.4 + + - +
132A PHE* 3.6 20.5 - + + +
133A PHE 3.2 23.7 + - - -
154A PRO 5.1 0.2 - - - -
155A VAL 4.8 0.4 - - - -
156A ILE* 3.3 40.2 - - + +
167A LEU* 3.7 45.3 - - + -
168A VAL* 5.1 0.4 - - - -
169A PHE* 3.5 58.6 - + + -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.3 34.8 - - + +
126A SER* 3.6 7.4 + - - +
127A ASP 3.2 0.8 - - - -
128A PHE* 1.3 98.8 - + - +
130A GLN* 1.3 56.7 + - - +
133A PHE* 3.3 20.4 - - - +
147A ALA* 4.0 16.7 - - + +
149A GLU* 3.3 54.0 - - + +
154A PRO* 3.4 40.2 - - + -
155A VAL 3.7 19.3 - - - -
156A ILE* 4.2 8.5 - - + -
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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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126A SER* 3.2 16.1 + - - +
127A ASP* 3.2 19.7 + - - +
129A PHE* 1.3 80.3 - - - +
131A SER* 1.3 88.3 + - - +
132A PHE 3.8 0.2 - - - -
133A PHE* 3.6 4.2 - - - +
134A GLU* 3.0 32.7 + - - +
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Residues in contact with SER 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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74A TRP* 3.0 20.0 + - - -
78A VAL* 4.1 10.8 - - - +
127A ASP* 2.9 17.8 + - - +
130A GLN* 1.3 89.8 + - - +
132A PHE* 1.3 65.4 + - - -
133A PHE 3.1 0.7 - - - -
134A GLU* 2.8 23.7 + - - +
135A LYS* 2.8 12.6 + - - +
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Residues in contact with PHE 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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67A LEU* 4.2 9.0 - - + -
70A LEU* 4.2 6.7 - - + -
71A VAL* 3.5 42.6 - - + -
74A TRP* 3.2 56.0 - + + +
127A ASP 3.5 1.8 + - - -
128A PHE* 3.6 26.9 - + - +
131A SER* 1.3 76.8 + - - +
133A PHE* 1.3 66.9 + - - +
135A LYS* 3.0 16.7 + - + +
136A LEU* 3.0 51.2 + - + +
156A ILE* 4.9 0.7 - - + -
167A LEU* 3.7 16.2 - - + -
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Residues in contact with PHE 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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128A PHE 3.2 10.2 + - - +
129A PHE 3.3 27.4 - - - +
130A GLN* 3.6 5.2 - - - +
131A SER 3.1 0.6 - - - -
132A PHE* 1.3 76.0 - - - +
134A GLU* 1.3 75.9 + - - +
136A LEU* 4.7 2.9 - - - +
137A LYS* 3.5 24.2 + - + +
145A LEU* 3.6 31.5 - - + +
146A ARG* 3.7 13.0 - - - -
147A ALA* 3.5 37.0 - - + -
156A ILE* 3.7 26.5 - - + -
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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
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130A GLN 3.0 17.7 + - - +
131A SER* 2.8 14.7 + - - +
133A PHE* 1.3 88.9 - - - +
135A LYS* 1.3 65.2 + - - +
137A LYS* 3.1 49.1 + - - +
138A HIS* 3.6 27.0 + - + -
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Residues in contact with LYS 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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70A LEU* 4.3 13.6 - - + +
73A GLU* 3.1 41.1 + - - -
74A TRP* 3.7 28.5 - - + +
77A ASP* 3.7 15.7 - - - -
131A SER 2.8 11.4 + - - +
132A PHE* 3.0 19.5 + - + +
134A GLU* 1.3 77.8 - - - +
136A LEU* 1.3 62.9 + - + +
138A HIS* 3.3 15.0 + - - +
139A GLN* 3.4 30.8 + - + +
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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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67A LEU* 4.5 7.9 - - + -
70A LEU* 4.1 15.3 - - + -
132A PHE* 3.0 53.3 + - + +
133A PHE* 4.1 1.3 - - - +
134A GLU 3.3 0.4 - - - -
135A LYS* 1.3 76.9 - - + +
137A LYS* 1.3 67.0 + - - +
138A HIS 2.9 1.6 + - - -
139A GLN* 2.9 13.2 + - - +
142A ILE* 3.6 38.4 - - + +
145A LEU* 3.9 16.2 - - + -
156A ILE* 4.1 17.5 - - + -
158A PHE* 3.6 33.7 - - + -
167A LEU* 5.0 0.2 - - + -
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Residues in contact with LYS 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 PHE* 3.5 18.3 + - + +
134A GLU* 3.1 42.2 + - - +
135A LYS 3.3 0.6 - - - -
136A LEU* 1.3 77.9 - - - +
138A HIS* 1.3 76.4 + - + +
139A GLN 4.2 3.1 - - - +
142A ILE* 5.1 6.5 - - - +
145A LEU* 3.5 16.9 - - + +
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Residues in contact with HIS 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 GLU* 3.6 22.3 + - + -
135A LYS* 3.3 9.6 + - - +
136A LEU 3.0 0.8 - - - -
137A LYS* 1.3 97.4 - - + +
139A GLN* 1.3 66.4 + - - +
140A ASP* 3.6 3.1 + - - +
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Residues in contact with GLN 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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66A LYS* 5.8 3.8 - - - +
70A LEU* 3.3 45.7 - - + +
73A GLU* 4.9 2.4 + - - -
135A LYS* 3.4 24.6 + - + +
136A LEU 2.9 13.5 + - - +
137A LYS 4.2 2.8 - - - +
138A HIS* 1.3 80.6 - - - +
140A ASP* 1.3 72.9 + - - +
141A GLY 3.7 0.7 - - - -
142A ILE* 3.6 25.4 + - + +
160A PHE* 4.9 9.7 - - + -
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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