Contacts of the helix formed by residues 126 - 134 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82F TRP* 4.7 7.0 - - + -
87F CYS 5.2 0.2 - - - +
88F THR* 4.0 15.0 - - + +
101F TRP* 6.3 5.4 - - + -
123F LEU* 3.8 46.0 - - + +
124F GLY 2.8 16.3 + - - +
125F PRO* 1.3 74.7 - - - +
127F TYR* 1.3 83.8 + - + +
128F GLY 5.0 1.1 - - - +
129F PHE 2.8 15.6 + - - -
130F GLN* 3.3 7.3 + - - -
182F MET* 3.8 25.4 - - + -
183F ALA 4.5 1.3 - - - +
184F LEU* 4.0 13.2 - - + +
186F PRO* 5.7 1.1 - - + -
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Residues in contact with TYR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TRP* 5.4 0.2 - + - -
83F PHE* 3.5 33.7 - + + -
101F TRP* 3.7 29.6 - + - -
126F VAL* 1.3 85.0 - - + +
128F GLY* 1.3 67.2 + - - +
130F GLN* 3.1 2.9 + - - +
131F TRP* 2.9 32.8 + - - +
173F ALA* 3.9 22.4 - - + +
184F LEU 5.8 2.5 - - - -
185F PRO 4.3 1.1 + - - -
186F PRO* 3.5 19.9 - - + +
187F CYS* 2.7 28.9 + - - +
188F HIS* 3.2 53.4 - + + -
600F UMP 3.7 7.4 - - - -
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Residues in contact with GLY 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TRP* 6.2 0.2 - - - -
83F PHE* 3.1 34.8 - - - +
86F GLY* 3.3 21.8 - - - -
87F CYS 4.5 5.5 + - - -
126F VAL* 3.1 3.4 + - - +
127F TYR* 1.3 78.6 - - - +
129F PHE* 1.3 62.2 + - - +
131F TRP* 3.4 5.5 + - - +
132F ARG* 3.1 18.9 + - - +
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Residues in contact with PHE 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLY 3.6 11.0 + - - +
88F THR* 3.6 18.4 - - + +
125F PRO* 3.4 28.0 - - + -
126F VAL 2.8 15.8 + - - +
128F GLY* 1.3 72.3 - - - -
130F GLN* 1.3 59.8 + - - +
133F HIS* 2.7 61.2 + + + +
135F GLY 5.3 0.9 - - - -
136F ALA* 3.8 38.1 - - + -
138F TYR* 3.6 27.8 - + + -
145F TYR* 3.6 38.8 - + - -
178F ASP* 4.2 6.7 - - - -
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Residues in contact with GLN 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F PRO* 3.0 31.0 + - - +
126F VAL 4.0 5.6 - - - +
127F TYR 3.1 4.3 + - - +
129F PHE* 1.3 81.3 - - - +
131F TRP* 1.3 61.1 + - - +
134F PHE* 3.2 34.1 + - + +
135F GLY 4.5 0.2 + - - -
152F GLN* 2.8 19.9 + - - -
172F SER 4.0 1.8 - - - +
173F ALA* 3.2 37.7 - - - +
175F ASN* 3.0 26.0 + - + +
178F ASP* 2.9 33.1 + - - +
182F MET* 4.1 1.7 - - + +
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Residues in contact with TRP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 4.5 8.5 - - + -
83F PHE* 3.5 45.5 - + + -
84F VAL* 4.3 11.2 - - + -
127F TYR* 2.9 23.4 + - + +
128F GLY* 3.6 9.4 - - - +
130F GLN* 1.3 77.4 - - - +
132F ARG* 1.3 64.4 + - + +
152F GLN* 3.0 33.0 + - - +
153F LEU* 3.4 13.0 + - + -
171F LEU* 3.8 38.2 + - + +
172F SER* 4.0 8.9 - - - +
173F ALA* 3.8 25.3 - - + +
188F HIS* 4.4 9.1 + + - -
190F PHE* 6.3 0.2 - - - +
230F SER* 6.1 0.2 - - - -
231F TYR* 3.4 27.3 + + - -
234F LEU* 4.0 22.9 - - + -
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Residues in contact with ARG 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F VAL* 3.0 32.2 + - - +
85F SER* 4.8 1.7 - - - +
86F GLY* 4.2 5.4 - - - +
128F GLY 3.1 15.8 + - - +
131F TRP* 1.3 85.8 - - + +
133F HIS* 1.3 88.0 + - + +
148F LYS 4.0 1.7 - - - +
149F GLY 4.7 0.3 - - - +
150F VAL 3.3 12.4 - - - +
151F ASP* 2.8 57.2 + - - +
153F LEU* 3.6 21.1 - - - +
154F GLN* 4.3 9.5 - - - +
292F ILE* 4.0 7.2 - - - +
293F ASP* 2.4 44.5 + - - -
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Residues in contact with HIS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F SER 5.2 2.4 + - - -
86F GLY* 4.7 11.0 + - - -
129F PHE* 2.7 51.3 + + + +
132F ARG* 1.3 97.4 + - + +
134F PHE* 1.3 67.6 + - - +
135F GLY 3.1 0.2 + - - -
136F ALA* 2.9 21.4 + - + +
145F TYR* 3.1 39.3 + + + +
146F LYS* 4.2 6.7 - - - -
147F GLY 4.6 3.1 + - - -
148F LYS 2.9 26.9 + - - +
149F GLY* 3.8 3.1 - - - -
150F VAL 3.7 1.6 - - - -
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 3.9 16.6 - + - -
175E ASN* 3.6 15.7 - - - -
176E PRO* 3.4 43.7 - - + -
177E LYS* 3.9 8.9 - - + +
130F GLN* 3.2 42.3 + - - +
133F HIS* 1.3 75.3 - - - +
135F GLY* 1.3 64.2 + - - +
149F GLY* 3.3 2.8 - - - -
150F VAL* 2.8 38.8 + - + +
152F GLN* 3.6 20.6 - - - +
172F SER* 4.3 6.3 - - - -
174F TRP 3.4 20.9 - - - -
175F ASN* 3.5 20.9 - - - -
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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