Contacts of the helix formed by residues 136 - 152 (chain A) in PDB entry 1M1D
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 GLY 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL 3.6 0.8 - - - -
135A ARG* 1.3 79.3 - - - +
137A TYR* 1.3 61.8 + - - +
139A THR* 3.5 7.6 + - - -
140A ARG* 3.0 34.5 + - - +
14B LYX 2.8 22.5 + - - -
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.3 29.2 - - + +
99A ILE* 4.0 23.1 - - + +
101A LYS* 5.3 3.6 - - + +
107A ILE* 3.4 26.0 - - + -
128A VAL* 4.5 4.3 - - + -
132A GLU* 3.3 44.7 + - + -
135A ARG* 3.8 28.0 + - + -
136A GLY* 1.3 79.1 - - - +
138A GLY* 1.3 61.5 + - - +
140A ARG* 3.2 23.7 + - - +
141A LEU* 2.8 30.5 + - - +
14B LYX 3.7 6.3 + - - +
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 6.0 0.9 - - - -
128A VAL* 4.0 9.8 - - - +
137A TYR* 1.3 73.5 - - - +
139A THR* 1.3 56.0 + - - +
141A LEU* 3.5 7.6 + - - +
142A MET 3.1 19.2 + - - -
168A TYR* 2.8 27.0 + - - -
14B LYX 2.7 35.8 + - - -
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 3.5 10.5 + - - -
137A TYR 3.2 0.4 - - - -
138A GLY* 1.3 76.1 - - - +
140A ARG* 1.3 65.3 + - + +
142A MET* 3.3 2.4 + - - +
143A ASN* 3.0 39.2 + - - +
172A GLN* 3.4 28.8 + - - +
14B LYX 3.2 32.7 + - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.2 29.7 + - - +
51A PHE* 4.1 29.3 - - + -
99A ILE* 6.6 0.2 - - + -
135A ARG 5.7 0.4 - - - -
136A GLY 3.0 27.3 + - - +
137A TYR* 3.7 26.4 - - - +
139A THR* 1.3 79.4 - - + +
141A LEU* 1.3 61.6 + - - +
143A ASN* 3.4 8.1 + - - +
144A LYS* 3.0 23.9 + - - +
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Residues in contact with LEU 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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51A PHE* 3.9 12.5 - - + -
97A MET* 3.9 37.9 - - + +
98A VAL 4.8 0.2 - - - -
99A ILE* 4.2 21.1 - - + -
109A GLY* 3.4 40.2 - - - +
110A ILE* 3.9 9.2 - - + +
126A LEU* 3.6 17.7 - - + -
127A ALA 4.9 1.6 - - - +
128A VAL* 5.4 1.1 - - + -
137A TYR 2.8 17.4 + - - +
138A GLY* 3.7 7.0 - - - +
140A ARG* 1.3 76.1 - - - +
142A MET* 1.3 58.6 + - - +
144A LYS* 3.1 4.5 + - - +
145A PHE* 2.8 28.5 + - - +
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Residues in contact with MET 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 5.9 2.9 - - + -
123A VAL* 5.6 4.7 - - + -
126A LEU* 4.4 11.6 - - + +
138A GLY 3.1 17.6 + - - +
139A THR 3.3 4.0 + - - +
141A LEU* 1.3 77.6 - - - +
143A ASN* 1.3 57.6 + - - +
145A PHE* 3.1 23.9 + - + +
146A LYS* 2.8 52.3 + - - +
157A LEU* 4.3 5.8 - - - -
168A TYR* 3.6 18.4 - - + +
169A PHE* 3.9 17.9 - - + -
172A GLN* 4.1 17.5 - - + +
174A PHE* 3.5 35.9 - - + -
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Residues in contact with ASN 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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139A THR* 3.0 35.9 + - - +
140A ARG* 3.8 7.1 - - - +
142A MET* 1.3 76.4 - - - +
144A LYS* 1.3 57.5 + - - +
146A LYS* 3.5 20.7 + - - +
147A ASP* 3.1 26.9 + - - +
172A GLN* 4.7 6.1 - - - +
208A TYR* 3.6 34.7 + - + +
209A GLY* 5.8 0.7 - - - -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.8 46.1 - - + +
97A MET* 3.7 21.0 - - + +
140A ARG 3.0 14.1 + - - +
141A LEU 3.4 8.3 - - - +
143A ASN* 1.3 77.8 - - - +
145A PHE* 1.3 62.1 + - - +
147A ASP* 3.5 22.6 + - + +
148A HIS* 3.2 18.8 + - - +
209A GLY* 6.2 4.9 - - - -
210A ARG* 5.8 11.2 - - - +
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Residues in contact with PHE 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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97A MET* 3.7 18.4 - - + -
110A ILE* 4.2 17.3 - - + -
