Contacts of the helix formed by residues 124 - 146 (chain A) in PDB entry 1R1M
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 SER 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLY* 1.3 76.0 - - - +
125A ASP* 1.3 65.5 + - - +
126A LYS* 3.5 8.0 + - - +
127A TYR* 2.9 29.6 + - - +
128A ASN* 2.8 22.1 + - - -
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 3.9 0.4 + - - +
124A SER* 1.3 72.8 - - - +
126A LYS* 1.3 57.4 + - - +
128A ASN* 3.9 1.0 - - - +
129A GLN* 2.9 33.4 + - - +
160A GLU* 3.4 29.3 - - - +
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Residues in contact with LYS 126 (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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124A SER* 3.2 7.5 - - - +
125A ASP* 1.3 79.6 - - - +
127A TYR* 1.3 62.8 + - - +
129A GLN* 3.9 5.0 + - - +
130A ALA* 3.1 26.6 + - + +
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET 4.9 5.2 - - - -
123A GLY* 4.1 10.8 - - - -
124A SER* 2.9 23.9 + - - +
126A LYS* 1.3 78.6 - - - +
128A ASN* 1.3 74.1 + - - +
130A ALA* 3.4 4.5 + - + +
131A LEU* 3.0 60.7 + - + +
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Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 3.1 29.3 + - - +
120A ASP* 3.4 17.2 + - - +
121A PHE 4.4 0.4 + - - -
122A MET 4.4 1.0 - - - -
123A GLY* 3.0 35.9 + - - +
124A SER 2.8 12.0 + - - +
125A ASP 3.9 0.2 - - - +
127A TYR* 1.3 84.6 - - - +
129A GLN* 1.3 61.2 + - - +
131A LEU* 4.7 0.7 - - - +
132A SER* 2.8 34.1 + - - -
159A GLY* 3.6 4.8 - - - -
160A GLU* 2.9 30.9 + - - +
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Residues in contact with GLN 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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125A ASP 2.9 18.6 + - - +
126A LYS* 3.9 5.7 + - - +
127A TYR 3.3 0.2 - - - -
128A ASN* 1.3 76.8 - - - +
130A ALA* 1.3 67.8 + - - +
132A SER* 3.1 6.4 + - - -
133A GLU* 2.9 50.8 + - - +
157A GLY* 3.5 23.2 + - - +
158A LEU 5.5 0.7 - - - -
159A GLY* 4.1 6.4 - - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 3.1 19.3 + - + +
127A TYR* 3.9 4.7 - - + +
129A GLN* 1.3 84.1 - - - +
131A LEU* 1.3 64.8 + - - +
133A GLU* 3.4 3.8 + - - +
134A ARG* 3.0 24.8 + - - +
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Residues in contact with LEU 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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87A LYS* 3.9 34.1 - - + +
119A THR* 4.4 14.1 - - + -
127A TYR* 3.0 51.1 + - + +
128A ASN 4.0 2.2 - - - +
130A ALA* 1.3 75.6 - - - +
132A SER* 1.3 59.6 + - - +
134A ARG* 3.3 6.0 + - + +
135A ARG* 3.0 68.5 + - + +
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Residues in contact with SER 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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117A GLY* 3.3 32.8 - - - -
118A HIS 4.0 0.9 - - - +
119A THR* 3.9 13.2 - - - +
128A ASN 2.8 24.5 + - - -
129A GLN 3.1 8.7 + - - -
131A LEU* 1.3 77.9 - - - +
133A GLU* 1.3 55.4 + - - +
135A ARG* 3.8 4.9 - - - +
136A ALA* 2.9 30.0 + - - +
157A GLY* 3.1 6.9 - - - -
159A GLY 3.0 18.2 + - - -
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Residues in contact with GLU 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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129A GLN* 2.9 40.9 + - - +
130A ALA* 3.8 4.6 - - - +
131A LEU 3.3 0.2 - - - -
132A SER* 1.3 75.2 + - - +
134A ARG* 1.3 60.8 + - - +
136A ALA* 3.3 1.7 + - - +
137A TYR* 2.8 31.5 + - + +
155A ALA* 4.6 13.3 - - + +
156A VAL* 4.3 1.6 - - - -
157A GLY* 3.6 19.3 - - - +
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Residues in contact with ARG 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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87A LYS* 4.4 14.6 - - + +
88A ASP* 2.7 39.8 + - + +
130A ALA 3.0 17.9 + - - +
131A LEU* 3.6 6.7 - - - +
133A GLU* 1.3 77.5 - - - +
135A ARG* 1.3 58.4 + - + +
137A TYR* 3.2 31.5 + - - +
138A VAL* 2.9 50.0 + - - +
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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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79A ALA* 3.4 24.3 - - - +
83A PHE* 3.4 37.4 - - + +
84A GLY 5.6 1.6 + - - -
86A ASP 3.2 25.3 + - - -
87A LYS* 2.8 24.4 + - - +
88A ASP* 5.0 2.7 - - + -
117A GLY* 5.5 0.4 - - - -
118A HIS 5.6 5.6 + - - -
119A THR* 6.0 2.3 - - - +
131A LEU* 3.0 48.3 + - + +
132A SER* 3.9 7.0 - - - +
134A ARG* 1.3 75.0 - - + +
136A ALA* 1.3 64.3 + - - +
138A VAL* 3.4 4.4 + - - +
139A VAL* 3.2 28.2 + - - +
197A ARG* 5.1 9.3 - - - +
199A VAL* 4.2 11.4 - - + -
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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
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115A VAL* 3.4 26.2 - - + +
