Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 1EFA
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LEU* 1.3 74.4 - - - +
130A ASP* 1.3 61.4 + - - +
131A GLN* 3.5 2.2 - - + +
132A ASP* 3.1 24.4 + - - +
133A ALA* 2.8 25.6 + - - +
192A VAL* 4.4 0.7 - - - +
195A ARG* 2.8 35.0 + - - +
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Residues in contact with ASP 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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128A LEU 4.9 0.5 - - - +
129A ASP* 1.3 72.9 - - - +
131A GLN* 1.3 62.3 + - + +
133A ALA* 3.3 3.1 + - - +
134A ILE* 2.9 36.0 + - + +
151A SER* 4.3 9.1 + - - -
153A GLN* 4.1 20.8 + - - +
154A THR* 2.7 36.3 + - + +
155A PRO* 4.7 6.3 - - + +
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Residues in contact with GLN 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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129A ASP* 3.5 2.2 - - - +
130A ASP* 1.3 79.7 - - + +
132A ASP* 1.3 60.6 + - - +
134A ILE* 3.2 14.4 + - + +
135A ALA* 2.8 29.3 + - - +
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Residues in contact with ASP 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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104A VAL* 3.0 44.8 - - + +
128A LEU* 4.2 8.1 - - + -
129A ASP* 3.1 29.6 + - - +
131A GLN* 1.3 76.2 - - - +
133A ALA* 1.3 61.7 + - - +
135A ALA* 3.1 8.1 + - - +
136A VAL* 2.8 32.9 + - - +
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Residues in contact with ALA 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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128A LEU* 3.9 16.3 - - + +
129A ASP 2.8 16.5 + - - +
130A ASP 3.5 4.9 - - - +
132A ASP* 1.3 77.2 - - - +
134A ILE* 1.3 50.2 + - - +
136A VAL* 3.2 2.8 + - - +
137A GLU* 2.8 36.2 + - - +
147A PHE* 3.6 5.4 - - + -
150A VAL* 3.9 17.5 - - + -
154A THR* 4.0 4.3 - - + -
156A ILE* 3.6 27.1 - - + -
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Residues in contact with ILE 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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130A ASP* 2.9 24.6 + - + +
131A GLN* 3.5 13.7 - - + +
133A ALA* 1.3 74.4 - - - +
135A ALA* 1.3 59.3 + - - +
137A GLU* 3.5 11.3 - - + +
138A ALA* 2.9 29.0 + - + +
154A THR* 4.8 0.9 - - + -
155A PRO* 3.4 37.5 - - + +
156A ILE* 4.5 10.1 - - + -
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Residues in contact with ALA 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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108A LYS* 4.1 26.2 - - - +
131A GLN 2.8 14.1 + - - +
132A ASP* 3.1 13.0 + - - +
134A ILE* 1.3 74.5 - - - +
136A VAL* 1.3 64.8 + - - +
138A ALA* 2.9 17.4 + - - +
139A ALA* 3.0 14.1 + - - +
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Residues in contact with VAL 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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104A VAL* 4.5 6.5 - - + -
107A CYS* 4.3 10.8 - - - -
108A LYS* 4.3 22.9 - - + +
111A VAL* 3.8 27.8 - - + -
124A ILE* 4.2 8.1 - - + -
128A LEU* 4.0 17.0 - - + -
132A ASP 2.8 16.9 + - - +
133A ALA 3.6 6.7 - - - +
135A ALA* 1.3 73.4 - - - +
137A GLU* 1.3 65.8 + - - +
139A ALA* 2.8 21.6 + - - +
140A CYS* 3.2 13.7 + - - -
147A PHE* 4.0 20.0 - - + -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ALA 2.8 20.5 + - - +
134A ILE* 3.5 9.0 - - + +
136A VAL* 1.3 74.0 - - - +
138A ALA* 1.3 64.9 + - + +
140A CYS* 3.4 22.0 + - - +
143A VAL 5.1 3.3 - - - +
144A PRO* 6.0 0.3 - - - +
145A ALA* 4.2 22.2 + - - +
147A PHE* 3.9 16.8 - - + -
156A ILE* 4.0 26.6 - - + +
157A ASN* 4.8 7.1 + - - -
314A LYS* 5.7 1.7 + - - -
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Residues in contact with ALA 138 (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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134A ILE* 2.9 16.7 + - + +
135A ALA* 2.9 12.3 + - - +
137A GLU* 1.3 82.8 - - + +
139A ALA* 1.3 61.5 + - - +
140A CYS 3.2 5.4 + - - +
141A THR* 4.2 2.8 + - - -
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Residues in contact with ALA 139 (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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108A LYS* 5.7 9.9 - - + -
111A VAL* 4.8 10.8 - - + -
115A LEU* 3.3 12.7 - - + +
135A ALA 3.0 10.0 + - - +
136A VAL* 2.8 13.8 + - - +
138A ALA* 1.3 77.2 - - - +
140A CYS* 1.3 51.0 + - - +
141A THR* 2.6 27.4 + - - -
46B ASN* 5.1 1.6 + - - -
48B ILE* 5.8 0.2 - - - +
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Residues in contact with CYS 140 (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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111A VAL* 3.9 6.5 - - - -
115A LEU* 4.1 5.2 - - - -
122A LEU* 3.6 30.3 - - - -
124A ILE* 5.3 0.4 - - - -
136A VAL* 3.5 19.5 - - - -
137A GLU* 3.5 12.5 - - - +
138A ALA 3.1 4.6 - - - +
139A ALA* 1.3 72.2 - - - +
141A THR* 1.3 65.2 + - - +
142A ASN* 2.8 5.7 + - - -
143A VAL* 3.2 35.3 + - + +
145A ALA* 3.9 20.9 - - + -
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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