Contacts of the helix formed by residues 163 - 173 (chain A) in PDB entry 1SFE
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 VAL 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.7 39.5 - - + +
157A SER* 5.3 2.0 - - - -
159A TYR* 5.2 0.2 - - - -
162A GLY* 1.3 70.1 - - - -
164A SER* 1.3 66.2 + - - +
166A LYS* 3.8 1.7 - - - +
167A ALA* 2.8 35.5 + - + +
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Residues in contact with SER 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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162A GLY* 3.4 0.6 - - - -
163A VAL* 1.3 86.1 - - - +
165A ARG* 1.3 61.2 + - - +
167A ALA* 3.9 4.4 - - - +
168A GLN* 3.0 34.8 + - - +
171A ARG* 5.1 1.4 + - - -
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Residues in contact with ARG 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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23A LEU* 3.2 35.7 + - + +
40A LEU* 3.7 34.5 + - + +
41A GLY* 3.4 23.8 + - - +
42A ASP* 2.6 40.4 + - - -
159A TYR* 3.9 10.3 - - + -
161A TRP* 2.6 44.8 + - - +
162A GLY* 3.3 3.2 + - - -
163A VAL 3.3 0.4 - - - -
164A SER* 1.3 80.0 - - - +
166A LYS* 1.3 63.2 + - - +
168A GLN* 3.2 9.1 + - - +
169A LEU* 2.8 33.8 + - + +
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Residues in contact with LYS 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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115A TYR* 4.9 3.6 + - - -
146A CYS 4.5 4.9 + - - -
147A HIS* 3.5 21.6 + - + +
149A VAL 2.6 25.9 + - - -
150A VAL* 4.2 7.3 - - - +
156A LEU* 3.4 41.7 - - + +
157A SER 3.6 15.8 + - - -
158A GLY 4.9 0.4 - - - -
159A TYR* 3.5 45.6 - - + +
162A GLY 3.1 9.1 + - - +
163A VAL* 3.8 5.6 - - - +
165A ARG* 1.3 78.0 - - - +
167A ALA* 1.3 57.1 + - - +
169A LEU* 3.3 4.9 + - - +
170A LEU* 3.0 38.5 + - + +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.6 27.8 - - + +
163A VAL* 2.8 21.3 + - + +
164A SER* 3.9 4.9 - - - +
166A LYS* 1.3 77.2 - - - +
168A GLN* 1.3 63.3 + - - +
170A LEU* 3.6 2.3 + - - +
171A ARG* 3.1 38.3 + - - +
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Residues in contact with GLN 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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22A GLU* 3.2 31.1 + - - +
23A LEU* 3.5 25.0 - - + +
164A SER* 3.0 26.2 + - - +
165A ARG* 3.2 9.6 + - - +
167A ALA* 1.3 78.4 - - - +
169A LEU* 1.3 61.5 + - - +
171A ARG* 3.6 30.2 + - - +
172A ARG* 3.2 24.3 + - - +
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Residues in contact with LEU 169 (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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23A LEU* 4.0 15.9 - - + -
40A LEU* 5.1 2.0 - - + -
142A ILE* 3.6 26.2 - - + -
147A HIS* 3.6 34.1 - - + +
159A TYR* 3.2 29.2 - - + +
165A ARG 2.8 23.9 + - - +
166A LYS 3.7 2.9 - - - +
168A GLN* 1.3 73.2 - - - +
170A LEU* 1.3 63.4 + - - +
172A ARG* 3.2 49.1 + - - +
173A GLU* 3.2 20.4 + - - +
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Residues in contact with LEU 170 (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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110A GLY 6.4 0.9 - - - -
111A GLU 5.1 1.8 - - - +
112A THR* 3.6 30.1 - - + -
147A HIS* 3.4 33.0 - - + +
148A ARG* 4.2 4.9 - - + -
150A VAL* 4.5 0.7 - - + -
156A LEU* 3.6 31.9 - - + -
166A LYS* 3.0 24.3 + - + +
167A ALA* 4.2 3.8 - - - +
169A LEU* 1.3 75.7 - - - +
171A ARG* 1.3 58.0 + - - +
173A GLU* 3.5 15.2 + - + +
174A ALA* 3.1 31.7 + - - +
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Residues in contact with ARG 171 (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 SER 5.1 1.4 + - - -
167A ALA* 3.1 31.6 + - - +
168A GLN* 3.6 40.3 - - - +
169A LEU 3.2 0.2 - - - -
170A LEU* 1.3 77.6 - - - +
172A ARG* 1.3 63.7 + - - +
174A ALA* 3.3 20.3 - - - +
175A GLU* 4.2 5.2 + - - +
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Residues in contact with ARG 172 (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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22A GLU* 4.0 6.9 + - - +
23A LEU* 3.5 17.9 - - - +
78A LEU 2.9 30.1 + - - -
79A ASN 3.8 11.8 + - - -
80A GLN 3.4 20.6 + - - -
81A ARG* 3.3 41.9 + - + +
142A ILE* 3.9 15.6 - - - +
168A GLN 3.2 13.5 + - - +
169A LEU* 3.2 36.9 + - - +
171A ARG* 1.3 79.5 - - - +
173A GLU* 1.3 70.1 + - + +
175A GLU* 3.6 14.5 - - - +
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Residues in contact with GLU 173 (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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81A ARG* 2.5 40.8 + - - +
109A CYS* 3.5 14.4 - - - -
110A GLY* 3.3 19.9 + - - +
111A GLU 5.2 0.2 - - - +
142A ILE* 5.8 1.0 - - - +
147A HIS* 2.9 27.6 + - - -
148A ARG* 2.8 50.0 + - - +
169A LEU* 3.2 13.6 + - - +
170A LEU* 4.2 9.0 - - + +
172A ARG* 1.3 90.5 + - + +
174A ALA* 1.3 59.2 + - - +
175A GLU 3.3 1.8 - - - -
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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