112A PHE* 3.3 61.0 - + + -
121A ALA* 4.3 2.2 - - + -
123A VAL* 3.8 18.4 - - + -
141A LEU 2.8 14.1 + - - +
142A MET* 3.4 20.0 - - - +
144A LYS* 1.3 75.8 - - - +
146A LYS* 1.3 60.4 + - - +
148A HIS* 3.2 2.3 + - - +
149A MET* 2.9 52.5 + - + +
157A LEU* 3.6 35.2 - - + -
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Residues in contact with LYS 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 MET* 2.8 40.8 + - + +
143A ASN* 3.8 16.6 + - - +
144A LYS 3.4 0.2 - - - -
145A PHE* 1.3 72.7 - - - +
147A ASP* 1.3 57.8 + - - +
149A MET* 3.2 2.6 + - - +
150A GLN* 2.8 32.1 + - - +
157A LEU* 4.3 8.3 - - + -
172A GLN* 2.6 35.4 + - - +
173A GLY* 4.9 0.4 - - - -
174A PHE* 4.8 0.2 - - - -
200A CYS* 3.9 18.6 - - - -
202A ILE* 4.0 22.7 - - + +
208A TYR* 3.5 41.1 - - + +
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Residues in contact with ASP 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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143A ASN 3.1 18.2 + - - +
144A LYS* 3.5 23.3 + - + +
146A LYS* 1.3 78.7 - - - +
148A HIS* 1.3 63.0 + - - +
150A GLN* 3.3 12.8 - - - +
151A LYS* 2.9 54.3 + - - +
207A ASP* 4.6 1.9 - - - +
208A TYR* 4.0 13.8 + - + +
209A GLY* 4.5 7.7 + - - +
210A ARG* 3.7 26.8 + - - +
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Residues in contact with HIS 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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53A ILE* 3.3 39.2 - - + +
95A GLU* 4.8 3.8 - - - -
97A MET* 4.0 13.2 - - + +
112A PHE* 4.8 3.9 - + - -
114A GLN* 4.4 5.6 - - - -
144A LYS* 3.2 12.5 + - - +
145A PHE 3.7 6.7 - - - +
146A LYS 3.2 0.2 - - - -
147A ASP* 1.3 82.7 + - - +
149A MET* 1.3 83.8 + - + +
151A LYS* 3.1 12.5 + - + +
152A GLN* 2.9 59.1 + - + +
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Residues in contact with MET 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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112A PHE* 3.8 21.3 - - + -
114A GLN* 3.8 13.9 - - - +
121A ALA* 3.7 21.3 - - - -
145A PHE* 2.9 32.8 + - + +
146A LYS* 3.7 4.9 - - - +
148A HIS* 1.3 100.8 - - + +
150A GLN* 1.3 59.7 + - - +
152A GLN* 2.8 20.3 + - + +
154A ILE* 2.9 48.1 + - + -
157A LEU* 3.8 18.6 - - + -
202A ILE* 4.3 10.8 - - + -
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Residues in contact with GLN 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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146A LYS 2.8 17.4 + - - +
147A ASP* 3.3 15.4 - - - +
149A MET* 1.3 76.8 - - - +
151A LYS* 1.3 67.3 + - + +
153A ASN* 3.3 15.8 + - - +
154A ILE 4.3 2.5 - - - -
202A ILE* 4.0 14.1 - - + +
203A HIS 2.6 29.2 + - - +
204A PRO* 3.1 26.9 + - + +
205A TYR* 4.7 0.9 - - - -
206A VAL 2.8 29.5 + - - +
207A ASP* 5.2 0.2 - - - -
208A TYR* 3.5 12.5 + - - -
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Residues in contact with LYS 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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147A ASP* 2.9 42.5 + - - +
148A HIS* 3.1 17.7 + - + +
150A GLN* 1.3 85.4 + - + +
152A GLN* 1.3 66.1 + - - +
153A ASN* 3.2 7.9 + - - +
210A ARG* 3.0 45.6 + - - +
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Residues in contact with GLN 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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114A GLN* 3.4 32.7 + - - +
116A LYS* 4.9 11.1 + - - +
148A HIS* 2.9 46.9 + - + +
149A MET* 2.8 9.0 + - + +
151A LYS* 1.3 83.4 + - - +
153A ASN* 1.3 74.2 + - - +
154A ILE* 3.3 11.2 + - + +
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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