Contacts of the helix formed by residues 121 - 142 (chain D) in PDB entry 1AV1
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 PRO 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D GLN 4.0 9.9 - - - +
118D LYS 4.2 9.6 - - - +
119D VAL* 3.0 9.4 - - - +
120D GLU* 1.3 93.6 - - + +
122D LEU* 1.3 63.7 + - + +
124D ALA* 3.0 22.1 + - + +
125D GLU* 3.1 12.0 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 4.1 28.0 - - + -
140C LYS* 5.3 17.3 - - + +
141C LEU* 4.6 10.1 - - + -
118D LYS 5.4 2.0 - - - +
119D VAL* 2.8 35.4 + - + +
121D PRO* 1.3 75.0 - - + +
123D ARG* 1.3 64.0 + - + +
124D ALA 2.9 5.2 - - - -
125D GLU* 3.9 22.6 - - + +
126D LEU* 2.8 31.2 + - + +
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.1 19.6 + - + +
243A GLN* 3.6 28.1 + - - +
229B PHE* 3.2 57.5 - - + -
116D ARG* 4.1 17.6 - - - +
119D VAL* 4.7 2.2 - - + +
120D GLU* 2.7 63.0 + - - +
122D LEU* 1.3 77.0 - - - +
124D ALA* 1.3 49.3 + - - +
126D LEU* 2.9 12.6 - - + +
127D GLN* 2.7 46.3 + - - +
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLU 3.6 0.9 + - - +
121D PRO* 3.0 14.6 + - + +
122D LEU 2.9 0.6 - - - -
123D ARG* 1.3 77.2 - - - +
125D GLU* 1.3 64.6 + - - +
126D LEU 2.7 5.5 + - - -
127D GLN* 2.9 4.2 + - - -
128D GLU* 2.9 31.3 + - + +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LYS* 5.8 1.6 + - - -
140C LYS* 5.7 3.7 + - - -
121D PRO 3.1 8.3 + - - +
122D LEU* 3.2 24.1 + - + +
124D ALA* 1.3 77.7 - - - +
126D LEU* 1.3 59.2 + - + +
128D GLU* 4.4 4.6 - - - +
129D GLY* 4.1 10.2 + - - -
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TYR* 3.5 25.1 - - - +
240A LEU* 4.9 14.4 - - + -
229B PHE* 6.0 3.1 - - + +
233B LEU* 4.2 20.4 - - + -
133C LYS* 6.3 3.4 - - + -
134C LEU* 5.9 1.1 - - + -
137C LEU* 5.8 3.8 - - + -
122D LEU* 2.8 10.5 + - + +
123D ARG* 2.9 29.2 - - + +
124D ALA 2.7 0.6 + - - -
125D GLU* 1.3 78.2 - - - +
127D GLN* 1.3 85.6 + - + +
128D GLU 3.0 2.5 + - - -
129D GLY* 3.1 4.0 + - - -
130D ALA* 3.0 23.0 + - + +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A THR* 5.8 1.0 - - + +
240A LEU* 3.4 38.9 - - + +
241A ASN* 3.0 36.1 + - - +
123D ARG* 2.7 36.4 + - - +
124D ALA* 2.9 4.2 + - - +
126D LEU* 1.3 78.8 - - + +
128D GLU* 1.3 61.2 + - - +
130D ALA* 3.4 7.2 - - - +
131D ARG* 3.2 24.3 + - + +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ALA* 2.9 18.1 + - + +
125D GLU* 4.4 5.4 - - - +
127D GLN* 1.3 74.5 - - - +
129D GLY* 1.3 66.6 + - - +
130D ALA 3.0 1.2 + - - -
131D ARG* 3.2 7.7 + - - +
132D GLN* 3.2 32.2 + - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LYS* 4.8 15.9 - - - -
125D GLU 4.1 6.1 + - - -
126D LEU 3.1 7.0 + - - -
128D GLU* 1.3 78.4 - - - +
130D ALA* 1.3 61.5 + - - +
132D GLN* 3.2 28.6 - - - +
133D LYS* 3.5 16.8 + - - +
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 5.8 5.8 - - + +
236A TYR* 4.2 26.0 - - + +
237A THR* 4.4 12.1 - - + -
240A LEU* 5.1 0.2 - - + -
126D LEU* 3.0 12.2 + - + +
127D GLN* 3.4 15.5 - - - +
128D GLU 3.0 0.2 + - - -
129D GLY* 1.3 74.5 - - - +
131D ARG* 1.3 67.5 + - - +
132D GLN 3.0 1.8 + - - -
133D LYS* 3.4 4.6 + - - +
134D LEU* 3.2 17.9 + - - +
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A THR* 5.3 4.2 - - + +
127D GLN* 3.2 11.2 + - + +
128D GLU* 3.2 7.6 + - - +
130D ALA* 1.3 78.3 - - - +
132D GLN* 1.3 63.8 + - - +
134D LEU* 2.9 38.6 - - + +
135D HIS* 3.6 17.5 + - + -
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Residues in contact with GLN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU* 3.2 19.8 + - - +
