Contacts of the helix formed by residues 134 - 152 (chain A) in PDB entry 3M93
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 4.6 2.0 - - - -
131A ASP* 3.5 19.0 + - + -
133A GLN* 1.3 81.9 - - + +
135A ARG* 1.3 60.9 + - - +
136A ALA* 3.4 2.4 + - - -
137A GLN* 3.7 26.5 + - - +
138A LEU* 3.4 34.1 + - + +
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Residues in contact with ARG 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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96A SER* 3.0 48.6 + - - +
98A LEU 4.3 2.0 + - - -
100A TRP* 5.3 14.8 - - - -
130A VAL* 3.6 10.3 - - + -
131A ASP 3.0 16.7 + - - +
132A LYS* 3.5 17.5 - - - +
133A GLN 3.2 1.0 - - - -
134A LYS* 1.3 75.5 - - - +
136A ALA* 1.3 70.7 + - - +
137A GLN 3.2 0.2 + - - -
139A LEU* 3.0 34.3 + - + +
169A VAL* 3.3 31.3 - - - +
170A ARG 5.1 2.0 + - - -
174A ASP* 2.5 31.7 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 5.2 8.5 - - - -
133A GLN 4.5 6.6 + - - +
134A LYS 3.4 0.6 - - - -
135A ARG* 1.3 86.1 - - - +
137A GLN* 1.3 62.4 + - + +
139A LEU 4.7 1.6 + - - -
140A ASP* 5.1 9.2 + - - +
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Residues in contact with GLN 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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134A LYS* 3.7 29.2 + - - +
135A ARG 3.3 0.6 - - - -
136A ALA* 1.3 78.7 - - + +
138A LEU* 1.3 72.7 + - - +
140A ASP 5.6 0.2 - - - -
141A HIS* 4.6 8.5 + - - +
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Residues in contact with LEU 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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130A VAL* 4.4 13.0 - - + -
131A ASP* 5.7 3.1 - - + +
134A LYS* 3.4 27.9 + - + +
135A ARG 3.2 1.6 + - - +
137A GLN* 1.3 93.4 - - - +
139A LEU* 1.3 69.3 + - - +
140A ASP 3.4 2.0 - - - -
141A HIS* 3.0 20.7 + - + +
142A TYR* 3.0 56.8 + - + +
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Residues in contact with LEU 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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95A ALA* 4.1 12.6 - - + +
96A SER* 3.8 33.4 - - - +
130A VAL* 3.7 28.2 - - + +
135A ARG* 3.0 27.8 + - + +
136A ALA 4.7 0.2 + - - -
137A GLN 4.0 0.2 - - - -
138A LEU* 1.3 77.8 - - - +
140A ASP* 1.3 64.6 + - - +
142A TYR* 3.1 4.3 + - - +
143A TRP* 3.1 21.7 + - - +
167A VAL* 4.3 11.0 - - + -
169A VAL* 4.7 2.9 - - + -
174A ASP* 3.7 31.4 - - + +
176A VAL* 4.0 17.9 - - + -
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Residues in contact with ASP 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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89A TYR* 4.1 9.8 + - - +
94A ALA* 4.0 11.3 - - - +
95A ALA* 3.5 14.0 - - - +
96A SER* 2.9 49.0 + - - -
136A ALA 5.1 7.0 + - - +
137A GLN 5.6 0.4 - - - -
138A LEU 3.4 0.4 - - - -
139A LEU* 1.3 76.5 - - - +
141A HIS* 1.3 56.8 + - - +
143A TRP* 4.2 5.6 - - - +
144A LEU* 3.1 32.1 + - - +
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Residues in contact with HIS 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 GLN 4.6 8.9 + - - +
138A LEU* 3.0 15.5 + - + +
140A ASP* 1.3 75.7 - - - +
142A TYR* 1.3 69.4 + - - +
144A LEU* 4.9 2.5 - - - -
145A GLU* 2.7 70.8 + - + +
199A LYS 4.8 3.8 - - - -
200A LEU 4.5 12.3 - - - -
201A GLU* 4.4 19.6 + - + -
6C ARG* 5.4 2.3 + - - -
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Residues in contact with TYR 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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128A VAL* 4.2 20.9 - - + -
129A VAL 5.3 2.5 - - - -
130A VAL* 3.9 25.8 - - + -
138A LEU* 3.0 49.0 + - + +
139A LEU 3.4 8.3 - - - +
141A HIS* 1.3 84.6 - - - +
143A TRP* 1.3 56.8 + - - +
146A LEU* 3.1 25.3 + - - +
176A VAL* 4.5 12.7 - - + +
200A LEU* 3.1 58.7 + - + +
201A GLU 4.5 2.2 + - - -
202A ILE* 3.9 26.2 - - + +
203A PRO* 4.5 4.9 - - - +
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Residues in contact with TRP 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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58A LEU* 5.2 3.7 - - + +
89A TYR* 4.3 20.9 - + - -
92A ILE* 6.0 1.4 - - - +
95A ALA* 4.1 21.8 - - + -
104A TYR* 3.5 43.0 - + + -
105A TYR 4.9 0.7 - - - -
106A LEU* 4.3 6.3 - - + -
139A LEU 3.1 15.7 + - - +
140A ASP* 4.2 4.0 - - - +
142A TYR* 1.3 74.5 - - - +
144A LEU* 1.3 68.3 + - - +
146A LEU* 3.2 12.8 + - + +
147A LEU* 2.9 57.9 + - + +
165A ALA* 3.4 34.3 - - + -
166A VAL 3.6 22.4 - - - -
167A VAL* 3.7 25.4 - - + -
