Contacts of the helix formed by residues 134 - 152 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU 3.1 7.9 + - - -
130C PHE* 3.7 37.2 + - + +
131C LYS 5.5 1.1 - - - +
132C ASP 3.7 3.2 + - - -
133C HIS* 1.3 73.5 - - - +
135C SER* 1.3 55.6 + - - +
137C TYR* 3.7 11.0 - - + -
138C VAL* 2.9 49.5 + - + +
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C HIS* 4.0 7.6 + - - +
134C LYS* 1.3 77.0 - - - +
136C GLN* 1.3 64.3 + - - +
138C VAL* 3.5 6.3 + - - +
139C LYS* 3.0 24.8 + - - +
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Residues in contact with GLN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 4.1 24.7 - - + +
133C HIS* 2.8 43.6 + - + +
135C SER* 1.3 75.4 + - - +
137C TYR* 1.3 67.0 + - - +
139C LYS* 3.1 20.8 + - + +
140C ARG* 2.9 29.3 + - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 4.1 13.4 - - + +
48C TYR* 2.8 34.4 + - - -
77C PHE* 3.6 30.5 - + - -
79C PRO* 4.6 8.7 - - + -
116C PRO* 4.0 13.3 - - + +
126C ALA 3.8 16.2 - - - -
129C LEU* 3.9 10.7 - - + +
130C PHE* 3.5 50.3 - + + +
133C HIS 3.1 4.9 + - - -
134C LYS* 3.5 9.9 - - + +
136C GLN* 1.3 74.7 - - - +
138C VAL* 1.3 84.4 + - + +
140C ARG* 3.0 5.9 + - - +
141C VAL* 2.9 43.3 + - + +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 3.7 22.0 - - + -
134C LYS* 2.9 34.4 + - + +
135C SER* 3.7 6.5 - - - +
137C TYR* 1.3 90.0 - - + +
139C LYS* 1.3 63.5 + - - +
141C VAL* 3.2 5.8 + - - +
142C LYS* 3.0 38.4 + - + +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER 3.0 14.6 + - - +
136C GLN* 3.3 23.0 - - + +
138C VAL* 1.3 77.6 - - - +
140C ARG* 1.3 74.6 + - - +
142C LYS* 3.1 8.5 + - - +
143C GLU* 3.1 45.7 + - + +
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 3.6 39.3 - - + -
125C GLU* 3.2 36.8 + - - -
129C LEU* 3.7 17.2 - - - +
136C GLN* 2.9 16.5 + - - +
137C TYR 3.4 7.9 - - - +
139C LYS* 1.3 83.9 - - - +
141C VAL* 1.3 62.0 + - - +
143C GLU* 3.2 36.7 + - - +
144C THR* 3.3 19.2 + - + +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 3.2 31.0 - - + +
48C TYR* 3.4 28.9 - - + +
77C PHE* 3.8 20.0 - - + +
137C TYR* 2.9 52.3 + - + +
138C VAL 3.6 7.2 - - - +
139C LYS 3.2 0.4 - - - -
140C ARG* 1.3 74.2 - - - +
142C LYS* 1.3 62.9 + - - +
144C THR* 2.6 27.9 + - - -
145C VAL* 3.0 7.8 + - - +
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR 4.5 4.0 + - - -
47C PRO* 3.4 28.0 + - - +
49C GLU* 5.2 7.9 + - - +
138C VAL* 3.0 38.2 + - + +
139C LYS* 3.4 9.4 - - - +
141C VAL* 1.3 76.3 - - - +
143C GLU* 1.3 57.4 + - + +
145C VAL* 3.2 11.4 + - + +
146C GLU* 3.0 32.0 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLU* 5.1 3.8 - - - +
139C LYS* 3.1 48.9 + - + +
140C ARG* 3.3 28.8 - - - +
141C VAL 3.1 0.2 - - - -
142C LYS* 1.3 77.3 - - + +
144C THR* 1.3 58.4 + - + +
146C GLU* 3.4 8.1 + - - +
147C LYS* 3.0 27.2 + - - +
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 4.9 1.6 - - - -
