Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 1MRJ
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU* 1.3 79.4 - - - +
129A LEU* 1.3 68.2 + - - -
130A PRO* 3.4 4.3 - - - -
131A ALA* 3.0 12.6 + - - +
132A LEU* 3.1 12.0 + - - +
153A VAL* 5.3 0.2 - - - +
157A SER* 5.2 2.7 + - - -
171A ILE* 4.1 17.6 - - - +
174A ARG* 3.8 20.9 - - - -
177A LYS 4.2 2.5 - - - -
179A PHE* 3.8 2.9 - - - -
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Residues in contact with LEU 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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4A PHE* 4.3 14.6 - - + -
6A LEU* 3.5 16.6 - - + +
9A ALA* 4.0 27.1 - - + -
10A THR 4.4 12.3 - - - +
14A TYR* 3.9 35.0 - - + -
55A TYR* 4.1 2.0 - - - +
128A GLY* 1.3 73.0 - - - -
130A PRO* 1.4 64.8 - - + +
132A LEU* 3.0 20.0 + - + +
133A ASP* 3.0 10.6 + - - +
171A ILE* 4.5 12.6 - - + +
172A GLY 4.9 2.7 - - - +
174A ARG 2.8 21.5 + - - +
175A VAL* 3.9 25.6 - - + +
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Residues in contact with PRO 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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55A TYR* 3.7 17.3 - - + +
128A GLY 3.5 1.3 - - - -
129A LEU* 1.4 89.8 - - - +
131A ALA* 1.3 59.0 + - - +
133A ASP* 3.4 7.5 + - + +
134A SER* 3.2 22.3 + - - -
174A ARG 3.5 0.4 - - - +
175A VAL 3.3 23.8 - - - +
176A ASP* 3.8 15.5 - - - +
177A LYS 3.4 22.9 - - - +
178A THR* 4.1 9.2 - - + -
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Residues in contact with ALA 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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126A PRO* 3.4 28.0 - - + +
127A LEU* 3.7 12.1 - - - -
128A GLY 3.0 13.0 + - - +
130A PRO* 1.3 78.4 - - - +
132A LEU* 1.3 56.6 + - - +
134A SER* 3.4 7.8 + - - -
135A ALA* 3.0 28.6 + - - +
153A VAL* 3.7 11.6 - - + +
178A THR* 3.7 13.0 - - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.2 29.4 - - + -
6A LEU* 4.0 10.1 - - + -
14A TYR* 4.9 4.7 - - + -
17A PHE* 5.7 1.6 - - + -
52A LEU* 4.6 9.6 - - + -
128A GLY 3.1 10.2 + - - +
129A LEU* 3.0 20.7 + - + +
131A ALA* 1.3 74.1 - - - +
133A ASP* 1.3 64.6 + - - +
135A ALA* 3.2 4.3 + - + +
136A ILE* 2.9 37.6 + - + +
153A VAL* 4.0 7.1 - - + +
154A LEU* 4.3 27.6 - - + -
157A SER* 4.0 32.3 - - - +
158A THR* 5.5 1.1 - - + -
171A ILE* 6.3 0.4 - - + -
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Residues in contact with ASP 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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6A LEU* 3.5 18.6 - - + +
54A ASN* 3.0 14.2 + - - +
55A TYR* 3.0 61.2 + - + +
56A ALA 4.6 0.3 + - - -
129A LEU 3.0 8.5 + - - +
130A PRO 3.5 10.4 - - - +
132A LEU* 1.3 75.5 - - - +
134A SER* 1.3 59.6 + - - +
136A ILE* 3.3 4.3 + - - +
137A THR* 3.0 34.9 + - - -
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Residues in contact with SER 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 PRO 3.2 10.7 + - - -
131A ALA* 3.6 11.9 - - - -
133A ASP* 1.3 81.1 + - - +
135A ALA* 1.3 66.2 + - - +
137A THR* 3.3 8.0 + - - -
138A THR* 3.0 30.8 + - - -
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Residues in contact with ALA 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 ALA 3.0 17.7 + - - +
132A LEU* 3.2 8.5 + - + +
134A SER* 1.3 76.4 - - - +
136A ILE* 1.3 63.0 + - - +
138A THR* 3.3 1.8 + - - -
139A LEU* 2.9 32.1 + - + +
150A ALA* 3.5 36.8 - - + +
153A VAL* 4.0 15.9 - - + -
154A LEU* 4.6 5.2 - - + +
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Residues in contact with ILE 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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6A LEU* 3.4 32.1 - - + -
52A LEU* 3.8 31.2 - - + +
54A ASN* 4.0 16.6 - - + +
58A GLU 3.8 22.4 - - - +
60A ILE* 4.1 34.4 - - + +
132A LEU* 2.9 26.5 + - + +
133A ASP 3.6 5.6 - - - +
135A ALA* 1.3 74.6 - - - +
137A THR* 1.3 57.4 + - - +
139A LEU* 3.4 0.5 + - - +
140A PHE* 2.8 33.7 + - + +
154A LEU* 5.6 1.1 - - + -
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Residues in contact with THR 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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54A ASN* 3.0 21.8 + - - +
56A ALA* 6.0 0.2 - - - +
58A GLU* 4.0 7.1 + - - +
133A ASP* 3.0 17.5 + - - -
134A SER* 3.6 10.6 - - - -
136A ILE* 1.3 76.3 - - - +
138A THR* 1.3 58.8 + - - +
140A PHE* 3.6 3.1 - - - +
141A TYR* 2.9 49.7 + - + +
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Residues in contact with THR 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 SER* 3.0 20.1 + - - -
135A ALA* 3.6 4.3 - - - -
137A THR* 1.3 79.0 - - - +
139A LEU* 1.3 57.9 + - - +
141A TYR* 3.2 22.8 - - - +
142A TYR* 3.5 6.1 - - - -
143A ASN* 3.8 2.3 + - + +
146A SER* 3.3 40.5 - - - +
147A ALA* 4.2 3.3 - - - +
150A ALA* 3.8 21.1 - - + -
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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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60A ILE* 4.2 13.9 - - + -
74A TYR* 2.7 53.8 + - + +
76A ALA* 4.2 1.6 - - - +
81A TYR* 4.7 0.3 - - - -
135A ALA 2.9 21.4 + - - +
136A ILE 4.0 2.5 - - - +
138A THR* 1.3 76.1 - - - +
140A PHE* 1.3 66.5 + - - +
142A TYR* 3.4 9.3 + - + +
147A ALA* 4.0 24.0 - - + +
150A ALA* 3.9 16.4 - - + +
151A LEU* 4.0 25.6 - - + -
154A LEU* 3.9 28.5 - - + -
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Residues in contact with PHE 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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58A GLU* 4.0 20.2 - - + -
59A THR 3.3 43.5 - - - -
60A ILE* 4.0 6.6 - - + +
76A ALA* 3.9 24.8 - - + +
77A GLY* 4.9 9.4 - - - -
81A TYR* 5.2 1.6 + - - -
136A ILE* 2.8 23.7 + - + +
137A THR* 3.6 6.7 - - - +
139A LEU* 1.3 74.9 - - - +
141A TYR* 1.3 96.6 + + - +
142A TYR* 3.4 3.3 + - - +
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Residues in contact with TYR 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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58A GLU* 2.8 40.8 + - - +
137A THR* 2.9 35.5 + - + +
138A THR* 3.2 8.9 - - - +
140A PHE* 1.3 97.6 - + - +
142A TYR* 1.3 66.4 + - - +
143A ASN* 3.0 8.3 + - - +
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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