Contacts of the helix formed by residues 156 - 168 (chain A) in PDB entry 4ED5
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 LYS 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.6 22.2 - - + +
103A ILE* 5.1 0.7 - - + -
106A ALA* 3.7 4.7 - - - +
154A PHE* 3.7 4.9 - - - +
155A ASP* 1.3 97.7 + - - +
157A ARG* 1.3 65.5 + - - +
158A SER* 4.0 3.4 - - - +
159A GLU* 3.0 46.2 + - - +
160A ALA 3.6 3.6 + - - -
158B SER* 6.1 1.6 - - - -
161B GLU* 3.6 30.5 - - + +
162B GLU* 5.0 14.0 - - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL 3.3 11.0 + - - +
104A LYS 3.6 11.9 - - - +
105A ASP* 3.1 46.8 + - - +
106A ALA* 3.7 12.0 - - - +
156A LYS* 1.3 72.3 - - - +
158A SER* 1.3 62.3 + - - +
160A ALA* 3.1 3.8 + - - +
161A GLU* 3.0 26.6 + - - +
183A PHE* 3.4 44.6 - - + +
101B GLU* 5.6 2.6 + - - +
105B ASP* 2.8 26.6 + - - -
157B ARG* 3.4 31.6 - - - +
161B GLU* 3.5 1.7 + - - +
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Residues in contact with SER 158 (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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156A LYS* 4.0 6.9 - - - +
157A ARG* 1.3 75.4 - - - +
159A GLU* 1.3 63.9 + - - +
161A GLU* 3.5 15.0 + - - +
162A GLU* 3.1 34.1 + - - +
102B VAL* 4.0 6.3 - - - +
157B ARG* 4.2 2.2 - - - +
158B SER* 3.6 31.6 - - - -
161B GLU* 2.6 37.4 + - - -
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Residues in contact with GLU 159 (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 PHE* 3.2 31.0 - - - +
130A GLY* 3.8 16.7 - - - -
131A ARG* 3.8 7.3 + - - +
154A PHE* 3.6 13.4 - - + +
155A ASP* 3.3 17.7 + - - +
156A LYS* 3.0 54.4 + - + +
157A ARG 3.2 0.4 - - - -
158A SER* 1.3 81.9 - - - +
160A ALA* 1.3 64.8 + - - +
162A GLU* 3.3 8.6 + - - +
163A ALA* 3.1 17.5 + - - +
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 3.8 23.8 - - - +
108A LEU* 3.8 13.2 - - + +
154A PHE* 3.6 16.4 - - + -
156A LYS 3.6 2.3 + - - +
157A ARG 3.1 9.1 + - - +
159A GLU* 1.3 78.3 - - - +
161A GLU* 1.3 63.1 + - - +
163A ALA* 3.2 4.0 + - - +
164A ILE* 3.0 26.7 + - - +
183A PHE* 3.7 20.6 - - + -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.0 23.8 + - - +
158A SER* 3.6 8.1 - - - +
160A ALA* 1.3 75.3 - - - +
162A GLU* 1.3 60.7 + - - +
164A ILE* 3.3 8.0 + - - +
165A THR* 3.1 26.7 + - - -
183A PHE* 3.5 15.5 - - + -
101B GLU* 3.5 28.9 - - + +
102B VAL* 3.3 25.0 - - - +
105B ASP* 2.5 34.8 - - - +
157B ARG* 3.3 27.4 - - - +
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Residues in contact with GLU 162 (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 PHE* 3.9 19.1 - - + +
158A SER* 3.1 22.5 + - - +
159A GLU* 3.6 10.1 - - - +
160A ALA 3.3 0.2 - - - -
161A GLU* 1.3 74.8 - - - +
163A ALA* 1.3 61.0 + - - +
165A THR* 3.5 5.8 + - - +
166A SER* 2.9 31.9 + - - -
102B VAL* 3.6 30.5 - - + +
156B LYS* 4.3 11.4 + - - +
158B SER* 5.1 3.0 + - - -
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Residues in contact with ALA 163 (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 LEU* 3.8 19.5 - - + -
126A PHE* 3.9 13.9 - - + -
129A PHE* 3.8 29.3 - - + -
154A PHE* 3.9 3.6 - - + -
159A GLU 3.1 11.6 + - - +
160A ALA 3.2 8.7 + - - +
162A GLU* 1.3 74.5 - - - +
164A ILE* 1.3 59.6 + - - +
166A SER* 3.3 1.4 + - - -
167A PHE* 2.9 35.2 + - - +
181A VAL* 4.4 2.0 - - - -
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Residues in contact with ILE 164 (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 LEU* 3.6 24.7 - - + -
160A ALA 3.0 14.0 + - - +
161A GLU* 3.6 8.5 - - - +
163A ALA* 1.3 74.9 - - - +
165A THR* 1.3 62.6 + - - +
168A ASN* 2.8 41.3 + - + +
181A VAL* 3.6 31.2 - - + +
182A LYS* 4.2 1.8 - - - -
183A PHE* 3.5 44.2 - - + +
101B GLU* 4.1 21.8 - - + +
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Residues in contact with THR 165 (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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161A GLU 3.1 11.4 + - - -
162A GLU* 4.1 7.6 - - - +
164A ILE* 1.3 79.1 - - - +
166A SER* 1.3 62.2 + - - +
168A ASN 4.8 1.6 + - - +
170A HIS* 4.1 11.3 - - - -
99B SER 4.5 5.2 - - - +
100B SER* 3.7 22.2 - - - -
101B GLU* 3.1 29.3 + - - +
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Residues in contact with SER 166 (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 ARG* 3.9 14.9 + - - -
129A PHE* 3.3 31.2 - - - -
162A GLU* 2.9 20.7 + - - +
163A ALA 3.8 0.2 - - - -
165A THR* 1.3 77.8 - - - +
167A PHE* 1.3 61.2 + - - +
170A HIS* 2.7 26.1 + - - +
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Residues in contact with PHE 167 (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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125A MET* 3.4 49.4 - - + -
126A PHE* 3.4 26.0 - + - -
128A ARG* 3.8 25.8 - - - -
129A PHE* 3.3 24.9 - + - -
163A ALA 2.9 15.2 + - - +
166A SER* 1.3 80.7 - - - +
168A ASN* 1.3 67.1 + - - +
169A GLY 3.2 0.3 + - - -
170A HIS* 3.0 25.7 + - + +
179A ILE* 3.6 13.9 - - + +
181A VAL* 3.8 15.7 - - + -
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Residues in contact with ASN 168 (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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164A ILE* 2.8 30.4 + - + +
165A THR 5.0 1.2 - - - +
167A PHE* 1.3 72.9 - - - +
169A GLY* 1.3 62.6 + - - +
170A HIS* 3.4 12.1 + - - -
179A ILE 3.8 2.9 - - - -
180A THR* 3.4 15.1 + - - +
181A VAL* 3.0 43.7 + - - +
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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