Contacts of the helix formed by residues 125 - 146 (chain A) in PDB entry 5HOO
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 ASN 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 5.3 0.6 + - - -
124A LEU* 1.3 75.8 - - - +
126A GLU* 1.3 65.9 + - - +
127A ARG* 3.7 11.7 - - + +
128A GLN* 2.7 45.3 + - - +
129A MET* 3.1 25.5 + - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASN* 1.3 75.2 - - - +
127A ARG* 1.3 68.9 + - - +
129A MET* 3.6 16.9 - - + +
130A GLU* 3.5 32.7 + - - +
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASN* 3.2 6.7 - - + +
126A GLU* 1.3 83.7 + - - +
128A GLN* 1.3 61.1 + - + +
129A MET 3.1 2.0 - - - -
130A GLU* 2.8 20.5 + - + +
131A ARG* 2.8 71.4 + - + +
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A HIS* 4.1 7.6 + - - -
123A GLU 3.8 4.7 - - - +
124A LEU* 3.5 19.6 - - + +
125A ASN* 2.7 54.2 + - - +
127A ARG* 1.3 80.2 - - + +
129A MET* 1.3 56.4 + - - +
131A ARG* 3.6 11.4 - - + +
132A ARG* 3.0 32.8 + - + +
275A ALA* 5.1 6.5 + - + +
276A TYR* 3.3 38.4 - - - +
-2G G 4.6 7.5 + - - +
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Residues in contact with MET 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.9 24.0 - - + +
125A ASN 3.1 18.2 + - - +
126A GLU* 3.6 17.3 - - + +
127A ARG 2.9 1.2 + - - -
128A GLN* 1.3 77.2 - - - +
130A GLU* 1.3 52.2 + - - +
132A ARG* 2.8 8.7 + - - +
133A LYS 2.7 30.8 + - - -
340A ASP* 3.3 27.1 - - + +
341A GLY* 3.3 19.7 - - - -
342A LYS* 3.3 44.6 - - + +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 3.5 34.6 + - - +
127A ARG* 2.8 24.9 + - - +
129A MET* 1.3 76.2 - - - +
131A ARG* 1.3 60.5 + - - +
133A LYS* 3.9 13.2 - - + -
134A ASN* 2.7 43.7 + - - +
340A ASP 4.3 2.7 + - - +
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 2.8 52.3 + - + +
128A GLN* 3.6 12.6 - - - +
130A GLU* 1.3 76.4 - - - +
132A ARG* 1.3 60.1 + - - +
134A ASN* 4.0 4.3 - - - +
135A THR* 3.0 50.7 + - - +
250A ASN* 5.1 4.0 - - - +
272A PRO* 5.6 4.0 - - - +
273A HIS 4.2 14.1 + - - +
274A ALA* 4.2 21.0 - - + +
275A ALA* 5.3 3.8 - - + +
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Residues in contact with ARG 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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124A LEU* 3.7 19.1 - - - +
128A GLN* 3.0 11.7 + - - +
129A MET 2.8 14.0 + - - +
131A ARG* 1.3 69.8 - - - +
133A LYS* 1.3 65.3 + - - +
135A THR* 3.3 3.8 + - - -
136A CYS* 3.2 30.6 + - - -
274A ALA* 3.6 24.7 - - + -
275A ALA 4.3 8.5 - - - +
276A TYR 4.5 2.7 - - - -
277A SER* 3.5 15.2 + - - +
279A ASP* 2.7 38.0 + - - -
280A LEU* 4.0 15.7 - - + +
336A CYS* 4.2 7.4 - - - -
341A GLY* 3.0 26.7 + - - +
342A LYS 3.3 13.3 + - - -
343A TYR* 3.4 25.9 - - - +
344A PHE* 4.1 7.5 - - - -
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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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129A MET 2.7 16.8 + - - +
130A GLU* 3.4 13.2 + - + +
132A ARG* 1.3 71.4 - - - +
134A ASN* 1.3 62.5 + - - +
136A CYS* 3.6 2.5 + - - +
137A GLU* 2.9 52.9 + - - +
336A CYS* 4.4 5.6 - - - -
337A VAL* 3.6 34.3 - - + +
340A ASP* 3.5 27.2 + - + +
341A GLY* 3.7 20.3 - - - +
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Residues in contact with ASN 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 GLU* 2.7 40.0 + - - +
131A ARG* 4.0 4.7 - - - +
132A ARG 3.3 0.2 - - - -
133A LYS* 1.3 78.3 - - - +
135A THR* 1.3 56.8 + - - +
137A GLU* 3.1 17.3 + - - +
138A ILE* 2.8 47.6 + - + +
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Residues in contact with THR 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 ARG* 3.0 33.2 + - - -
132A ARG 3.3 6.4 + - - -
134A ASN* 1.3 76.2 - - - +
136A CYS* 1.3 67.1 + - - +
138A ILE* 3.4 4.3 + - - +
139A LEU* 3.0 38.1 + - + +
272A PRO* 3.2 44.8 - - + +
273A HIS* 4.0 6.7 - - - +
274A ALA* 3.8 9.8 - - - +
280A LEU* 6.2 1.6 - - + -
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Residues in contact with CYS 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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132A ARG 3.2 8.9 + - - -
