Contacts of the helix formed by residues 126 - 133 (chain A) in PDB entry 3EDY
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 ILE 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.4 1.3 - - - +
41A ALA* 3.6 32.3 - - + +
42A ASP 3.2 27.6 - - - +
43A PRO* 3.4 5.1 + - + +
45A GLU* 2.8 28.6 + - + +
47A LEU* 4.0 25.8 - - + -
124A LEU 4.0 0.4 + - - -
125A SER* 1.3 70.9 - - - +
127A ARG* 1.3 62.3 + - - +
129A ALA* 3.3 5.1 + - - +
130A GLU* 3.1 49.9 + - + +
138A PHE* 3.9 14.1 - - + -
151A VAL* 4.4 4.3 - - + -
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Residues in contact with ARG 127 (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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43A PRO* 3.0 45.4 + - + +
44A GLU* 2.9 30.1 + - - +
125A SER* 3.8 4.0 - - - +
126A ILE* 1.3 76.7 - - - +
128A GLN* 1.3 64.5 + - - +
130A GLU* 3.3 8.3 + - - +
131A LEU* 3.2 35.6 + - + +
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Residues in contact with GLN 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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46A GLU* 4.8 1.0 - - - +
106A ALA* 3.3 24.2 + - - +
107A GLY* 3.6 28.9 + - - +
124A LEU* 4.0 9.3 - - + -
125A SER* 3.0 40.3 + - - +
127A ARG* 1.3 80.0 - - + +
129A ALA* 1.3 58.0 + - - +
131A LEU* 3.4 12.4 + - + +
132A LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 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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47A LEU* 4.0 19.7 - - + -
49A LEU* 4.2 13.9 - - + -
124A LEU* 4.2 10.3 - - + +
125A SER 2.8 15.3 + - - +
126A ILE 3.7 4.9 - - - +
128A GLN* 1.3 78.0 - - - +
130A GLU* 1.3 57.9 + - - +
132A LEU* 3.4 7.1 + - - +
133A LEU* 3.0 33.1 + - - +
136A ALA* 4.7 0.5 - - - +
138A PHE* 4.0 16.8 - - + -
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Residues in contact with GLU 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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40A ARG* 2.7 44.2 + - - -
126A ILE* 3.1 28.8 + - - +
127A ARG* 4.0 5.8 - - - +
128A GLN 3.3 0.4 - - - -
129A ALA* 1.3 74.5 - - - +
131A LEU* 1.3 63.7 + - - +
133A LEU 3.6 17.1 - - - +
134A PRO* 3.7 9.9 - - - +
135A GLY 4.7 1.2 + - - -
136A ALA* 3.4 20.7 - - - +
138A PHE* 3.0 28.7 + - + -
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Residues in contact with LEU 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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106A ALA* 6.4 0.7 - - + -
127A ARG* 3.2 31.8 + - + +
128A GLN* 3.7 11.7 - - + +
130A GLU* 1.3 78.0 - - - +
132A LEU* 1.3 65.2 + - - +
133A LEU 3.2 0.7 + - - -
134A PRO* 3.5 15.8 - - - +
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Residues in contact with LEU 132 (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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51A PHE* 3.5 36.6 - - + -
102A TRP* 3.3 49.0 + - + +
103A LEU* 3.8 9.6 - - + -
106A ALA* 3.5 29.8 - - + +
124A LEU* 4.0 14.8 - - + -
128A GLN 3.0 19.0 + - - +
129A ALA* 3.4 4.7 + - - +
131A LEU* 1.3 76.4 - - - +
133A LEU* 1.3 72.2 + - + +
134A PRO* 3.3 7.3 - - - +
158A GLN 4.2 1.6 - - - +
160A PRO* 4.7 4.0 - - - +
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Residues in contact with LEU 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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49A LEU* 4.0 16.6 - - + -
102A TRP* 4.0 3.6 - - + -
129A ALA 3.0 15.8 + - - +
130A GLU 3.6 4.7 - - - +
132A LEU* 1.3 102.7 - - + +
134A PRO* 1.3 69.5 - - - +
136A ALA* 3.0 27.2 + - + +
138A PHE* 5.4 0.9 - - + -
157A TYR* 4.0 14.0 - - + +
158A GLN 3.6 4.5 - - - +
159A LEU* 3.4 32.8 - - + -
170A VAL* 4.0 32.1 - - + -
173A LEU* 4.2 13.7 - - + -
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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