Contacts of the helix formed by residues 134 - 152 (chain B) in PDB entry 1AYZ
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 LYS 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU 3.1 7.4 + - - -
130B PHE* 3.5 48.2 + - + +
131B LYS 5.7 0.7 - - - +
132B ASP 3.7 3.2 + - - -
133B HIS* 1.3 73.5 - - - +
135B SER* 1.3 60.9 + - - +
137B TYR* 3.6 10.5 - - + +
138B VAL* 3.0 41.9 + - + +
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B HIS* 4.1 6.8 + - - +
134B LYS* 1.3 76.9 - - - +
136B GLN* 1.3 69.4 + - - +
138B VAL* 3.5 6.7 + - - +
139B LYS* 3.1 24.7 + - - +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.4 20.3 - - + +
133B HIS* 2.8 43.0 + - + +
135B SER* 1.3 82.8 + - - +
137B TYR* 1.3 55.2 + - - +
139B LYS* 3.0 25.1 + - + +
140B ARG* 2.8 36.5 + - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 4.2 14.1 - - + +
48B TYR* 2.9 31.9 + - - -
77B PHE* 3.8 21.1 - + - -
79B PRO* 4.3 9.6 - - + -
116B PRO* 3.5 15.8 - - + +
126B ALA 3.8 21.1 - - - -
129B LEU* 4.0 12.2 - - + +
130B PHE* 3.5 51.6 - + + +
133B HIS 3.1 4.8 + - - +
134B LYS* 3.6 11.0 - - + +
136B GLN* 1.3 72.4 - - - +
138B VAL* 1.3 77.3 + - + +
140B ARG* 3.0 5.2 + - - +
141B VAL* 2.9 50.4 + - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 3.7 25.8 - - + -
134B LYS* 3.0 28.8 + - + +
135B SER* 3.6 6.1 - - - +
137B TYR* 1.3 89.9 - - + +
139B LYS* 1.3 62.4 + - - +
141B VAL* 3.2 7.2 + - - +
142B LYS* 2.9 44.0 + - + +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER 3.1 13.7 + - - +
136B GLN* 3.0 28.3 + - + +
138B VAL* 1.3 76.2 - - - +
140B ARG* 1.3 78.8 + - - +
142B LYS* 3.2 9.9 + - - +
143B GLU* 3.2 46.8 + - + +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.5 41.0 - - + -
125B GLU* 3.1 37.3 + - - -
129B LEU* 4.1 13.8 - - + +
136B GLN* 2.8 12.9 + - - +
137B TYR 3.4 8.3 - - - +
139B LYS* 1.3 87.7 - - - +
141B VAL* 1.3 61.3 + - - +
143B GLU* 3.3 36.6 + - - +
144B THR* 3.4 15.6 + - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 3.1 37.7 - - + +
48B TYR* 3.4 23.1 - - + +
77B PHE* 3.5 26.7 - - + +
137B TYR* 2.9 43.4 + - + +
138B VAL 3.2 7.6 + - - +
140B ARG* 1.3 76.3 - - - +
142B LYS* 1.3 61.5 + - - +
144B THR* 2.5 25.1 + - - -
145B VAL* 3.2 6.9 + - - +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR 4.5 3.2 + - - -
47B PRO* 3.6 28.8 + - - +
49B GLU* 5.3 6.9 + - - +
138B VAL* 2.9 37.8 + - + +
139B LYS* 3.2 10.3 + - + +
141B VAL* 1.3 73.9 - - - +
143B GLU* 1.3 63.8 - - - +
145B VAL* 3.0 11.0 + - + +
146B GLU* 3.0 30.7 + - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 5.0 4.7 - - - +
139B LYS* 3.2 42.4 + - + +
140B ARG* 3.5 26.9 + - - +
141B VAL 3.3 0.2 - - - -
142B LYS* 1.3 76.5 - - - +
144B THR* 1.3 57.1 + - + +
146B GLU* 3.4 15.5 + - - +
