Contacts of the helix formed by residues 124 - 132 (chain F) in PDB entry 2AJQ
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 ALA 124 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F HIS* 4.1 3.6 - - - -
92F LEU* 5.4 0.7 - - - -
119F ARG* 5.7 3.1 - - - -
122F SER* 3.0 17.3 + - - +
123F HIS* 1.3 84.5 - - - +
125F LEU* 1.3 65.0 + - - +
126F GLU* 4.4 4.9 - - + +
127F ALA* 3.3 9.3 + - + +
128F TRP* 3.1 18.4 + - - -
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Residues in contact with LEU 125 (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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5F ALA* 5.9 2.0 - - + -
59F HIS* 3.5 40.9 + - + +
124F ALA* 1.3 69.6 - - - +
126F GLU* 1.3 68.7 + - - +
128F TRP* 3.0 7.2 + - + +
129F GLY* 2.8 19.4 + - - -
135F MET* 5.8 0.2 - - - -
174F ASP* 3.4 49.6 - - + +
177F VAL* 3.4 37.4 - - + +
178F THR* 3.6 16.2 - - - +
181F LEU* 4.6 7.0 - - + -
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Residues in contact with GLU 126 (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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119F ARG* 3.1 31.6 - - - +
124F ALA* 4.4 4.6 - - + +
125F LEU* 1.3 77.3 - - - +
127F ALA* 1.3 56.6 + - - +
129F GLY* 2.6 27.9 + - - -
130F TYR* 3.2 10.3 + - - -
135F MET* 4.2 17.0 - - - -
138F GLU* 4.7 8.7 - - + +
174F ASP* 5.6 2.4 + - - -
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Residues in contact with ALA 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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119F ARG* 3.8 24.4 - - + +
122F SER* 3.4 32.3 - - - +
124F ALA* 3.3 10.2 + - + +
125F LEU 3.2 0.2 - - - -
126F GLU* 1.3 79.2 - - - +
128F TRP* 1.3 60.7 + - - +
130F TYR* 3.2 14.4 + - - +
131F ARG* 3.2 33.7 + - - +
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Residues in contact with TRP 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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95F SER* 2.8 24.5 + - - -
99F HIS* 3.3 51.4 - + + -
102F LEU* 4.3 7.9 - - + -
123F HIS* 3.4 27.0 + - - +
124F ALA 3.1 6.2 + - - +
125F LEU 3.0 9.8 + - - +
127F ALA* 1.3 70.8 - - - +
129F GLY* 1.3 66.3 + - - +
130F TYR 3.0 2.5 - - - -
131F ARG* 2.9 61.3 + - + +
132F LEU* 3.0 41.8 + - + +
177F VAL* 4.7 3.8 - - + -
181F LEU* 3.8 41.3 - - + -
184F LYS* 4.9 7.9 - - + -
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Residues in contact with GLY 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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125F LEU 2.8 9.9 + - - -
126F GLU 2.6 16.5 + - - -
128F TRP* 1.3 72.3 - - - +
130F TYR* 1.3 55.1 + - - -
132F LEU* 4.1 0.4 - - - -
133F GLY* 3.3 2.1 + - - -
134F GLU* 2.8 31.7 + - - -
135F MET* 3.0 32.1 + - - -
177F VAL* 4.0 11.1 - - - +
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Residues in contact with TYR 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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114F LYS* 3.2 41.0 - - - +
115F LEU* 4.8 1.8 - - + -
116F PRO* 3.5 36.7 - - + +
119F ARG* 3.9 14.4 - - + -
126F GLU 3.2 14.3 + - - -
127F ALA* 3.2 9.5 + - - +
128F TRP 3.0 1.0 - - - -
129F GLY* 1.3 75.8 - - - +
131F ARG* 1.3 63.0 + - + +
132F LEU 3.2 2.1 + - - -
133F GLY* 3.6 9.1 + - - +
135F MET* 3.4 27.7 - - + +
137F GLY* 5.9 1.9 - - - -
138F GLU* 3.2 27.6 + - - +
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Residues in contact with ARG 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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102F LEU* 3.7 17.4 - - - +
105F THR* 6.1 1.6 - - - -
106F ASP* 2.5 46.7 + - - +
109F LEU* 3.5 24.0 - - + +
114F LYS* 4.6 14.2 + - - +
115F LEU* 6.1 2.9 - - + -
119F ARG 4.5 2.8 + - - -
122F SER 2.5 34.3 + - - +
127F ALA* 3.2 30.6 + - - +
128F TRP* 2.9 52.5 + - + +
130F TYR* 1.3 79.8 - - + +
132F LEU* 1.3 63.5 + - - +
133F GLY 3.5 0.2 - - - -
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Residues in contact with LEU 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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114F LYS* 6.2 0.2 - - - -
128F TRP* 3.0 35.5 + - + +
131F ARG* 1.3 82.8 - - - +
133F GLY* 1.3 64.9 + - - +
134F GLU* 3.9 20.2 - - + +
177F VAL* 4.6 4.3 - - + +
180F ALA* 3.6 38.6 - - + +
181F LEU* 3.8 14.6 - - + +
184F LYS* 3.5 32.5 - - + -
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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