53C PHE* 3.7 16.7 - - - -
75C GLU* 3.5 41.6 - - + +
76C MET* 4.1 6.0 - - - -
77C PHE* 4.0 23.4 + - + -
140C ARG* 3.4 16.6 - - + +
141C VAL* 2.6 20.9 + - - +
143C GLU* 1.3 74.6 - - + +
145C VAL* 1.3 60.9 + - - +
147C LYS* 3.8 6.5 - - - +
148C SER* 2.9 29.6 + - - -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO 3.4 23.8 - - - +
48C TYR* 3.9 12.6 - - - +
49C GLU 3.5 22.2 - - - +
51C GLY* 3.6 15.3 - - - -
53C PHE* 4.1 9.2 - - + -
141C VAL 3.0 17.2 + - - +
142C LYS* 3.3 12.8 - - + +
144C THR* 1.3 76.9 + - - +
146C GLU* 1.3 62.4 + - - +
148C SER* 2.6 26.2 + - - -
149C TRP* 3.4 25.6 + - + -
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS 3.0 14.9 + - - +
143C GLU* 3.6 10.7 - - - +
145C VAL* 1.3 75.4 - - + +
147C LYS* 1.3 60.1 + - - +
149C TRP* 2.8 53.5 + - + +
150C GLU* 3.1 26.7 + - - +
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLU* 3.5 47.9 + - + +
143C GLU 3.0 17.4 + - - +
144C THR* 4.0 6.3 - - - +
145C VAL 3.4 0.2 - - - -
146C GLU* 1.3 74.9 - - - +
148C SER* 1.3 62.4 + - - +
150C GLU* 3.2 20.0 + - + +
151C ASP* 3.0 46.0 + - - +
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLY* 3.6 2.1 - - - -
52C THR* 2.8 57.7 + - - +
53C PHE* 4.2 11.7 - - - -
54C ARG* 4.5 0.3 + - - +
74C SER* 4.8 6.1 - - - -
144C THR 2.9 14.4 + - - -
145C VAL 2.6 18.9 + - - -
146C GLU 3.1 0.4 - - - -
147C LYS* 1.3 76.8 - - - +
149C TRP* 1.3 59.9 + - - +
151C ASP* 3.5 20.2 - - - +
152C ASP* 3.5 8.1 - - - +
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Residues in contact with TRP 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU 4.5 0.9 - - - -
50C ASP* 2.8 37.7 + - + -
52C THR* 3.8 15.7 - - + +
145C VAL* 3.5 28.9 + - + -
146C GLU* 2.8 37.3 + - + +
148C SER* 1.3 86.4 + - - +
150C GLU* 1.3 66.5 + - + +
151C ASP 3.1 1.8 - - - -
152C ASP* 3.0 20.7 + - - +
153C MET* 3.5 13.7 + - + +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLU* 3.1 33.4 + - - +
147C LYS* 3.2 21.0 + - + +
149C TRP* 1.3 76.1 - - + +
151C ASP* 1.3 60.8 + - - +
152C ASP 3.3 0.2 - - - -
153C MET* 3.2 21.1 + - + +
154C ASP* 2.9 22.1 - - - +
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Residues in contact with ASP 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ARG* 5.5 7.0 - - - +
74C SER* 4.7 16.5 + - - -
75C GLU 5.2 0.9 + - - -
147C LYS* 3.0 44.1 + - - +
148C SER* 3.5 16.9 - - - +
149C TRP 3.1 0.2 - - - -
150C GLU* 1.3 79.2 - - - +
152C ASP* 1.3 63.7 + - - +
153C MET 3.5 0.2 + - - -
154C ASP* 3.6 22.4 + - - +
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 5.3 0.2 - - - +
52C THR* 3.1 26.7 + - - +
54C ARG* 2.9 36.0 + - - -
148C SER 3.5 8.8 - - - +
149C TRP* 3.0 8.9 + - - +
151C ASP* 1.3 74.7 - - - +
153C MET* 1.3 63.6 + - + +
154C ASP 3.1 11.6 + - - -
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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