147B LYS* 2.9 30.8 + - - +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 5.0 2.1 - - - -
53B PHE* 3.8 15.9 - - - -
75B GLU* 3.5 38.9 - - + +
76B MET* 4.0 4.2 - - - +
77B PHE* 3.9 25.8 + - + +
140B ARG* 3.4 14.1 + - + +
141B VAL* 2.5 24.9 + - - +
143B GLU* 1.3 74.5 - - + +
145B VAL* 1.3 59.1 + - - +
147B LYS* 3.8 7.7 - - - +
148B SER* 3.0 27.9 + - - -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO 3.6 20.0 - - - +
48B TYR* 3.7 18.4 - - - +
49B GLU 3.7 8.5 - - - +
51B GLY* 3.5 13.9 - - - -
53B PHE* 4.0 10.3 - - + -
141B VAL 3.2 15.5 - - - +
142B LYS* 3.0 12.7 + - + +
144B THR* 1.3 75.5 + - - +
146B GLU* 1.3 66.0 + - + +
148B SER* 2.7 25.5 + - - -
149B TRP* 3.3 37.2 + - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 3.0 20.0 + - + +
143B GLU* 3.6 16.7 - - - +
145B VAL* 1.3 75.8 - - + +
147B LYS* 1.3 63.8 + - - +
149B TRP* 2.9 38.3 + - + +
150B GLU* 3.0 27.2 + - + +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 3.5 43.5 + - + +
143B GLU 2.9 16.6 + - - +
144B THR* 3.8 9.2 - - - +
146B GLU* 1.3 75.9 - - - +
148B SER* 1.3 61.3 + - - +
150B GLU* 3.3 21.1 + - + +
151B ASP* 3.1 49.0 + - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY* 3.6 3.3 - - - -
52B THR* 2.9 46.8 + - - -
53B PHE* 4.3 10.3 - - - -
54B ARG* 4.2 1.2 + - - -
74B SER* 4.7 6.5 - - - -
144B THR 3.0 15.5 + - - -
145B VAL 2.7 18.3 + - - -
147B LYS* 1.3 76.1 - - - +
149B TRP* 1.3 59.0 + - - +
151B ASP* 3.5 14.9 - - - +
152B ASP* 3.0 23.4 - - - +
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Residues in contact with TRP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU 5.1 0.9 - - - -
50B ASP* 2.7 40.4 + - + -
51B GLY* 4.0 1.2 - - - -
52B THR* 3.8 15.3 - - + +
145B VAL* 3.5 28.7 - - + -
146B GLU* 2.9 29.9 + - + +
148B SER* 1.3 84.6 - - - +
150B GLU* 1.3 60.8 + - + +
151B ASP 3.2 0.2 - - - -
152B ASP* 3.0 24.3 + - - +
153B MET* 3.2 15.9 + - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU* 3.0 30.3 + - + +
147B LYS* 3.6 26.0 + - + +
149B TRP* 1.3 76.9 - - + +
151B ASP* 1.3 63.6 + - - +
153B MET* 3.1 21.3 + - - +
154B ASP* 3.2 17.8 - - - +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 5.5 7.7 - - - +
74B SER* 4.7 16.5 + - - +
75B GLU* 5.1 2.6 + - - +
147B LYS* 3.1 45.7 + - - +
148B SER* 3.5 16.4 - - - +
149B TRP 3.2 0.2 - - - -
150B GLU* 1.3 76.1 - - - +
152B ASP* 1.3 64.4 + - - +
154B ASP* 3.6 25.5 + - - +
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET* 5.2 0.2 - - - +
52B THR* 3.1 23.6 + - - +
54B ARG* 2.6 35.7 + - - -
148B SER 3.0 12.2 - - - +
149B TRP* 3.0 12.5 + - - +
151B ASP* 1.3 77.4 - - - +
153B MET* 1.3 58.4 + - + +
154B ASP 2.9 17.2 + - - -
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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