Contacts of the helix formed by residues 128 - 148 (chain A) in PDB entry 4LDT
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 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY 3.7 3.1 - - - +
127A PHE* 1.4 89.1 - - + +
129A ASP* 1.3 69.2 + - - +
130A TRP 3.6 0.9 - - - -
131A THR* 3.6 15.0 - - - +
132A CYS* 3.3 24.4 + - - +
207A GLU* 6.1 1.3 - - - +
96C ALA* 3.7 27.6 - - + +
97C LEU* 5.4 5.6 - - + -
98C THR* 6.1 1.3 - - + -
101C LYS* 4.8 20.6 - - - -
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 4.9 14.2 - - + +
127A PHE 3.3 7.1 + - - +
128A PRO* 1.3 74.2 - - - +
130A TRP* 1.3 66.7 + - + +
132A CYS* 4.3 0.7 - - - +
133A THR* 3.0 27.5 + - - -
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Residues in contact with TRP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 1.3 80.7 - - + +
131A THR* 1.3 72.6 + - + +
133A THR* 3.8 4.9 - - - -
134A ASP* 2.9 35.2 + - + +
5C ARG* 3.7 27.4 - - - -
8C LYS* 3.6 29.2 - - + -
9C GLU* 3.8 35.0 - - + -
12C ASP* 3.4 39.1 + - + -
98C THR* 3.7 29.6 - - + +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 3.6 13.4 - - - +
130A TRP* 1.3 90.8 - - + +
132A CYS* 1.3 67.7 + - - +
134A ASP* 3.2 5.6 + - - +
135A PHE* 3.1 29.8 + - - -
5C ARG* 3.5 28.5 - - - +
95C PRO 4.2 0.2 - - - -
96C ALA* 2.7 32.5 + - - +
98C THR* 3.5 31.0 - - + -
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Residues in contact with CYS 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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122A LEU* 4.3 13.2 - - + -
127A PHE* 3.9 22.7 - - + -
128A PRO* 3.3 20.9 + - - +
129A ASP 4.3 0.7 - - - +
130A TRP 3.4 0.2 - - - -
131A THR* 1.3 80.8 + - - +
133A THR* 1.3 57.6 + - - +
135A PHE* 3.4 4.4 + - - +
136A CYS* 3.1 34.1 + - - -
175A LEU* 3.7 38.4 - - + +
96C ALA* 4.0 19.7 - - - -
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Residues in contact with THR 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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119A THR* 4.3 15.0 + - + +
123A VAL* 4.0 18.7 - - - +
129A ASP 3.0 19.4 + - - -
130A TRP* 4.0 5.2 - - - -
132A CYS* 1.3 74.8 - - - +
134A ASP* 1.3 55.8 + - - +
136A CYS* 3.6 5.7 - - - +
137A ASP* 2.8 60.6 + - - +
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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
----------------------------------------------------------
130A TRP* 2.9 23.2 + - + +
131A THR* 3.3 9.4 - - - +
133A THR* 1.3 77.8 - - - +
135A PHE* 1.3 61.6 + - - +
137A ASP* 4.0 5.7 - - - +
138A PHE* 3.1 24.9 + - - +
168A TYR* 3.3 30.6 + - - -
5C ARG* 4.5 7.6 + - - -
8C LYS* 3.3 39.9 + - - +
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Residues in contact with PHE 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 THR* 3.1 27.4 + - - -
132A CYS* 3.7 5.2 - - - +
134A ASP* 1.3 73.6 - - - +
136A CYS* 1.3 64.8 + - - +
138A PHE* 3.4 2.8 + - - +
139A PHE* 3.1 24.5 + - - +
168A TYR* 3.4 63.7 - + - +
171A MET* 3.8 19.3 - - + -
172A PHE* 4.6 6.5 - - - +
175A LEU* 4.0 23.6 - - + -
5C ARG* 3.5 20.6 - - - -
61C PRO* 4.1 2.5 - - + -
62C PHE* 4.3 2.7 - + - -
95C PRO* 3.7 39.5 - - + -
96C ALA* 4.4 2.7 - - - -
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Residues in contact with CYS 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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119A THR* 3.2 41.7 - - + +
122A LEU* 3.5 28.3 - - - -
132A CYS 3.1 21.5 + - - +
133A THR 3.3 1.8 + - - +
135A PHE* 1.3 76.1 - - - +
137A ASP* 1.3 58.5 + - - +
139A PHE* 3.3 3.3 + - - +
140A ILE* 2.9 34.4 + - - +
172A PHE* 3.8 28.3 - - + -
175A LEU* 5.1 1.8 - - - -
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Residues in contact with ASP 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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119A THR* 4.4 9.0 - - - +
133A THR* 2.8 41.8 + - - +
134A ASP* 4.0 6.9 - - - +
136A CYS* 1.3 71.9 - - - +
138A PHE* 1.3 58.2 + - - +
140A ILE* 3.3 10.6 + - - +
141A GLU* 2.9 41.1 + - - +
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Residues in contact with PHE 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 19.1 + - - +
135A PHE 3.8 3.8 - - - +
136A CYS 3.3 0.2 - - - -
137A ASP* 1.3 75.9 - - - +
139A PHE* 1.3 64.3 + - - +
141A GLU* 3.5 14.9 + - + +
142A PHE* 3.1 23.8 + - + +
159A ILE* 5.5 1.8 - - + -
165A SER* 3.6 43.5 - - - -
168A TYR* 3.8 26.7 - + + -
169A ILE* 3.9 17.9 - - + -
1C MET* 3.6 29.8 - - + -
4C LYS* 6.1 0.4 - - - -
