Contacts of the helix formed by residues 134 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU 3.2 7.4 + - - -
130A PHE* 3.7 43.5 - - + +
131A LYS 5.3 1.8 - - - +
132A ASP 3.6 3.6 + - - -
133A HIS* 1.3 72.8 - - - +
135A SER* 1.3 61.2 + - - +
136A GLN 3.4 0.2 - - - -
137A TYR* 3.6 13.9 - - + +
138A VAL* 3.2 37.3 + - + +
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Residues in contact with SER 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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133A HIS* 4.1 7.4 + - - +
134A LYS* 1.3 79.8 - - - +
136A GLN* 1.3 68.6 + - - +
138A VAL* 3.6 5.9 + - - +
139A LYS* 3.1 24.1 + - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.1 23.9 - - + +
133A HIS* 2.9 41.1 + - + +
135A SER* 1.3 83.0 + - - +
137A TYR* 1.3 56.8 + - - +
139A LYS* 3.0 24.0 + - + +
140A ARG* 2.7 38.3 + - - +
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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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47A PRO* 3.9 19.6 - - + +
48A TYR* 3.3 30.7 + - - -
77A PHE* 3.9 15.7 - + - -
79A PRO* 4.8 8.5 - - + -
116A PRO* 3.4 18.4 - - + +
126A ALA 3.9 17.3 - - - -
129A LEU* 4.1 12.8 - - + +
130A PHE* 3.3 51.4 - + + +
133A HIS 3.1 9.8 + - - +
134A LYS* 3.6 11.4 - - + +
136A GLN* 1.3 75.1 - - - +
138A VAL* 1.3 71.6 + - + +
140A ARG* 3.1 4.7 + - - +
141A VAL* 2.8 52.6 + - + +
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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
----------------------------------------------------------
47A PRO* 3.7 28.3 - - + -
134A LYS* 3.2 27.2 + - + +
135A SER* 3.7 6.3 - - - +
137A TYR* 1.3 90.4 - - + +
139A LYS* 1.3 57.5 + - - +
141A VAL* 3.2 1.8 + - - +
142A LYS* 2.8 53.9 + - + +
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Residues in contact with LYS 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 SER 3.1 14.7 + - - +
136A GLN* 3.0 26.8 + - + +
138A VAL* 1.3 76.1 - - - +
140A ARG* 1.3 66.8 + - - +
142A LYS* 3.4 9.1 + - - +
143A GLU* 3.1 45.5 + - + +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.6 36.9 - - + -
125A GLU* 3.2 40.5 + - - -
129A LEU* 4.0 16.3 - - + +
136A GLN* 2.7 17.8 + - - +
137A TYR 3.4 7.4 - - - +
139A LYS* 1.3 76.0 - - - +
141A VAL* 1.3 65.1 + - - +
143A GLU* 3.0 43.4 + - - +
144A THR* 3.3 11.8 + - + +
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Residues in contact with VAL 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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47A PRO* 3.2 32.3 - - + +
48A TYR* 3.3 36.1 - - + +
77A PHE* 3.6 27.4 - - + +
137A TYR* 2.8 40.0 + - + +
138A VAL* 3.6 4.3 - - - +
140A ARG* 1.3 69.6 - - - +
142A LYS* 1.3 64.3 + - - +
144A THR* 2.9 24.9 + - - -
145A VAL* 3.1 7.8 + - - +
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Residues in contact with LYS 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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46A THR 4.8 2.2 + - - -
47A PRO* 3.7 25.3 + - - +
49A GLU* 5.5 6.5 + - - +
138A VAL* 2.8 48.9 + - + +
139A LYS* 3.5 9.2 - - - +
141A VAL* 1.3 73.6 - - - +
143A GLU* 1.3 61.8 - - - +
145A VAL* 3.1 10.6 + - + +
146A GLU* 3.1 31.0 + - - +
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Residues in contact with GLU 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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75A GLU* 5.0 4.0 - - - +
139A LYS* 3.1 47.7 + - + +
140A ARG* 3.0 33.1 + - - +
142A LYS* 1.3 78.0 - - + +
144A THR* 1.3 56.9 + - + +
146A GLU* 3.5 8.7 + - - +
147A LYS* 3.1 25.8 + - - +
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Residues in contact with THR 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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48A TYR* 4.9 2.4 - - - -
