Contacts of the helix formed by residues 126 - 134 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82K TRP* 4.7 7.2 - - + -
87K CYS 5.3 0.7 - - - +
88K THR* 4.0 17.4 - - + +
101K TRP* 6.2 4.5 - - + -
123K LEU* 3.8 43.3 - - + +
124K GLY 2.8 16.3 + - - +
125K PRO* 1.3 74.3 - - - +
127K TYR* 1.3 83.5 + - + +
128K GLY 4.9 0.9 - - - +
129K PHE 2.8 16.5 + - - -
130K GLN* 3.3 6.4 + - - -
182K MET* 3.8 25.1 - - + -
183K ALA* 4.6 1.6 - - + +
184K LEU* 4.1 13.0 - - + +
186K PRO* 6.0 0.9 - - + -
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Residues in contact with TYR 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K TRP* 5.4 0.2 - + - -
83K PHE* 3.4 34.8 - + + -
101K TRP* 3.6 30.1 - + - -
126K VAL* 1.3 84.6 - - + +
128K GLY* 1.3 66.7 + - - +
130K GLN* 3.0 3.5 + - - +
131K TRP* 2.9 32.2 + - - +
173K ALA* 4.0 23.3 - - + +
184K LEU 5.8 2.0 - - - -
185K PRO 4.3 1.3 + - - -
186K PRO* 3.5 26.5 - - + +
187K CYS* 2.7 24.0 + - - -
188K HIS* 3.2 41.2 - + + -
450K UMP 3.4 17.8 - + - -
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Residues in contact with GLY 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K TRP* 6.2 0.2 - - - -
83K PHE* 3.1 33.7 - - - -
86K GLY* 3.3 21.4 - - - -
87K CYS 4.5 5.1 + - - -
126K VAL* 3.1 3.6 + - - +
127K TYR* 1.3 78.0 - - - +
129K PHE* 1.3 61.0 + - - +
131K TRP* 3.4 5.6 + - - +
132K ARG* 3.1 19.2 + - - +
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Residues in contact with PHE 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K GLY 3.7 10.9 + - - -
88K THR* 3.6 19.0 - - + +
125K PRO* 3.5 28.0 - - + -
126K VAL 2.8 16.4 + - - +
128K GLY* 1.3 71.9 - - - -
130K GLN* 1.3 64.1 + - - +
133K HIS* 2.7 61.3 + + + +
135K GLY 5.3 0.7 - - - -
136K ALA* 3.7 38.1 - - + -
138K TYR* 3.6 29.2 - + + -
145K TYR* 3.6 36.8 - + - -
178K ASP* 4.2 2.5 - - - -
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Residues in contact with GLN 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K PRO* 2.9 31.3 + - - +
126K VAL 3.3 5.4 + - - +
127K TYR 3.0 7.0 + - - +
129K PHE* 1.3 81.4 - - - +
131K TRP* 1.3 62.6 + - - +
134K PHE* 3.1 35.0 + - + +
135K GLY 4.4 0.2 + - - -
150K VAL 4.1 0.2 - - - +
152K GLN* 2.8 19.5 + - - -
172K SER 4.1 1.8 - - - +
173K ALA* 3.2 35.2 - - - +
175K ASN* 3.0 27.5 + - + +
178K ASP* 2.9 31.8 + - - +
182K MET* 4.3 1.3 - - + +
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Residues in contact with TRP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K LEU* 4.5 8.5 - - + -
83K PHE* 3.5 45.1 - + + -
84K VAL* 4.4 10.3 - - + -
127K TYR* 2.9 21.2 + - + +
128K GLY* 3.5 9.0 - - - +
130K GLN* 1.3 77.9 - - - +
132K ARG* 1.3 65.3 + - + +
152K GLN* 3.0 34.4 + - - +
153K LEU* 3.4 12.6 + - + -
171K LEU* 3.8 39.8 + - + +
172K SER* 4.0 6.2 - - - +
173K ALA* 3.7 25.7 - - + +
188K HIS* 4.4 10.2 + + - -
189K MET 6.3 0.2 - - - -
190K PHE* 6.2 0.4 - - - +
230K SER* 6.0 0.4 - - - -
231K TYR* 3.4 27.4 + + - -
234K LEU* 4.0 24.5 - - + -
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Residues in contact with ARG 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE 4.5 0.2 - - - +
84K VAL* 2.6 47.9 + - - +
85K SER* 4.6 1.7 - - - +
86K GLY* 4.0 7.4 - - - +
128K GLY 3.1 16.0 + - - +
131K TRP* 1.3 78.6 - - + +
133K HIS* 1.3 87.1 + - + +
148K LYS 4.0 1.6 - - - +
149K GLY 4.7 0.2 - - - +
150K VAL 3.4 6.9 - - - +
151K ASP* 2.7 59.3 + - - +
153K LEU* 3.6 27.6 - - - +
154K GLN* 4.4 7.1 - - - +
292K ILE* 4.3 6.3 - - - +
293K ASP* 2.8 35.7 + - - -
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Residues in contact with HIS 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K SER 5.2 2.8 + - - -
86K GLY* 4.7 11.1 + - - -
129K PHE* 2.7 45.7 + + + +
132K ARG* 1.3 96.7 + - + +
134K PHE* 1.3 65.7 + - - +
135K GLY 3.2 0.2 + - - -
136K ALA* 3.0 26.4 + - + +
145K TYR* 3.0 41.5 + + + +
146K LYS* 4.2 6.5 - - - -
147K GLY 4.6 2.5 - - - -
148K LYS 2.9 26.5 + - - +
149K GLY* 3.8 2.2 - - - -
150K VAL 3.8 1.8 - - - -
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Residues in contact with PHE 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K GLN* 3.1 42.2 + - - +
133K HIS* 1.3 73.8 - - - +
135K GLY* 1.3 66.5 + - - +
149K GLY* 3.3 2.9 - - - -
150K VAL* 2.8 38.9 + - + +
152K GLN* 3.6 21.3 - - - +
172K SER* 4.3 6.5 - - - -
174K TRP 3.4 22.4 - - - -
175K ASN* 3.4 21.3 - - - -
134L PHE* 3.9 16.6 - + - -
175L ASN* 3.6 15.3 - - - -
176L PRO* 3.4 41.3 - - + -
177L LYS* 4.0 7.5 - - + +
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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