Contacts of the helix formed by residues 126 - 134 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82J TRP* 4.7 7.6 - - + -
87J CYS 5.3 0.2 - - - +
88J THR* 3.9 17.4 - - + +
101J TRP* 6.2 4.3 - - + -
123J LEU* 3.8 42.4 - - + +
124J GLY 2.8 15.7 + - - +
125J PRO* 1.3 73.6 - - - +
127J TYR* 1.3 84.2 + - + +
128J GLY 5.0 1.1 - - - +
129J PHE 2.8 16.1 + - - -
130J GLN* 3.3 6.2 + - - -
182J MET* 3.8 26.7 - - + -
183J ALA* 4.5 1.6 - - + +
184J LEU 4.1 11.4 - - - +
186J PRO* 6.0 0.7 - - + -
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Residues in contact with TYR 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J TRP* 5.3 0.7 - + - -
83J PHE* 3.4 35.4 - + + -
101J TRP* 3.6 31.4 - + - -
126J VAL* 1.3 84.7 - - + +
128J GLY* 1.3 66.9 + - - +
130J GLN* 3.0 2.8 + - - +
131J TRP* 2.9 33.2 + - - +
173J ALA* 3.9 22.6 - - + +
184J LEU 5.8 2.5 - - - -
185J PRO 4.3 1.1 + - - -
186J PRO* 3.5 27.2 - - + +
187J CYS* 2.7 23.4 + - - -
188J HIS* 3.2 40.6 - + + -
400J UMP 3.4 18.2 - - - -
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Residues in contact with GLY 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J PHE* 3.1 34.4 - - - +
86J GLY* 3.2 23.0 - - - -
87J CYS 4.5 5.3 + - - -
126J VAL* 3.1 3.2 + - - +
127J TYR* 1.3 77.8 - - - +
129J PHE* 1.3 61.1 + - - +
131J TRP* 3.4 5.2 + - - +
132J ARG* 3.2 18.9 + - - +
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Residues in contact with PHE 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J GLY 3.6 11.3 + - - +
88J THR* 3.6 18.6 - - + +
125J PRO* 3.5 28.0 - - + -
126J VAL 2.8 15.5 + - - +
128J GLY* 1.3 72.5 - - - +
130J GLN* 1.3 64.8 + - - +
133J HIS* 2.7 61.2 + + + +
135J GLY 5.3 0.7 - - - -
136J ALA* 3.7 35.9 - - + -
138J TYR* 3.6 29.6 - + + -
145J TYR* 3.6 35.4 - + - -
178J ASP* 4.3 3.4 - - - -
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Residues in contact with GLN 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J PRO* 2.9 32.0 + - - +
126J VAL 3.3 5.8 + - - +
127J TYR 3.0 6.7 + - - +
129J PHE* 1.3 81.0 - - - +
131J TRP* 1.3 62.3 + - - +
134J PHE* 3.1 33.1 + - + +
135J GLY 4.4 0.2 + - - -
150J VAL 4.1 0.3 - - - +
152J GLN* 2.8 19.6 + - - -
172J SER 4.0 1.6 - - - +
173J ALA* 3.2 35.9 - - - +
175J ASN* 3.1 26.7 + - - +
178J ASP* 2.9 31.3 + - - +
182J MET* 4.2 1.7 - - + +
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Residues in contact with TRP 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J LEU* 4.6 8.5 - - + -
83J PHE* 3.5 45.3 - + + -
84J VAL* 4.4 11.2 - - + -
127J TYR* 2.9 20.9 + - + +
128J GLY* 3.6 9.6 - - - +
130J GLN* 1.3 77.4 - - - +
132J ARG* 1.3 64.1 + - + +
152J GLN* 3.0 35.0 + - - +
153J LEU* 3.4 12.7 + - + -
171J LEU* 3.8 40.2 + - + +
172J SER* 4.0 7.0 - - - +
173J ALA* 3.8 25.7 - - + +
188J HIS* 4.4 10.0 + + - -
189J MET 6.3 0.2 - - - -
190J PHE* 6.2 0.4 - - - +
230J SER* 6.0 0.2 - - - -
231J TYR* 3.4 27.4 + + - -
234J LEU* 4.0 23.8 - - + -
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Residues in contact with ARG 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J VAL 2.7 41.5 + - - +
85J SER* 4.6 1.9 - - - +
86J GLY* 4.0 5.8 - - - -
128J GLY 3.2 16.4 + - - +
131J TRP* 1.3 80.5 - - + +
133J HIS* 1.3 85.2 + - + +
148J LYS 4.0 1.7 - - - +
149J GLY 4.7 0.2 - - - +
150J VAL 3.4 8.3 - - - +
151J ASP* 2.7 57.9 + - - +
153J LEU* 3.6 33.5 - - - +
154J GLN* 4.4 7.9 - - - +
292J ILE* 4.3 6.0 - - - +
293J ASP* 2.8 36.2 + - - -
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Residues in contact with HIS 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J SER 5.2 3.0 + - - -
86J GLY* 4.8 10.8 + - - -
129J PHE* 2.7 46.0 + + + +
132J ARG* 1.3 97.5 + - + +
134J PHE* 1.3 66.7 + - - +
135J GLY 3.2 0.3 + - - -
136J ALA* 3.0 25.5 + - + +
145J TYR* 3.0 41.5 + + + +
146J LYS* 4.2 6.7 - - - -
147J GLY 4.6 2.7 - - - -
148J LYS 2.9 27.0 + - - +
149J GLY* 3.8 2.7 - - - -
150J VAL 3.8 1.8 - - - -
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Residues in contact with PHE 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I PHE* 3.9 17.7 - + - -
174I TRP 5.0 0.2 - - - -
175I ASN* 3.6 15.5 - - - -
176I PRO* 3.5 37.9 - - + -
177I LYS* 4.0 8.6 - - + +
130J GLN* 3.1 36.5 + - + +
133J HIS* 1.3 73.6 - - - +
135J GLY* 1.3 64.0 + - - +
149J GLY* 3.3 2.9 - - - -
150J VAL* 2.8 43.7 + - + +
152J GLN* 3.6 22.9 - - - +
172J SER* 4.3 5.4 - - - -
174J TRP 3.4 22.9 - - - -
175J ASN* 3.4 25.1 - - + -
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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