53A PHE* 3.7 16.9 - - - -
75A GLU* 3.5 39.0 - - + +
76A MET* 4.2 2.9 - - - -
77A PHE* 4.0 28.0 + - + +
140A ARG* 3.5 15.7 - - + +
141A VAL* 2.9 17.4 + - - +
143A GLU* 1.3 74.8 - - + +
145A VAL* 1.3 60.4 + - - +
147A LYS* 3.6 8.3 - - - +
148A SER* 3.0 28.6 + - - -
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Residues in contact with VAL 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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47A PRO 3.5 20.6 - - - +
48A TYR* 3.6 19.1 - - - +
49A GLU 3.8 10.3 - - - +
51A GLY* 3.5 22.0 - - - +
53A PHE* 3.8 11.7 - - + -
141A VAL 3.1 15.9 + - - +
142A LYS* 3.1 10.3 + - + +
144A THR* 1.3 77.7 + - - +
146A GLU* 1.3 60.4 + - + +
148A SER* 2.8 23.6 + - - -
149A TRP* 3.5 26.0 + - + -
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Residues in contact with GLU 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 LYS* 3.1 18.8 + - + +
143A GLU* 3.8 9.4 - - - +
145A VAL* 1.3 76.5 - - + +
147A LYS* 1.3 56.2 + - - +
149A TRP* 2.7 48.8 + - + +
150A GLU* 3.1 24.8 + - - +
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Residues in contact with LYS 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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75A GLU* 4.2 39.8 + - + +
143A GLU 3.1 18.6 + - - +
144A THR* 3.6 10.1 - - - +
145A VAL 3.4 0.2 - - - -
146A GLU* 1.3 75.1 - - - +
148A SER* 1.3 61.0 + - - +
150A GLU* 3.3 25.1 + - - +
151A ASP* 3.2 44.8 + - - +
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Residues in contact with SER 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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51A GLY* 3.6 1.9 - - - -
52A THR* 2.8 48.6 + - - +
53A PHE* 4.3 11.0 - - - -
54A ARG* 4.3 0.3 + - - +
74A SER* 4.7 6.5 - - - -
144A THR 3.0 15.9 + - - -
145A VAL 2.8 15.1 + - - -
146A GLU 3.1 0.4 - - - -
147A LYS* 1.3 76.3 - - - +
149A TRP* 1.3 58.5 + - - +
151A ASP* 3.6 13.8 - - - +
152A ASP* 2.9 24.6 - - - +
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Residues in contact with TRP 149 (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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49A GLU 4.7 1.3 - - - -
50A ASP* 2.9 41.2 + - + -
51A GLY* 3.9 0.6 - - - -
52A THR* 3.8 14.9 - - + +
145A VAL* 3.5 27.6 + - + -
146A GLU* 2.7 34.1 + - + +
148A SER* 1.3 83.1 - - - +
150A GLU* 1.3 61.2 + - + +
151A ASP 3.2 0.2 - - - -
152A ASP* 3.3 16.4 + - - +
153A MET* 3.4 16.5 + - - +
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Residues in contact with GLU 150 (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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146A GLU* 3.1 28.9 + - - +
147A LYS* 3.3 26.0 + - + +
149A TRP* 1.3 73.4 - - + +
151A ASP* 1.3 66.5 + - - +
153A MET* 3.1 14.9 + - - +
154A ASP* 3.0 26.2 - - - +
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Residues in contact with ASP 151 (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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54A ARG* 5.3 9.0 - - - +
73A LEU 5.3 0.7 - - - +
74A SER* 4.3 19.8 + - - -
75A GLU 5.2 0.7 + - - -
147A LYS* 3.2 36.8 + - - +
148A SER* 3.6 15.4 - - - +
150A GLU* 1.3 78.9 - - - +
152A ASP* 1.3 64.8 + - - +
154A ASP* 3.2 26.6 + - - +
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Residues in contact with ASP 152 (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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52A THR* 3.1 22.5 + - - +
54A ARG* 2.8 33.6 + - - -
148A SER 2.9 14.0 - - - +
149A TRP* 3.3 9.9 + - - +
150A GLU 3.2 0.6 - - - -
151A ASP* 1.3 80.9 - - - +
153A MET* 1.3 63.7 + - + +
154A ASP 3.1 5.8 + - - -
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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