Contacts of the helix formed by residues 156 - 167 (chain D) in PDB entry 4S0N
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 ASN 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D PHE* 4.1 2.5 - - + -
126D LYS 4.7 4.6 + - - -
127D LEU* 3.7 47.7 + - + +
153D LYS* 2.8 29.0 + - - +
155D GLU* 1.3 88.9 - - - +
157D ARG* 1.3 64.5 + - - +
158D LYS 3.2 3.1 - - - -
159D ALA* 3.1 10.9 + - - +
160D VAL* 3.1 22.7 + - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 3.9 12.1 - - - +
59D LEU 3.0 21.8 + - - -
60D PHE* 3.1 58.4 + - + +
153D LYS 3.5 3.0 + - - -
154D GLU* 2.3 47.0 + - - +
156D ASN* 1.3 77.5 - - - +
158D LYS* 1.3 65.0 + - - +
160D VAL* 3.4 4.0 + - - +
161D SER* 3.2 27.2 + - - +
171D LEU* 5.6 1.5 - - + +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLU 4.7 1.6 + - - +
155D GLU 5.2 3.1 + - - +
156D ASN 3.2 1.2 - - - -
157D ARG* 1.3 78.5 - - - +
159D ALA* 1.3 60.1 + - - +
160D VAL 3.3 0.2 + - - -
161D SER* 3.3 7.2 + - - -
162D ASP* 3.0 55.0 + - - +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 5.5 1.5 - - + -
127D LEU* 4.0 26.6 - - + +
155D GLU 5.6 0.6 + - - +
156D ASN* 3.1 14.3 + - - +
158D LYS* 1.3 79.4 - - - +
160D VAL* 1.3 62.0 + - - +
162D ASP* 4.0 7.2 - - - +
163D GLN* 3.1 23.7 + - - +
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 3.7 23.3 - - + -
122D ILE* 4.0 20.2 - - + -
127D LEU* 3.9 25.1 - - + +
128D ALA* 4.1 5.2 - - + -
150D PHE* 4.2 19.5 - - + -
156D ASN 3.1 14.6 + - - +
157D ARG 3.7 7.0 - - - +
159D ALA* 1.3 75.1 - - - +
161D SER* 1.3 65.7 + - - +
163D GLN* 3.1 7.6 + - - +
164D LEU* 3.0 26.3 + - + +
171D LEU* 4.2 16.6 - - + -
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Residues in contact with SER 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ARG* 3.2 20.0 + - - +
158D LYS* 3.3 8.3 + - - -
160D VAL* 1.3 78.3 - - - +
162D ASP* 1.3 62.0 + - - +
164D LEU* 3.4 8.9 + - - +
165D LYS* 2.9 32.1 + - - +
169D PHE 4.9 0.2 - - - +
170D LYS* 5.7 1.3 - - - +
171D LEU* 4.2 20.1 + - - +
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Residues in contact with ASP 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LYS* 3.0 43.0 + - - +
159D ALA* 4.0 6.1 + - - +
161D SER* 1.3 81.3 - - - +
163D GLN* 1.3 58.0 + - - +
165D LYS* 4.0 23.7 + - - +
166D LYS* 3.1 26.5 + - - +
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Residues in contact with GLN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLY 4.2 2.0 + - - -
118D ALA* 3.0 30.0 + - - +
121D TYR* 3.6 38.4 - - + +
122D ILE* 3.7 20.2 - - + -
159D ALA 3.1 18.7 + - - +
160D VAL 3.1 5.7 + - - +
162D ASP* 1.3 75.2 - - - +
164D LEU* 1.3 64.1 + - - +
166D LYS* 3.2 23.7 + - - +
167D HIS* 3.3 34.1 + - - -
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Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 4.8 7.2 - - + -
118D ALA* 4.3 10.8 - - + -
119D LEU* 3.8 27.6 - - + -
122D ILE* 4.0 10.1 - - + -
150D PHE* 4.5 6.7 - - + -
160D VAL* 3.0 24.6 + - + +
161D SER* 3.8 4.7 - - - +
163D GLN* 1.3 76.8 - - - +
165D LYS* 1.3 53.6 + - - +
167D HIS* 2.9 14.7 + - - -
169D PHE* 2.7 52.7 + - + +
170D LYS* 4.4 4.3 - - - -
171D LEU* 3.7 44.0 - - + +
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Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D SER 2.9 17.6 + - - +
162D ASP* 4.1 24.2 + - - +
164D LEU* 1.3 76.2 - - - +
166D LYS* 1.3 62.0 + - - +
168D GLY* 3.3 11.4 + - - +
169D PHE 3.2 12.1 + - - +
170D LYS* 5.8 3.4 - - + -
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ASP 3.1 15.5 + - - +
163D GLN* 3.2 18.4 + - - +
165D LYS* 1.3 78.6 - - - +
167D HIS* 1.3 82.9 + - + +
168D GLY 3.8 0.3 + - - -
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Residues in contact with HIS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLU 4.4 5.8 - - - -
117D GLY* 3.1 29.9 + - - -
118D ALA* 3.5 10.3 - - + +
163D GLN* 3.3 30.4 + - - -
164D LEU 2.9 4.5 + - - +
166D LYS* 1.3 108.9 + - + +
168D GLY* 1.3 61.3 + - - +
169D PHE* 3.2 32.5 - - + -
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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