Contacts of the helix formed by residues 131 - 149 (chain A) in PDB entry 2Q8F
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 ASP 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 5.0 6.1 - - - +
128A SER* 2.7 32.5 + - - +
130A GLU* 1.4 68.7 - - - +
132A ALA* 1.4 58.5 + - - +
133A LYS* 2.7 41.9 + - - +
134A ALA* 3.2 35.5 + - + +
135A ILE* 3.4 7.8 + - - +
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Residues in contact with ALA 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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73A LYS* 4.5 8.7 - - - +
130A GLU 3.4 7.0 + - - +
131A ASP* 1.4 69.6 + - - +
133A LYS* 1.4 60.8 + - - +
135A ILE* 3.3 12.9 + - - +
136A TYR* 2.9 28.8 + - - +
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Residues in contact with LYS 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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127A LYS* 6.4 2.2 - - - +
131A ASP* 2.7 20.3 + - - +
132A ALA* 1.4 71.4 - - - +
134A ALA* 1.4 66.9 + - - +
135A ILE 3.1 0.2 - - - -
136A TYR* 4.2 9.9 - - + -
137A ASP* 3.0 54.5 + - - +
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Residues in contact with ALA 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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76A PHE* 4.7 7.6 - - + -
124A PHE* 3.4 15.4 - - + -
127A LYS* 3.9 30.1 - - + +
128A SER 3.8 13.5 - - - +
131A ASP* 3.2 28.1 + - - +
133A LYS* 1.4 79.5 - - - +
135A ILE* 1.3 58.8 + - - +
137A ASP* 3.3 1.1 + - - -
138A PHE* 3.0 27.6 + - - +
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Residues in contact with ILE 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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72A GLU* 3.6 40.6 - - + +
73A LYS* 3.9 26.5 - - + +
76A PHE* 3.3 38.4 - - + -
129A ALA* 3.4 22.2 - - - +
131A ASP 3.6 12.1 - - - +
132A ALA* 3.3 9.0 - - - +
133A LYS 3.1 0.6 - - - -
134A ALA* 1.3 76.0 - - - +
136A TYR* 1.3 63.6 + - - +
138A PHE* 3.2 9.3 + - - +
139A THR* 3.0 21.8 + - - -
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Residues in contact with TYR 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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72A GLU* 4.7 3.6 - - - -
132A ALA 2.9 19.1 + - - +
133A LYS* 3.7 10.1 - - + +
135A ILE* 1.3 72.8 - - - +
137A ASP* 1.4 70.8 + - - +
139A THR* 3.3 11.2 + - + +
140A ASP* 2.9 48.4 + - - +
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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
----------------------------------------------------------
124A PHE* 3.5 18.8 - - + -
127A LYS* 5.8 2.4 + - - +
133A LYS* 3.0 47.8 + - - +
134A ALA* 4.5 0.9 - - - -
136A TYR* 1.4 87.3 - - - +
138A PHE* 1.3 59.8 + - - +
140A ASP* 3.7 10.0 - - - +
141A THR* 2.5 38.9 + - - +
144A ARG* 5.3 0.2 + - - -
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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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76A PHE* 3.2 39.3 - + + -
79A LEU* 3.7 37.0 - - + -
80A ARG* 3.7 23.6 - - + -
83A LEU* 4.6 0.9 - - + -
121A LEU* 3.7 29.6 - - + -
124A PHE* 3.3 23.0 - + + -
134A ALA 3.0 10.9 + - - +
135A ILE 3.4 9.0 - - - +
137A ASP* 1.3 77.8 - - - +
139A THR* 1.3 50.7 + - - +
141A THR* 2.9 4.6 + - - -
142A VAL* 2.7 54.0 + - + +
198A HIS* 4.2 11.9 - + - -
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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
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72A GLU* 2.6 26.0 + - - +
135A ILE 3.0 8.4 + - - -
136A TYR* 3.6 11.2 - - + -
138A PHE* 1.3 76.1 - - - +
140A ASP* 1.3 62.4 + - - +
142A VAL* 3.3 3.2 + - - +
143A ILE* 3.1 37.0 + - + +
198A HIS* 2.9 32.9 + - + +
199A SER* 5.8 0.4 - - - -
202A PHE 3.7 28.5 - - - +
203A GLY* 4.4 0.9 - - - +
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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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136A TYR* 2.9 46.5 + - - +
137A ASP* 3.9 11.0 - - - +
