Contacts of the helix formed by residues 117 - 127 (chain A) in PDB entry 1EOD
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 SER 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASN* 2.4 32.4 + - - -
115A ARG 3.0 0.4 + - - -
116A PRO* 1.3 77.6 - - - +
118A PHE* 1.3 61.9 + - - +
119A ASP 3.5 0.2 - - - -
120A ALA* 3.4 11.3 + - - +
121A ILE* 3.3 17.6 + - - +
134A PRO* 4.9 0.4 - - - -
137A VAL* 3.4 21.9 - - - +
141A VAL* 4.0 0.2 - - - +
142A PHE* 3.5 21.3 - - - -
145A GLU* 3.6 25.1 - - - +
149A TYR* 6.1 1.1 - - - -
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Residues in contact with PHE 118 (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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70A ILE* 3.6 30.7 - - + -
72A VAL* 3.8 17.5 - - + -
77A PHE* 3.3 48.5 - + + -
92A LEU* 4.0 27.4 - - + -
111A PHE* 5.4 0.2 - + - -
114A ASN 4.1 5.3 + - - +
115A ARG 3.0 13.5 + - - +
117A SER* 1.3 74.7 - - - +
119A ASP* 1.3 66.7 + - - +
120A ALA 3.0 2.0 - - - -
121A ILE* 4.0 14.8 - - + +
122A LEU* 2.9 37.7 + - + +
149A TYR* 3.9 26.0 - + - -
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Residues in contact with ASP 119 (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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75A LEU* 6.0 0.8 - - - +
77A PHE* 3.5 25.4 - - - -
115A ARG 4.4 1.0 + - - -
116A PRO* 4.1 13.6 + - - +
117A SER 3.5 0.6 - - - -
118A PHE* 1.3 76.3 - - - +
120A ALA* 1.3 58.2 + - - +
122A LEU* 3.4 2.8 + - - +
123A TYR* 2.9 30.5 + - - +
134A PRO* 5.5 4.0 - - + +
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Residues in contact with ALA 120 (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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116A PRO 4.9 0.2 + - - -
117A SER 3.4 11.3 + - - +
118A PHE 3.0 0.4 - - - -
119A ASP* 1.3 79.5 - - - +
121A ILE* 1.3 65.4 - - - +
123A TYR* 4.1 6.4 - - - +
124A PHE* 3.2 20.3 + - - +
130A ARG 4.8 2.3 - - - +
131A LEU* 4.8 4.3 - - - +
132A ARG 3.3 27.4 + - - +
134A PRO* 3.9 12.5 - - + +
142A PHE* 3.6 17.9 - - + -
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Residues in contact with ILE 121 (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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92A LEU* 4.2 4.0 - - + -
117A SER 3.3 15.0 + - - +
118A PHE* 3.0 24.6 + - + +
120A ALA* 1.3 76.9 - - - +
122A LEU* 1.3 59.6 + - - +
124A PHE* 3.0 24.7 - - - +
125A TYR* 3.2 22.4 - - + -
131A LEU* 5.1 0.2 - - + -
142A PHE* 4.2 9.2 - - + -
145A GLU* 4.7 2.9 - - + -
146A ILE* 3.9 29.4 - - + +
149A TYR* 3.6 47.6 - - + -
151A LEU* 4.1 12.8 - - + -
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Residues in contact with LEU 122 (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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70A ILE* 5.4 1.8 - - + -
77A PHE* 4.0 31.2 - - + -
78A GLU 4.3 10.5 - - - +
79A THR* 3.9 30.1 - - + +
84A LEU* 4.7 12.1 - - + -
92A LEU* 6.3 0.4 - - + -
118A PHE* 2.9 30.3 + - + +
119A ASP* 3.8 2.7 - - - +
121A ILE* 1.3 74.8 - - - +
123A TYR* 1.3 65.5 + - - +
124A PHE 3.0 1.8 - - - -
125A TYR* 3.0 18.5 + - + -
126A GLN* 3.1 34.7 + - + +
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Residues in contact with TYR 123 (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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119A ASP 2.9 21.8 + - - +
120A ALA* 4.2 5.8 - - - +
121A ILE 3.4 0.2 - - - -
122A LEU* 1.3 70.6 - - - +
124A PHE* 1.3 55.2 + - - +
126A GLN* 3.6 23.3 + - + +
127A SER* 2.7 59.7 + - - -
130A ARG* 2.9 52.7 + - + -
132A ARG* 5.6 5.2 - - + -
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Residues in contact with PHE 124 (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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87A PHE* 3.7 34.0 - + + -
90A THR* 5.1 0.2 - - + -
120A ALA 3.2 12.4 + - - +
121A ILE* 3.0 16.4 - - - +
123A TYR* 1.3 79.4 - - - +
125A TYR* 1.3 69.9 + + - +
127A SER* 3.3 0.5 + - - -
129A GLY* 2.8 59.9 + - - -
130A ARG 3.6 10.3 + - - +
131A LEU* 3.8 22.2 - - + -
151A LEU* 4.1 47.8 - - + -
155A ALA* 4.1 10.1 - - + -
158A ARG* 3.6 13.7 - - - -
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Residues in contact with TYR 125 (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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83A THR* 3.6 23.9 - - + +
84A LEU* 3.6 40.2 - - + -
86A GLN* 3.3 20.8 + - - +
87A PHE* 3.6 26.2 - + + -
90A THR* 2.8 36.7 + - - -
92A LEU* 3.6 24.1 + - + +
93A GLY 4.5 1.6 - - - -
121A ILE* 3.2 33.4 - - + +
122A LEU* 3.0 11.6 + - + +
124A PHE* 1.3 83.7 - + - +
126A GLN* 1.3 63.8 + - - +
128A GLY 3.3 9.2 + - - -
149A TYR* 4.5 1.2 + - - +
151A LEU* 3.6 12.1 - - + +
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Residues in contact with GLN 126 (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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78A GLU 4.9 4.2 + - - -
79A THR* 4.5 6.0 + - - +
83A THR* 4.0 20.2 - - + -
86A GLN* 5.5 0.2 + - - -
122A LEU* 3.1 37.7 + - + +
123A TYR* 3.3 32.4 + - + +
125A TYR* 1.3 77.0 - - - +
127A SER* 1.3 60.8 + - - +
128A GLY 3.6 0.5 + - - -
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Residues in contact with SER 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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123A TYR* 2.7 49.3 + - - -
124A PHE 3.3 1.0 + - - -
126A GLN* 1.3 73.5 - - - +
128A GLY* 1.3 57.7 + - - +
130A ARG* 2.9 48.3 + - - +
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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