117A GLY 3.7 10.5 - - - +
132A SER 2.9 17.9 + - - +
133A GLU 3.7 4.0 - - - +
135A ARG* 1.3 75.7 - - - +
137A TYR* 1.3 58.1 + - - +
139A VAL 3.3 1.4 + - - -
140A ALA* 2.8 30.3 + - - +
155A ALA* 3.7 2.9 - - + -
156A VAL 3.4 26.9 - - - +
199A VAL* 4.4 4.4 - - - +
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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
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133A GLU* 2.8 21.0 + - + +
134A ARG* 3.5 36.6 - - - +
136A ALA* 1.3 78.3 - - - +
138A VAL* 1.3 56.6 + - + +
140A ALA* 3.2 0.7 + - + -
141A ASN* 2.7 51.3 + - + +
155A ALA* 3.6 16.3 - - + +
229A TRS 3.2 46.4 + - - -
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Residues in contact with VAL 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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83A PHE* 4.2 5.4 - - + -
88A ASP* 3.7 22.4 - - + +
90A LEU* 3.7 28.4 - - + +
134A ARG* 2.9 55.2 + - - +
135A ARG* 3.8 6.5 - - - +
137A TYR* 1.3 79.9 - - + +
139A VAL* 1.3 62.1 + - - +
141A ASN* 3.5 6.9 + - - +
142A ASN* 3.1 21.7 + - - +
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Residues in contact with VAL 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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77A LEU* 5.1 2.0 - - + -
82A LEU* 4.0 26.9 - - + -
83A PHE* 4.3 6.7 - - + -
90A LEU* 4.5 5.6 - - + -
98A LEU* 4.1 19.5 - - + -
115A VAL* 4.0 16.4 - - + -
135A ARG 3.2 13.9 + - - +
136A ALA 3.7 6.5 - - - +
138A VAL* 1.3 73.9 - - - +
140A ALA* 1.3 66.2 + - - +
142A ASN* 3.1 8.7 + - - +
143A LEU* 3.1 24.5 + - + +
199A VAL* 3.9 14.8 - - + -
201A VAL* 4.1 18.6 - - + -
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Residues in contact with ALA 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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115A VAL* 3.8 19.3 - - + +
136A ALA 2.8 17.3 + - - +
137A TYR* 3.6 3.6 - - - +
139A VAL* 1.3 76.8 - - - +
141A ASN* 1.3 63.2 + - - +
143A LEU* 3.2 4.7 + - - +
144A VAL* 3.0 27.3 + - - +
153A ILE* 3.5 20.4 - - + +
154A SER 4.3 1.3 - - - +
155A ALA* 3.9 15.5 - - + -
229A TRS 4.6 8.5 - - - +
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Residues in contact with ASN 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 TYR* 2.7 40.0 + - + +
138A VAL* 3.7 7.1 - - - +
140A ALA* 1.3 72.7 - - - +
142A ASN* 1.3 59.6 + - - +
144A VAL* 3.4 2.5 + - - +
145A SER* 2.9 30.3 + - - -
229A TRS 3.2 41.0 + - - -
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Residues in contact with ASN 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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90A LEU* 3.9 12.6 - - + +
95A GLN* 3.7 32.7 - - - +
98A LEU* 3.1 33.5 - - + +
138A VAL 3.1 14.7 + - - +
139A VAL 3.1 9.6 + - - +
141A ASN* 1.3 81.1 + - - +
143A LEU* 1.3 61.8 + - - +
145A SER* 2.6 25.8 + - - -
146A ASN* 3.0 25.7 + - - +
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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 LEU* 3.6 39.3 - - + +
101A LEU* 4.3 8.5 - - + -
102A ALA* 4.1 15.3 - - + +
105A LEU* 5.1 1.3 - - + -
113A VAL* 4.1 8.5 - - + -
115A VAL* 4.3 8.1 - - + -
139A VAL* 3.1 16.6 + - + +
140A ALA 3.2 6.3 + - - +
142A ASN* 1.3 76.7 - - - +
144A VAL* 1.3 62.2 + - - +
146A ASN* 3.0 9.5 + - - +
147A GLY 3.2 1.0 + - - -
148A VAL* 3.0 34.8 + - + +
153A ILE* 3.9 16.8 - - + -
201A VAL* 4.1 30.7 - - + -
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Residues in contact with VAL 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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140A ALA 3.0 16.3 + - - +
141A ASN* 3.6 11.2 - - - +
143A LEU* 1.3 76.9 - - - +
145A SER* 1.3 63.6 + - - +
147A GLY* 3.1 13.3 + - - -
148A VAL 3.4 19.5 + - - +
150A VAL* 3.6 27.4 - - + -
153A ILE* 3.8 26.9 - - + -
229A TRS 3.9 24.5 - - - +
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Residues in contact with SER 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 ASN* 2.9 19.4 + - - +
142A ASN* 2.6 26.8 + - - -
144A VAL* 1.3 78.0 - - - +
146A ASN* 1.3 67.9 + - - +
147A GLY 3.4 0.4 + - - -
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Residues in contact with ASN 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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95A GLN 4.6 0.8 + - - -
99A LYS* 3.5 45.9 - - + +
102A ALA* 3.4 32.9 - - + +
103A GLN* 4.6 7.0 + - + +
106A SER* 5.8 0.7 - - - -
142A ASN* 3.0 41.2 + - - +
143A LEU 3.0 3.8 + - - -
144A VAL 3.0 1.2 - - - -
145A SER* 1.3 85.3 + - - +
147A GLY* 1.3 54.7 + - - +
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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
------------------------------------------------------------
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