133A LYS 3.7 6.5 - - - +
135A THR* 1.3 79.5 - - - +
137A GLU* 1.3 63.3 + - - +
139A LEU* 3.1 5.9 + - - +
140A LEU* 2.9 26.5 + - - +
280A LEU* 3.4 23.6 - - - -
333A TRP* 3.6 36.3 - - - +
336A CYS* 2.9 36.6 - - - -
337A VAL* 3.8 6.3 - - + -
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Residues in contact with GLU 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 LYS* 2.9 45.4 + - - +
134A ASN* 3.4 23.9 + - - +
136A CYS* 1.3 72.3 - - - +
138A ILE* 1.3 70.1 + - + +
140A LEU* 3.5 7.2 + - + +
141A SER* 3.2 24.1 + - - -
337A VAL* 3.7 27.4 - - + +
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Residues in contact with ILE 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 ASN* 2.8 32.6 + - + +
135A THR* 3.9 4.9 - - - +
137A GLU* 1.3 79.2 - - + +
139A LEU* 1.3 65.2 + - + +
141A SER* 3.4 12.0 + - - +
142A ARG* 3.3 21.6 + - + +
272A PRO* 5.9 7.0 - - + -
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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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135A THR* 3.0 41.9 + - + +
136A CYS* 3.5 4.7 - - - +
138A ILE* 1.3 76.3 - - + +
140A LEU* 1.3 59.5 + - - +
142A ARG* 3.5 8.8 + - - +
143A TYR* 2.9 29.6 + - - +
148A PHE* 4.2 13.9 - - + -
271A LEU* 3.7 31.9 - - + -
272A PRO* 4.2 17.7 - - + +
333A TRP* 3.6 44.7 - - + +
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Residues in contact with LEU 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 CYS 2.9 12.4 + - - +
137A GLU* 3.7 8.5 - - - +
138A ILE 3.3 0.2 - - - -
139A LEU* 1.3 73.0 - - - +
141A SER* 1.3 65.7 + - - +
143A TYR* 3.8 7.1 - - + +
144A LYS* 3.1 47.0 + - - +
330A PRO* 3.6 29.6 - - + +
333A TRP* 3.7 15.5 - - + -
334A GLU* 3.8 35.9 - - + +
337A VAL* 3.8 30.3 - - + -
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Residues in contact with SER 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 GLU 3.2 12.3 + - - -
138A ILE* 3.5 16.8 - - - +
140A LEU* 1.3 78.4 - - - +
142A ARG* 1.3 62.3 + - - +
144A LYS* 3.6 11.6 + - - +
145A ARG* 3.4 26.4 + - - +
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Residues in contact with ARG 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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138A ILE* 3.3 12.8 + - - +
139A LEU* 3.9 6.8 - - - +
140A LEU 3.3 0.6 - - - -
141A SER* 1.3 77.5 - - - +
143A TYR* 1.3 64.3 + - - +
145A ARG* 3.2 10.6 + - + +
146A LYS 3.1 22.2 + - - +
148A PHE* 3.5 28.8 - - + +
151A ARG* 5.4 2.0 - - - +
245A ILE* 3.9 19.6 - - - +
269A GLU* 3.0 41.2 + - - -
271A LEU* 4.5 14.0 - - - +
272A PRO* 5.7 2.6 - - - +
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Residues in contact with TYR 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 LEU 2.9 18.9 + - - +
140A LEU* 3.4 10.5 + - + +
142A ARG* 1.3 76.1 - - - +
144A LYS* 1.3 70.3 + - + +
146A LYS* 3.1 24.3 - - - -
147A SER* 3.4 34.0 + - - -
148A PHE* 3.6 5.5 - - + -
149A LEU* 3.9 26.5 - - + +
327A HIS* 5.3 5.6 + - - -
330A PRO* 3.8 30.1 - - + +
333A TRP* 4.1 10.1 - - + -
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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
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140A LEU* 3.1 46.6 + - - +
141A SER* 3.6 10.5 - - - +
142A ARG 3.3 0.2 - - - -
143A TYR* 1.3 85.0 - - + +
145A ARG* 1.3 64.1 + - + +
146A LYS* 4.4 0.3 - - - -
334A GLU* 4.3 10.5 + - - +
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Residues in contact with ARG 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 SER* 3.4 16.7 + - - +
142A ARG* 3.2 11.3 + - + +
144A LYS* 1.3 79.2 - - + +
146A LYS* 1.3 68.2 + - - +
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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 ARG 3.1 13.5 + - - +
143A TYR 3.1 12.2 - - - +
144A LYS 4.4 0.4 - - - -
145A ARG* 1.3 80.9 - - - +
147A SER* 1.3 76.0 + - - +
148A PHE* 3.2 13.2 + - + +
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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
------------------------------------------------------------
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