129D GLY* 3.2 24.1 - - - +
130D ALA 3.0 0.6 - - - -
131D ARG* 1.3 78.9 - - - +
133D LYS* 1.3 66.9 - - + +
134D LEU 3.0 0.2 + - - -
135D HIS* 3.5 10.0 + - - +
136D GLU* 3.8 8.1 + - - +
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Residues in contact with LYS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 4.4 19.8 + - + +
126C LEU* 4.6 16.9 - - + +
129C GLY* 4.4 16.6 + - - -
133C LYS* 4.9 17.6 - - - +
129D GLY 3.9 12.6 - - - +
130D ALA* 3.4 7.0 + - - +
132D GLN* 1.3 82.1 - - + +
134D LEU* 1.3 63.4 + - - +
136D GLU* 2.8 43.4 + - + +
137D LEU* 3.1 21.7 + - + +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 5.0 14.9 - - + +
233A LEU* 5.7 11.9 - - + -
237A THR* 6.0 7.0 - - + +
130D ALA 3.2 9.9 + - - +
131D ARG* 2.9 30.7 - - + +
132D GLN 3.0 0.2 + - - -
133D LYS* 1.3 76.1 - - - +
135D HIS* 1.3 81.4 + - + +
137D LEU* 3.6 6.4 + - - +
138D GLN* 2.9 36.5 + - + +
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Residues in contact with HIS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ARG* 3.6 22.6 + - + -
132D GLN 3.5 4.7 + - - +
133D LYS 3.2 0.2 - - - -
134D LEU* 1.3 99.6 - - + +
136D GLU* 1.3 63.7 + - - +
137D LEU 2.9 1.8 - - - -
138D GLN* 3.0 25.5 + - - -
139D GLU* 2.7 58.8 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 4.3 15.5 - - - +
132D GLN* 3.8 6.0 + - - +
133D LYS* 3.0 40.6 + - - +
135D HIS* 1.3 76.5 - - - +
137D LEU* 1.3 61.3 + - + +
140D LYS* 2.6 46.7 - - + +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 6.1 7.2 - - + -
230A LEU* 5.6 10.3 - - + -
233A LEU* 5.9 8.7 - - + -
122C LEU* 5.0 10.3 - - + -
125C GLU* 3.7 21.3 - - - +
126C LEU* 3.7 35.0 - - + -
133D LYS* 3.1 21.9 + - + +
134D LEU* 4.0 5.4 - - - +
135D HIS 2.9 0.2 - - - -
136D GLU* 1.3 93.3 - - + +
138D GLN* 1.3 60.8 + - - +
139D GLU 3.3 1.3 - - - -
140D LYS* 4.6 5.2 - - + -
141D LEU* 2.7 42.8 + - + +
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LEU* 5.5 10.1 - - + +
134D LEU* 2.9 31.6 + - + +
135D HIS* 3.0 35.0 + - - -
137D LEU* 1.3 76.6 - - - +
139D GLU* 1.3 66.2 + - + +
141D LEU* 4.6 4.0 - - - +
142D SER* 2.9 27.8 + - - +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D HIS* 2.7 43.4 + - - +
138D GLN* 1.3 85.8 - - + +
140D LYS* 1.3 58.2 + - - -
141D LEU 3.3 1.1 - - - -
142D SER* 4.0 6.3 - - - -
143D PRO* 3.1 19.6 - - - +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 4.9 14.1 - - - +
122C LEU* 4.8 20.6 - - + +
125C GLU* 5.5 4.6 + - - -
135D HIS 3.7 0.4 + - - -
136D GLU* 2.6 33.4 + - + +
137D LEU* 4.6 5.6 - - + -
139D GLU* 1.3 77.7 - - - +
141D LEU* 1.3 58.5 + - - +
143D PRO* 3.0 19.1 - - - +
144D LEU* 4.2 9.5 - - + +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PHE* 6.2 0.2 - - + -
227A VAL* 3.5 25.8 - - + -
229A PHE* 5.1 6.3 - - + -
230A LEU* 4.7 15.3 - - + -
115C TYR* 3.9 30.1 - - + +
119C VAL* 5.1 8.1 - - + -
122C LEU* 6.0 8.1 - - + -
137D LEU* 2.7 26.3 + - + +
138D GLN* 5.2 2.5 - - - +
140D LYS* 1.3 77.0 - - - +
142D SER* 1.3 69.3 + - - +
143D PRO* 3.0 3.4 - - - -
144D LEU* 2.8 24.6 + - + -
145D GLY* 3.2 12.0 + - - +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLN* 2.9 22.8 + - - +
139D GLU* 4.0 9.0 - - - -
141D LEU* 1.3 80.3 - - - +
143D PRO* 1.3 66.5 - - - +
145D GLY* 3.2 12.7 + - - +
146D GLU* 3.4 21.7 + - - +
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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
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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