Contacts of the helix formed by residues 126 - 134 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TRP* 4.7 7.4 - - + -
87P CYS 5.2 0.2 - - - +
88P THR* 3.9 16.5 - - + +
101P TRP* 6.2 5.2 - - + -
123P LEU* 3.8 43.5 - - + +
124P GLY 2.8 16.1 + - - +
125P PRO* 1.3 75.6 - - - +
127P TYR* 1.3 83.5 + - + +
128P GLY 4.9 1.1 - - - +
129P PHE* 2.8 16.1 + - - +
130P GLN* 3.3 6.0 + - - -
182P MET* 3.9 25.4 - - + -
183P ALA 4.6 1.6 - - - +
184P LEU* 4.1 13.5 - - + +
186P PRO* 6.0 0.7 - - + -
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Residues in contact with TYR 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TRP* 5.3 0.2 - + - -
83P PHE* 3.4 34.1 - + + -
101P TRP* 3.7 29.6 - + - -
126P VAL* 1.3 84.6 - - + +
128P GLY* 1.3 66.5 + - - +
130P GLN* 3.0 3.1 + - - +
131P TRP* 2.9 33.5 + - - +
173P ALA* 3.9 23.1 - - + +
184P LEU 5.8 2.5 - - - -
185P PRO 4.3 1.3 + - - -
186P PRO* 3.5 26.0 - - + +
187P CYS* 2.7 24.0 + - - -
188P HIS* 3.2 41.3 - + + -
700P UMP 3.5 17.2 - - - -
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Residues in contact with GLY 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TRP* 6.2 0.2 - - - -
83P PHE* 3.1 34.2 - - - +
86P GLY* 3.3 21.8 - - - -
87P CYS 4.5 5.3 + - - -
126P VAL* 3.1 3.6 + - - +
127P TYR* 1.3 78.4 - - - +
129P PHE* 1.3 62.7 + - - +
131P TRP* 3.4 5.8 + - - +
132P ARG* 3.1 19.2 + - - +
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Residues in contact with PHE 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P GLY 3.6 11.4 + - - +
88P THR* 3.6 18.2 - - + +
125P PRO* 3.5 27.1 - - + -
126P VAL 2.8 16.0 + - - +
128P GLY* 1.3 71.2 - - - -
130P GLN* 1.3 64.8 + - - +
133P HIS* 2.7 62.1 + + + +
135P GLY 5.3 0.9 - - - -
136P ALA* 3.7 36.6 - - + -
138P TYR* 3.6 30.5 - + + -
145P TYR* 3.6 37.7 - + - -
178P ASP* 4.3 2.5 - - - -
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Residues in contact with GLN 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P PRO* 2.9 32.3 + - - +
126P VAL 4.1 5.4 - - - +
127P TYR 3.0 7.2 + - - +
129P PHE* 1.3 82.8 - - - +
131P TRP* 1.3 60.7 + - - +
134P PHE* 3.2 35.2 + - + +
135P GLY 4.5 0.2 + - - -
152P GLN* 2.8 20.0 + - - -
172P SER 4.1 1.8 - - - +
173P ALA* 3.2 35.7 - - - +
175P ASN* 3.0 27.5 + - + +
178P ASP* 2.9 31.1 + - - +
182P MET* 4.2 1.7 - - + +
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Residues in contact with TRP 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 4.5 8.7 - - + -
83P PHE* 3.6 45.8 - + + -
84P VAL* 4.4 11.7 - - + -
127P TYR* 2.9 21.6 + - + +
128P GLY* 3.5 9.6 - - - +
130P GLN* 1.3 77.6 - - - +
132P ARG* 1.3 65.3 + - - +
152P GLN* 3.0 30.5 + - - +
153P LEU* 3.4 15.3 + - + -
171P LEU* 3.8 37.0 + - + +
172P SER* 4.0 8.7 - - - +
173P ALA* 3.7 25.3 - - + +
188P HIS* 4.4 9.8 + + - -
190P PHE* 6.2 0.6 - - - +
230P SER* 6.1 0.2 - - - -
231P TYR* 3.4 27.4 + + - -
234P LEU* 4.0 23.1 - - + -
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Residues in contact with ARG 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P PHE 4.5 0.2 - - - +
84P VAL* 2.7 46.7 + - - +
85P SER* 4.7 1.7 - - - +
86P GLY* 4.1 5.8 - - - +
128P GLY 3.1 14.9 + - - +
131P TRP* 1.3 81.7 - - + +
133P HIS* 1.3 86.4 + - + +
148P LYS 4.0 1.6 - - - +
149P GLY 4.7 0.3 - - - +
150P VAL 3.4 6.9 - - - -
151P ASP* 2.7 59.2 + - - +
153P LEU* 3.6 27.3 - - - +
154P GLN* 4.4 7.5 - - - +
292P ILE* 4.3 6.3 - - - +
293P ASP* 2.7 36.6 + - - -
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Residues in contact with HIS 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P SER 5.2 3.0 + - - -
86P GLY* 4.8 11.0 - - - -
129P PHE* 2.7 51.0 + + + +
132P ARG* 1.3 97.1 + - + +
134P PHE* 1.3 66.9 + - - +
135P GLY 3.2 0.3 + - - -
136P ALA* 3.0 21.2 + - + +
145P TYR* 3.0 39.5 + + + +
146P LYS* 4.2 6.7 - - - -
147P GLY 4.6 3.1 + - - -
148P LYS 2.9 26.8 + - - +
149P GLY* 3.8 2.9 - - - -
150P VAL 3.8 1.6 - - - -
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Residues in contact with PHE 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O PHE* 3.9 17.3 - + - -
175O ASN* 3.7 15.0 - - - -
176O PRO* 3.6 36.3 - - + -
177O LYS* 4.1 7.6 - - + +
130P GLN* 3.2 36.3 + - + +
133P HIS* 1.3 75.3 - - - +
135P GLY* 1.3 66.2 + - - +
149P GLY* 3.3 2.9 - - - -
150P VAL* 2.8 43.8 + - + +
152P GLN* 3.6 21.5 - - - +
172P SER* 4.3 6.7 - - - -
174P TRP 3.4 20.9 - - - -
175P ASN* 3.4 26.7 - - - -
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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