176A VAL* 4.8 6.1 - - + -
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Residues in contact with LEU 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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85A PHE* 4.1 12.6 - - + -
86A TRP* 3.7 22.9 - - + -
89A TYR* 3.5 46.2 - - + +
140A ASP 3.1 17.7 + - - +
141A HIS* 4.1 2.0 - - - +
143A TRP* 1.3 80.0 - - - +
145A GLU* 1.3 66.2 + - + +
147A LEU* 2.9 16.8 + - + +
148A MET* 2.9 26.9 + - + +
10C MET* 4.9 7.9 - - + -
13C ARG* 4.2 16.6 - - - +
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Residues in contact with GLU 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 HIS* 2.7 63.0 + - + +
144A LEU* 1.3 73.9 - - + +
146A LEU* 1.3 56.6 + - - +
148A MET* 3.4 17.0 - - - +
149A ALA* 2.9 27.9 + - - +
199A LYS* 4.1 18.8 - - + +
200A LEU* 3.7 18.3 - - + +
6C ARG* 2.8 52.5 + - - +
10C MET* 4.1 2.6 - - - +
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Residues in contact with LEU 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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142A TYR 3.1 17.9 + - - +
143A TRP* 3.4 10.1 - - + +
144A LEU 3.1 0.8 - - - -
145A GLU* 1.3 73.3 - - - +
147A LEU* 1.3 62.1 + - + +
149A ALA* 2.9 7.5 + - + +
150A ILE* 2.8 63.2 + - + +
155A PHE* 4.9 4.0 - - + -
165A ALA* 3.7 23.3 - - + -
176A VAL* 3.8 26.0 - - + -
177A SER 4.1 13.0 - - - +
178A LEU* 3.9 20.6 - - + -
196A LEU* 4.2 19.3 - - + -
200A LEU* 3.7 4.9 - - + +
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Residues in contact with LEU 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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58A LEU* 4.9 7.4 - - + -
85A PHE* 3.9 29.6 - - + -
89A TYR* 4.7 9.2 - - + -
106A LEU* 3.4 34.5 - - + -
143A TRP* 2.9 65.5 + - + +
144A LEU* 2.9 12.0 + - - +
146A LEU* 1.3 72.0 - - - +
148A MET* 1.3 57.1 + - - +
150A ILE* 3.3 2.5 + - + +
151A ILE* 2.9 38.1 + - - +
165A ALA* 4.0 11.0 - - + -
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Residues in contact with MET 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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85A PHE* 4.5 9.2 - - + -
86A TRP* 4.0 29.6 - - + -
144A LEU* 2.9 31.0 + - + +
145A GLU* 3.4 35.9 - - - +
147A LEU* 1.3 74.7 - - - +
149A ALA* 1.3 65.4 + - - +
151A ILE* 4.1 2.7 - - - -
152A GLY* 3.1 22.3 + - - -
154A GLN* 4.5 1.6 - - - +
4C TYR 4.7 0.5 - - - +
6C ARG* 4.3 19.9 + - + +
9C LEU* 3.6 29.9 - - + +
10C MET* 4.1 22.4 - - + +
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Residues in contact with ALA 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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145A GLU 2.9 16.6 + - - +
146A LEU* 2.9 12.1 + - + +
148A MET* 1.3 77.4 - - - +
150A ILE* 1.3 60.5 + - - +
153A GLU 3.3 1.0 + - - -
154A GLN* 3.1 38.6 + - + +
155A PHE* 4.0 16.9 - - + -
199A LYS* 3.9 30.1 - - + -
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Residues in contact with ILE 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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56A TRP* 3.6 39.5 - - + -
106A LEU* 3.7 31.2 - - + +
146A LEU* 2.8 43.9 + - + +
147A LEU* 3.9 7.4 - - + +
149A ALA* 1.3 70.9 - - - +
151A ILE* 1.3 68.9 + - + +
153A GLU* 2.9 23.2 + - - +
155A PHE* 4.0 18.3 - - + -
162A ILE* 4.3 17.5 - - + -
164A GLY* 4.4 3.8 - - - -
165A ALA* 4.2 13.9 - - + +
178A LEU* 4.6 3.4 - - + -
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Residues in contact with ILE 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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52A LEU* 3.5 35.3 - - + +
53A GLN 4.9 2.1 + - - -
56A TRP* 3.7 34.7 + - + +
79A PHE* 4.3 6.1 - - + -
82A VAL* 5.5 0.9 - - - -
85A PHE* 3.6 47.1 - - + -
106A LEU* 3.9 21.8 - - + -
147A LEU 2.9 26.3 + - - +
148A MET* 4.0 5.2 - - - +
150A ILE* 1.3 72.2 - - + +
152A GLY* 1.3 60.8 + - - +
153A GLU* 3.2 11.1 + - - +
2C ILE 5.1 0.2 - - - +
4C TYR* 4.8 1.7 - - - -
9C LEU* 4.4 13.5 - - + -
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Residues in contact with GLY 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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148A MET 3.1 16.1 + - - -
149A ALA 3.8 1.1 - - - -
151A ILE* 1.3 76.4 - - - +
153A GLU* 1.3 62.3 + - - +
154A GLN* 2.6 26.2 + - - -
2C ILE 4.6 0.4 - - - -
3C ILE* 3.7 0.7 - - - -
4C TYR* 3.1 41.0 + - - +
9C LEU* 4.4 3.1 - - - -
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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