Contacts of the helix formed by residues 127 - 136 (chain A) in PDB entry 2A1X
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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU* 2.8 44.8 - - - +
88A ILE* 3.7 4.7 - - - +
93A VAL* 5.1 0.5 - - - +
95A PRO* 3.1 34.8 - - + +
124A PHE* 2.9 20.7 + - + +
125A GLN 4.8 0.2 - - - -
126A GLU* 1.3 77.2 - - - +
128A LYS* 1.3 60.8 + - - +
129A GLU 3.4 1.4 + - - -
130A LEU* 3.4 16.1 + - + -
131A PHE* 2.9 32.5 + - - +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU 4.1 2.2 + - - -
127A ASP* 1.3 73.5 + - - +
129A GLU* 1.3 73.5 + - + +
131A PHE* 3.6 5.1 + - - +
132A ARG* 3.3 25.8 + - - +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.0 56.3 + - + +
81A PHE* 3.2 22.7 - - - -
84A GLU* 3.8 36.3 - - + +
127A ASP* 3.4 1.8 + - - -
128A LYS* 1.3 79.8 - - + +
130A LEU* 1.3 67.1 + - - +
132A ARG* 3.4 16.3 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 4.0 23.8 - - + +
84A GLU* 3.5 28.5 - - + -
85A PHE* 4.4 2.9 - - - +
88A ILE* 3.9 24.9 - - + -
121A VAL* 4.6 9.2 - - + -
124A PHE* 3.4 51.9 - - + -
127A ASP* 3.4 10.4 + - - +
129A GLU* 1.3 82.3 - - - +
131A PHE* 1.3 60.8 + - - +
133A TYR* 3.1 25.1 + - - +
158A LEU* 4.5 8.7 - - + -
278A ILE* 4.2 9.5 - - + +
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.0 5.3 - - - +
125A GLN* 3.6 40.4 - - + +
127A ASP 2.9 21.2 + - - +
128A LYS* 3.6 5.4 + - - +
129A GLU 3.3 0.2 - - - -
130A LEU* 1.3 71.5 - - - +
132A ARG* 1.3 63.8 + - - +
133A TYR 3.0 2.5 - - - -
134A CYS* 3.0 41.9 + - + -
135A THR* 3.3 27.0 - - + +
153A ALA* 4.4 7.2 - - + -
156A THR* 4.9 1.8 - - + -
329A ARG* 3.9 21.3 - - + -
330A LEU 5.6 1.3 - - - -
331A VAL* 3.8 22.7 - - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 2.7 37.8 + - - +
80A ARG* 3.3 46.6 - - - +
81A PHE* 4.6 8.1 - - + -
128A LYS 3.3 17.7 + - - +
129A GLU* 3.5 18.3 + - - +
130A LEU 3.2 1.2 - - - -
131A PHE* 1.3 73.1 - - - +
133A TYR* 1.3 65.3 + - - +
135A THR* 3.1 15.1 + - + +
136A LEU* 2.9 42.2 + - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.7 5.4 - - + -
81A PHE* 3.8 26.1 - + + -
124A PHE* 5.1 2.5 - + + -
130A LEU 3.1 17.2 + - - +
132A ARG* 1.3 79.6 - - - +
134A CYS* 1.3 64.8 + - - +
136A LEU* 3.5 15.7 + - + +
139A ILE* 3.8 29.7 - - + +
192A ALA* 2.7 42.6 + - + +
193A TRP 3.6 0.2 + - - -
194A THR* 3.0 31.6 + - + -
278A ILE* 3.9 32.8 - - + -
279A SER* 3.9 7.0 - - - -
280A CYS* 3.7 27.1 - - + -
282A PHE* 5.1 2.0 - + - -
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Residues in contact with CYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.4 8.7 - - - -
131A PHE* 3.0 46.5 + - + +
133A TYR* 1.3 79.2 - - - +
135A THR* 1.3 56.9 + - - +
136A LEU 3.3 0.4 - - - -
139A ILE* 5.2 0.2 - - - +
140A LEU* 3.5 13.0 - - - +
153A ALA* 4.0 11.9 - - + -
156A THR* 3.7 23.8 - - - -
280A CYS* 4.0 15.3 - - - -
282A PHE* 3.7 12.4 - - + -
331A VAL* 3.0 22.0 - - + +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 3.3 39.7 - - + +
132A ARG* 3.1 22.2 + - + +
134A CYS* 1.3 77.2 - - + +
136A LEU* 1.3 65.2 + - - +
137A PRO* 3.3 7.4 - - - +
140A LEU* 3.8 13.6 - - - +
331A VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.1 36.3 - - + -
74A PRO* 5.0 0.9 - - + -
77A ASP* 3.9 22.7 - - + +
81A PHE* 5.2 3.1 - - + -
132A ARG* 2.9 31.5 + - - +
133A TYR* 3.5 13.9 - - + +
134A CYS 3.3 2.8 - - - -
135A THR* 1.3 77.1 - - - +
137A PRO* 1.3 75.0 - - + +
138A GLU* 3.2 30.1 - - + +
139A ILE* 3.0 22.3 + - + +
140A LEU* 3.1 12.5 + - - +
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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