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Residues in contact with PHE 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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98A ILE* 4.9 4.5 - - + -
101A MET* 4.9 3.6 - - + -
111A PHE* 3.9 8.3 - + - -
115A SER* 3.9 11.2 - - - -
135A PHE 3.1 17.2 + - - +
136A CYS 3.7 2.7 - - - +
138A PHE* 1.3 77.3 - - - +
140A ILE* 1.3 66.9 + - - +
142A PHE* 3.3 16.9 + + - +
143A LEU* 3.0 58.3 + - + +
169A ILE* 3.7 34.3 - - + -
172A PHE* 3.4 50.0 - + + -
173A PHE* 3.6 20.4 - + - -
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Residues in contact with ILE 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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112A ILE* 4.4 8.5 - - + +
115A SER* 3.8 22.0 - - - -
116A ARG* 3.8 41.7 - - + +
119A THR* 3.5 23.8 - - + +
136A CYS* 2.9 24.1 + - + +
137A ASP* 3.8 11.7 - - - +
139A PHE* 1.3 78.0 - - + +
141A GLU* 1.3 57.1 + - + +
143A LEU* 3.3 8.4 + - - +
144A GLU* 2.8 49.6 + - + +
172A PHE* 5.8 0.7 - - + -
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Residues in contact with GLU 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 ASP* 2.9 25.2 + - - +
138A PHE* 3.8 16.1 - - + +
140A ILE* 1.3 77.8 - - + +
142A PHE* 1.3 57.5 + - - +
144A GLU* 3.4 17.4 + - - +
145A LYS* 2.9 50.7 + - - +
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Residues in contact with PHE 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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98A ILE* 3.7 26.5 - - + -
138A PHE* 3.1 19.1 + + + +
139A PHE* 3.4 22.7 - + - +
141A GLU* 1.3 75.6 - - - +
143A LEU* 1.3 71.5 + - + +
145A LYS* 3.3 2.6 + - - -
146A ILE* 3.1 47.6 + - + +
151A HIS* 3.6 24.1 - + - -
156A VAL* 3.9 19.3 - - + -
159A ILE* 3.8 34.1 - - + -
160A LEU* 4.5 4.0 - - + -
169A ILE* 3.9 25.4 - - + -
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Residues in contact with LEU 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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98A ILE* 4.8 2.7 - - + -
101A MET* 4.1 17.3 - - + -
108A LEU* 3.8 17.4 - - + +
111A PHE* 3.9 19.7 - - + -
112A ILE* 3.7 26.4 - - + +
115A SER* 4.4 3.8 - - - +
139A PHE* 3.0 50.8 + - + +
140A ILE* 3.6 9.4 - - - +
142A PHE* 1.3 91.0 - - + +
144A GLU* 1.3 59.8 + - - +
146A ILE* 3.1 13.2 + - + +
147A HIS* 2.9 27.2 + - - +
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Residues in contact with GLU 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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112A ILE* 3.9 19.5 - - + +
116A ARG* 2.3 47.6 + - - +
140A ILE* 2.8 26.6 + - - +
141A GLU* 3.6 21.8 - - - +
143A LEU* 1.3 73.3 - - - +
145A LYS* 1.3 58.9 + - + +
147A HIS* 3.2 4.5 + - - +
148A SER* 2.8 30.4 + - - -
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Residues in contact with LYS 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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141A GLU* 2.9 34.3 + - - +
142A PHE* 5.2 0.2 - - - -
143A LEU 3.2 0.2 - - - -
144A GLU* 1.3 76.1 - - + +
146A ILE* 1.3 61.7 + - - +
148A SER* 3.6 6.5 - - - +
149A GLY 3.3 1.0 + - - -
150A VAL* 2.9 33.3 + - + -
151A HIS* 2.9 59.3 + - + +
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Residues in contact with ILE 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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98A ILE* 4.3 13.7 - - + -
101A MET* 5.4 2.2 - - + +
102A LEU* 3.8 26.2 - - + +
108A LEU* 3.9 17.0 - - + -
142A PHE* 3.1 36.5 + - + +
143A LEU* 3.1 16.9 + - + +
145A LYS* 1.3 74.0 - - - +
147A HIS* 1.3 65.7 + - - +
149A GLY* 3.1 12.1 + - - -
151A HIS* 4.0 16.9 - - + +
156A VAL* 3.6 30.7 - - + -
301A EDO 3.6 18.5 + - - -
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Residues in contact with HIS 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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105A ARG* 2.9 70.0 + - + +
108A LEU* 3.7 25.3 - - + +
109A GLU* 3.6 42.1 + - + -
112A ILE* 4.1 11.0 - - + -
143A LEU 2.9 13.2 + - - +
144A GLU* 3.2 10.0 + - - +
146A ILE* 1.3 78.5 - - - +
148A SER* 1.3 62.4 + - - +
149A GLY 3.4 0.3 + - - -
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Residues in contact with SER 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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105A ARG* 5.2 0.7 - - - +
144A GLU 2.8 17.9 + - - -
145A LYS* 3.4 8.3 + - - +
147A HIS* 1.3 76.7 - - - +
149A GLY* 1.3 59.8 + - - +
150A VAL* 3.3 28.7 + - - +
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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