139A THR* 1.3 77.0 - - - +
141A THR* 1.3 56.9 + - - +
143A ILE* 3.5 14.2 + - - +
144A ARG* 3.1 38.4 + - - +
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Residues in contact with THR 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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120A GLU* 3.9 18.2 - - + +
121A LEU* 4.5 6.7 - - + -
124A PHE* 3.5 23.3 - - + -
137A ASP* 2.5 29.0 + - - +
138A PHE* 3.4 4.0 - - - -
140A ASP* 1.3 71.1 - - - +
142A VAL* 1.3 64.4 + - - +
144A ARG* 3.5 30.2 + - - +
145A ILE* 3.0 42.4 + - + +
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Residues in contact with VAL 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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79A LEU* 4.8 0.7 - - + -
83A LEU* 4.5 13.9 - - + -
121A LEU* 5.1 2.2 - - + -
138A PHE* 2.7 49.0 + - + +
139A THR 3.6 7.9 - - - +
141A THR* 1.3 74.5 - - - +
143A ILE* 1.3 55.7 + - - +
145A ILE* 3.8 4.1 - - - +
146A ARG* 3.0 27.9 + - - +
195A LEU* 3.8 27.3 - - + +
198A HIS* 3.9 24.7 - - + -
199A SER* 3.3 20.0 - - - +
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Residues in contact with ILE 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* 3.1 33.2 + - + +
140A ASP* 3.8 15.0 - - - +
142A VAL* 1.3 73.0 - - - +
144A ARG* 1.3 64.5 + - - +
146A ARG* 3.2 12.5 + - - +
147A ASN* 3.1 37.7 + - - +
199A SER* 3.7 24.2 - - - +
203A GLY* 4.3 16.6 - - - +
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Residues in contact with ARG 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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120A GLU* 3.3 27.3 + - - +
137A ASP 5.3 0.2 + - - -
140A ASP* 3.1 27.5 + - - +
141A THR* 3.6 33.9 + - - +
142A VAL 3.4 0.2 - - - -
143A ILE* 1.3 77.4 - - - +
145A ILE* 1.3 57.4 + - - +
147A ASN* 3.4 7.1 + - - +
148A ARG* 2.9 54.8 + - - +
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Residues in contact with ILE 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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87A LEU* 5.8 2.5 - - + -
117A SER* 3.7 35.2 - - - +
120A GLU* 4.1 4.0 - - - +
121A LEU* 3.7 37.2 - - + -
141A THR* 3.0 32.9 + - + +
142A VAL* 3.8 4.3 - - - +
144A ARG* 1.3 73.2 - - - +
146A ARG* 1.3 67.8 + - - +
148A ARG* 3.2 15.2 + - - +
149A HIS* 2.9 35.3 + - + +
191A ILE* 5.9 1.6 - - + -
195A LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 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 VAL 3.0 19.0 + - - +
143A ILE* 3.2 13.5 + - - +
145A ILE* 1.3 77.9 - - - +
147A ASN* 1.3 70.9 + - - +
150A ASN* 3.3 9.0 + - - +
192A ARG* 2.6 46.8 + - - +
195A LEU* 3.9 20.2 - - + -
196A ASN* 3.0 36.2 + - - +
199A SER* 3.8 28.1 + - - +
200A LEU* 4.3 18.8 - - - +
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Residues in contact with ASN 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 ILE* 3.1 29.8 + - - +
144A ARG* 3.8 6.5 - - - +
146A ARG* 1.3 85.9 + - - +
148A ARG* 1.3 66.5 + - - +
150A ASN* 3.1 35.7 + - - +
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Residues in contact with ARG 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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113A TRP* 3.7 58.6 - - + +
116A GLN* 3.4 25.8 + - - +
117A SER* 3.2 31.4 + - - +
120A GLU* 2.9 41.8 + - - -
144A ARG* 2.9 40.7 + - + +
145A ILE* 3.2 13.0 + - - +
147A ASN* 1.3 72.4 - - - +
149A HIS* 1.3 63.8 + - + +
150A ASN 3.3 0.9 + - - -
151A ASP 4.7 0.9 + - - -
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Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.3 8.7 - - + +
113A TRP* 3.4 11.7 + - + -
114A TYR* 3.5 43.4 + + - -
117A SER* 2.7 35.3 + - - -
145A ILE* 2.9 30.1 + - + +
147A ASN 3.1 0.2 - - - -
148A ARG* 1.3 87.1 - - + +
150A ASN* 1.3 63.2 + - - +
151A ASP 3.1 4.7 + - - -
152A VAL* 3.2 23.3 + - + +
188A ARG* 3.0 17.6 + - + +
191A ILE* 5.3 7.2 - - + +
192A ARG* 3.3 13.0 - - - +
195A LEU* 5.2 2.2 - - + +
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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