Contacts of the helix formed by residues 126 - 134 (chain M) in PDB entry 2AAZ
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 VAL 126 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82M TRP* 4.7 7.2 - - + -
87M CYS 5.3 0.4 - - - +
88M THR* 4.0 14.1 - - + +
101M TRP* 6.2 4.5 - - + -
123M LEU* 3.8 45.3 - - + +
124M GLY 2.8 16.3 + - - +
125M PRO* 1.3 74.2 - - - +
127M TYR* 1.3 83.9 + - + +
128M GLY 5.0 1.8 - - - +
129M PHE 2.8 16.5 + - - -
130M GLN* 3.3 6.2 + - - -
182M MET* 3.8 26.5 - - + -
183M ALA* 4.5 1.8 - - + +
184M LEU* 4.1 12.3 - - + +
186M PRO* 6.0 0.7 - - + -
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Residues in contact with TYR 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M TRP* 5.4 0.4 - + - -
83M PHE* 3.5 34.8 - + + -
101M TRP* 3.7 30.5 - + - -
126M VAL* 1.3 83.3 - - + +
128M GLY* 1.3 66.2 + - - +
130M GLN* 3.0 3.1 + - - +
131M TRP* 2.9 33.3 + - - +
173M ALA* 3.9 22.4 - - + +
184M LEU 5.8 2.2 - - - -
185M PRO 4.3 1.3 + - - -
186M PRO* 3.5 26.3 - - + +
187M CYS* 2.7 23.8 + - - -
188M HIS* 3.2 40.5 - + + -
550M UMP 3.5 17.4 - + - -
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Residues in contact with GLY 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M PHE* 3.1 34.4 - - - +
86M GLY* 3.3 21.3 - - - -
87M CYS 4.5 5.7 + - - -
126M VAL* 3.1 3.2 + - - +
127M TYR* 1.3 78.1 - - - +
129M PHE* 1.3 61.2 + - - +
131M TRP* 3.4 5.9 + - - +
132M ARG* 3.2 18.9 + - - +
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Residues in contact with PHE 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M GLY 3.7 10.6 + - - +
88M THR* 3.6 18.4 - - + +
125M PRO* 3.5 28.7 - - + -
126M VAL 2.8 16.1 + - - +
128M GLY* 1.3 73.0 - - - -
130M GLN* 1.3 65.4 + - - +
133M HIS* 2.7 57.9 + + + +
135M GLY 5.3 0.4 - - - -
136M ALA* 3.7 38.6 - - + -
138M TYR* 3.6 30.1 - + + -
145M TYR* 3.6 37.5 - + - -
178M ASP* 4.3 2.9 - - - -
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Residues in contact with GLN 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M PRO* 2.9 31.5 + - - +
126M VAL 3.3 5.8 + - - +
127M TYR 3.0 7.0 + - - +
129M PHE* 1.3 81.4 - - - +
131M TRP* 1.3 62.0 + - - +
134M PHE* 3.1 35.4 + - + +
135M GLY 4.4 0.2 + - - -
152M GLN* 2.8 19.4 + - - -
172M SER 4.0 1.6 - - - +
173M ALA* 3.2 35.9 - - - +
175M ASN* 3.0 26.7 + - - +
178M ASP* 3.0 31.7 + - - +
182M MET* 4.2 1.7 - - + +
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Residues in contact with TRP 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M LEU* 4.5 8.1 - - + -
83M PHE* 3.6 45.1 - + + -
84M VAL* 4.4 11.7 - - + -
127M TYR* 2.9 21.2 + - + +
128M GLY* 3.6 8.7 - - - +
130M GLN* 1.3 78.2 - - - +
132M ARG* 1.3 64.5 + - + +
152M GLN* 3.0 34.2 + - - +
153M LEU* 3.4 12.4 + - + -
171M LEU* 3.8 39.8 + - + +
172M SER* 4.0 7.3 - - - +
173M ALA* 3.8 25.1 - - + +
188M HIS* 4.4 10.0 + + - -
189M MET 6.3 0.2 - - - -
190M PHE* 6.3 0.6 - - - +
230M SER* 6.0 0.4 - - - -
231M TYR* 3.4 28.7 + + - -
234M LEU* 4.0 23.6 - - + -
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Residues in contact with ARG 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M PHE 4.5 0.2 - - - +
84M VAL* 2.6 47.4 + - - +
85M SER 4.7 1.3 - - - -
86M GLY* 4.1 5.2 - - - -
128M GLY 3.2 16.0 + - - +
131M TRP* 1.3 80.3 - - + +
133M HIS* 1.3 86.3 + - + +
148M LYS 4.0 1.7 - - - +
149M GLY 4.7 0.3 - - - +
150M VAL 3.4 7.6 - - - +
151M ASP* 2.7 59.4 + - - +
153M LEU* 3.6 28.1 - - - +
154M GLN* 4.4 6.5 - - - +
292M ILE* 4.3 6.5 - - - +
293M ASP* 2.8 35.7 + - - -
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Residues in contact with HIS 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M SER 5.2 2.8 + - - -
86M GLY* 4.7 11.9 + - - -
129M PHE* 2.7 45.5 + + + +
132M ARG* 1.3 96.9 + - + +
134M PHE* 1.3 66.4 + - - +
135M GLY 3.2 0.5 + - - -
136M ALA* 3.0 25.6 + - + +
145M TYR* 3.0 39.8 + + + +
146M LYS* 4.2 6.5 - - - -
147M GLY 4.6 2.4 + - - -
148M LYS 2.9 27.8 + - - +
149M GLY* 3.8 3.6 - - - -
150M VAL 3.8 1.3 - - - -
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Residues in contact with PHE 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M GLN* 3.1 40.8 + - - +
133M HIS* 1.3 74.4 - - - +
135M GLY* 1.3 64.6 + - - +
149M GLY* 3.3 3.1 - - - -
150M VAL* 2.8 43.1 + - + +
152M GLN* 3.6 21.3 - - - +
172M SER* 4.3 5.6 - - - -
174M TRP 3.4 22.9 - - - -
175M ASN* 3.4 21.1 - - - -
134N PHE* 4.0 17.0 - + - -
174N TRP 5.0 0.2 - - - -
175N ASN* 3.7 15.5 - - - -
176N PRO* 3.5 36.6 - - + -
177N LYS* 4.1 7.3 - - + +
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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