Contacts of the helix formed by residues 154 - 167 (chain A) in PDB entry 3PEJ
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 THR 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A MET* 1.3 75.5 - - - +
155A LYS* 1.3 59.3 + - - +
156A VAL* 3.7 8.3 + - - +
157A ASP* 3.2 34.3 + - - +
158A LEU* 2.9 29.9 + - - +
210A ASN* 3.4 26.9 - - - +
212A ASP* 4.2 12.3 - - + +
213A ASP* 3.6 28.7 - - + -
216A TYR* 5.3 1.3 - - - -
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Residues in contact with LYS 155 (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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154A THR* 1.3 70.7 - - - +
156A VAL* 1.4 60.0 + - + +
158A LEU* 3.5 8.0 + - - +
159A ILE* 2.9 34.1 + - + +
213A ASP* 3.1 18.0 + - - +
216A TYR* 3.6 49.7 + - + +
228A ILE* 4.7 18.5 - - + +
229A TYR* 5.8 1.1 - - - +
230A LYS* 5.2 5.1 - - - +
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Residues in contact with VAL 156 (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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154A THR* 3.2 8.2 + - - +
155A LYS* 1.4 76.7 - - + +
157A ASP* 1.4 62.1 + - - +
159A ILE* 3.4 2.8 + - - -
160A ASN* 2.8 61.0 + - - +
213A ASP* 4.7 1.1 + - - +
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Residues in contact with ASP 157 (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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152A GLY 4.9 1.6 - - - +
153A MET* 4.6 5.1 - - + -
154A THR* 3.2 39.5 + - - +
156A VAL* 1.4 80.3 - - - +
158A LEU* 1.3 56.0 + - - +
160A ASN* 4.2 3.4 + - - +
161A ASN* 3.0 34.1 + - - +
210A ASN* 5.0 3.8 + - - -
1001A BC2 3.4 35.1 - - - +
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Residues in contact with LEU 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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153A MET* 3.8 23.8 - - + +
154A THR 2.9 16.7 + - - +
155A LYS* 3.7 6.3 - - - +
157A ASP* 1.3 75.9 - - - +
159A ILE* 1.3 59.2 + - - +
161A ASN* 4.1 1.9 - - + +
162A LEU* 3.0 41.2 + - + +
208A THR* 4.4 20.2 - - + -
216A TYR* 5.1 5.6 - - + -
218A TRP* 3.7 52.0 - - + +
228A ILE* 4.1 27.4 - - + -
1001A BC2 4.7 3.8 - - + -
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Residues in contact with ILE 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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155A LYS* 2.9 20.8 + - + +
156A VAL* 4.1 3.1 - - - +
158A LEU* 1.3 72.6 - - - +
160A ASN* 1.4 62.9 + - - +
162A LEU* 3.5 5.6 + - - +
163A GLY* 3.0 25.3 + - - -
228A ILE* 5.2 9.1 - - + +
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Residues in contact with ASN 160 (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 VAL* 2.8 45.7 + - - +
157A ASP* 4.2 3.6 + - - +
159A ILE* 1.4 74.0 - - - +
161A ASN* 1.4 55.9 + - - +
163A GLY* 3.1 4.3 + - - -
164A THR* 3.0 32.5 + - + +
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Residues in contact with ASN 161 (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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157A ASP 3.0 22.6 + - - +
158A LEU* 4.1 3.6 - - + +
160A ASN* 1.4 72.5 - - - +
162A LEU* 1.4 64.4 + - + +
164A THR* 2.7 25.4 + - - +
165A ILE* 3.3 16.7 + - + +
1001A BC2 3.6 41.0 - - + +
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Residues in contact with LEU 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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77A TYR* 3.4 37.0 - - + +
158A LEU* 3.0 24.1 + - + +
159A ILE* 3.9 5.2 - - - +
161A ASN* 1.4 76.0 - - + +
163A GLY* 1.3 59.4 - - - +
165A ILE* 3.7 9.0 + - + +
166A ALA* 3.4 17.5 + - - +
195A TYR* 3.7 7.9 - - - +
218A TRP* 3.4 52.5 - - + +
226A PHE* 3.8 14.4 - - + -
228A ILE* 3.7 24.2 - - + -
1001A BC2 5.6 1.6 - - + -
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Residues in contact with GLY 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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159A ILE 3.0 14.3 + - - -
160A ASN* 3.1 6.7 + - - -
162A LEU* 1.3 76.7 - - - +
164A THR* 1.4 62.4 + - - +
166A ALA* 3.6 7.7 + - - +
167A LYS* 3.3 29.3 + - - +
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Residues in contact with THR 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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160A ASN* 3.0 18.9 + - + +
161A ASN* 2.7 24.7 + - - +
163A GLY* 1.4 74.4 - - - +
165A ILE* 1.4 61.2 + - - +
167A LYS* 3.6 10.1 + - + +
168A SER* 2.6 35.7 + - - -
1001A BC2 6.1 0.5 - - - -
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Residues in contact with ILE 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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77A TYR* 4.2 9.2 - - + -
80A GLU* 3.4 16.8 - - + +
81A VAL* 4.2 4.7 - - + -
84A LEU* 4.2 22.4 - - + -
161A ASN* 3.3 16.4 + - + +
162A LEU* 3.7 15.3 - - + +
163A GLY 3.4 0.2 - - - -
164A THR* 1.4 77.9 + - - +
166A ALA* 1.3 61.1 + - - +
168A SER* 3.4 16.4 + - - -
170A THR* 5.1 1.6 + - - -
191A GLY 4.3 10.8 - - - +
192A VAL* 4.8 6.5 - - + -
195A TYR* 3.5 31.2 - - + +
1001A BC2 3.7 30.1 - - + +
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Residues in contact with ALA 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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74A SER* 5.3 4.0 - - - +
76A GLN* 3.3 30.5 - - + +
77A TYR* 3.7 36.3 - - + +
80A GLU* 4.1 10.6 - - - +
162A LEU 3.4 14.3 + - - +
163A GLY* 3.7 9.6 - - - +
164A THR 3.4 0.2 - - - -
165A ILE* 1.3 80.5 - - - +
167A LYS* 1.3 57.3 + - - +
168A SER 3.9 0.5 + - - -
169A GLY 4.8 1.7 + - - -
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Residues in contact with LYS 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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76A GLN* 3.3 24.5 - - - +
163A GLY 3.3 18.6 - - - +
164A THR* 4.0 11.0 - - + +
165A ILE 3.4 0.2 - - - -
166A ALA* 1.3 75.6 - - - +
168A SER* 1.4 59.6 + - - +
169A GLY 3.7 1.1 - - - -
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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