Contacts of the helix formed by residues 152 - 170 (chain F) in PDB entry 4XCS
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 152 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F PHE* 4.0 1.1 - - - -
150F GLY 3.6 2.4 + - - -
151F ARG* 1.3 74.0 - - - +
153F VAL* 1.3 62.6 + - - +
154F ASP* 3.3 11.4 + - - +
155F GLU* 3.0 44.3 + - - +
156F THR* 2.9 24.6 + - - -
158F ARG* 4.9 0.9 + - - -
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Residues in contact with VAL 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F ALA* 3.8 32.5 - - + +
59F PHE* 3.6 32.1 - - + -
62F ARG* 3.4 42.0 - - + +
66F PHE* 4.0 22.0 - - + -
151F ARG 3.5 2.1 + - - +
152F SER* 1.3 71.2 - - - +
154F ASP* 1.3 63.6 + - - +
156F THR* 3.0 2.4 + - - -
157F LEU* 2.8 26.5 + - + +
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Residues in contact with ASP 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG* 3.2 31.1 + - - +
152F SER* 3.3 8.7 + - - +
153F VAL* 1.3 79.9 - - - +
155F GLU* 1.3 62.6 + - - +
157F LEU* 3.2 8.8 + - - +
158F ARG* 3.1 46.1 + - - +
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Residues in contact with GLU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 3.3 44.9 - - + +
158E ARG* 4.2 9.9 + - - +
151F ARG* 4.6 13.1 + - - +
152F SER* 3.0 27.1 + - - +
154F ASP* 1.3 80.0 - - - +
156F THR* 1.3 60.3 + - - +
158F ARG* 3.3 21.9 + - - +
159F LEU* 2.9 28.2 + - - +
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Residues in contact with THR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL* 4.2 21.3 - - + -
59F PHE* 3.6 18.6 - - + -
66F PHE* 4.1 11.9 - - + -
130F LEU* 4.9 8.1 - - + -
132F ILE* 5.6 1.1 - - + -
151F ARG* 3.0 31.2 + - - +
152F SER 2.9 16.8 + - - -
153F VAL 3.0 5.6 + - - -
155F GLU* 1.3 78.8 - - - +
157F LEU* 1.3 63.3 + - - +
159F LEU* 3.2 10.1 + - + +
160F VAL* 3.0 23.5 + - + +
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ARG* 3.7 14.6 - - - +
65F GLU* 3.4 45.5 - - + +
66F PHE* 3.5 40.8 - - + -
69F LEU* 4.1 10.4 - - + +
153F VAL* 2.8 23.2 + - + +
154F ASP* 3.6 9.0 - - - +
156F THR* 1.3 77.9 - - - +
158F ARG* 1.3 62.9 + - + +
160F VAL* 3.3 5.9 + - - +
161F GLN* 3.0 33.0 + - - +
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Residues in contact with ARG 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E GLU* 4.3 9.8 + - - +
158E ARG* 5.3 6.3 - - - +
152F SER* 4.9 0.6 + - - -
154F ASP* 3.1 35.7 + - - +
155F GLU* 3.5 37.6 + - - +
157F LEU* 1.3 76.5 - - + +
159F LEU* 1.3 58.4 + - - +
161F GLN* 3.3 16.8 + - - +
162F ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ASN* 5.0 0.4 - - - +
147E LEU* 3.8 17.9 - - + -
130F LEU* 4.7 9.2 - - + -
132F ILE* 3.0 33.0 - - + -
141F GLN* 3.5 32.3 - - - +
151F ARG* 4.9 7.9 - - - +
155F GLU 2.9 17.7 + - - +
156F THR* 3.2 8.0 + - + +
158F ARG* 1.3 77.6 - - - +
160F VAL* 1.3 63.3 + - - +
162F ALA* 3.2 6.4 + - - +
163F PHE* 3.0 37.6 + - + -
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Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F TYR* 4.3 10.3 - - + -
40F VAL* 3.7 29.6 - - + -
66F PHE* 4.6 5.2 - - + -
69F LEU* 4.1 15.3 - - + -
71F CYS* 4.2 17.9 - - + -
132F ILE* 5.0 13.0 - - + -
156F THR* 3.0 18.0 + - + +
157F LEU* 3.3 7.6 + - - +
159F LEU* 1.3 75.1 - - - +
161F GLN* 1.3 59.7 + - - +
163F PHE* 3.2 8.7 + - - +
164F GLN* 2.9 50.1 + - - +
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Residues in contact with GLN 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.8 33.9 - - + +
157F LEU* 3.0 19.9 + - - +
158F ARG* 3.7 18.4 - - - +
159F LEU 3.3 0.2 - - - -
160F VAL* 1.3 76.7 - - - +
162F ALA* 1.3 53.5 + - - +
164F GLN* 3.2 9.5 + - - +
165F PHE* 2.7 36.7 + - - +
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Residues in contact with ALA 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU* 3.7 21.3 - - + -
149E VAL* 4.8 9.9 - - + -
158F ARG 2.9 16.7 + - - +
159F LEU* 3.5 7.6 - - + +
161F GLN* 1.3 72.1 - - - +
163F PHE* 1.3 59.4 + - - +
165F PHE* 3.8 5.1 - - - +
166F THR* 2.8 35.9 + - - +
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Residues in contact with PHE 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ASN* 4.1 1.3 - - + -
146E ASP* 3.9 3.6 - - - -
147E LEU* 3.6 33.8 - - + +
38F TYR* 3.2 21.1 - + + +
132F ILE* 3.7 35.2 - - + -
140F ARG* 3.5 60.6 - - + -
141F GLN* 3.7 17.7 - - + -
159F LEU* 3.0 35.1 + - + -
160F VAL* 3.6 5.8 - - - +
162F ALA* 1.3 75.2 - - - +
164F GLN* 1.3 58.9 + - - +
166F THR* 3.1 5.2 + - - -
167F ASP* 2.8 33.6 + - - +
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Residues in contact with GLN 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F TYR* 3.6 36.2 - - + +
69F LEU* 2.8 43.9 + - - +
70F ASN* 4.7 4.0 + - - +
160F VAL* 2.9 28.2 + - - +
161F GLN* 3.6 10.2 - - - +
163F PHE* 1.3 74.5 - - - +
165F PHE* 1.3 67.2 + - - +
167F ASP* 3.3 15.9 + - - +
168F LYS* 3.4 16.6 + - - +
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Residues in contact with PHE 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F GLN 2.7 21.0 + - - +
162F ALA* 3.8 6.3 - - - +
164F GLN* 1.3 72.8 - - - +
166F THR* 1.3 57.0 + - + +
168F LYS* 3.1 1.8 + - - -
169F HIS* 2.7 85.6 + + + +
170F GLY 4.7 2.0 - - - -
171F GLU 6.0 0.2 - - - -
172F VAL* 3.9 28.0 - - + -
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Residues in contact with THR 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU* 3.6 10.9 - - - +
148E PRO* 3.7 23.9 - - + +
149E VAL* 3.6 28.3 - - + -
140F ARG* 5.3 1.2 + - - -
162F ALA 2.8 24.2 + - - +
163F PHE* 3.1 8.8 + - - -
165F PHE* 1.3 78.1 - - + +
167F ASP* 1.3 66.1 + - - +
170F GLY* 3.1 40.7 + - - +
172F VAL* 4.0 10.1 - - + -
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Residues in contact with ASP 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F TYR* 2.6 32.3 + - - -
134F ASP* 4.5 2.2 - - - +
135F ASP* 4.1 6.8 - - - +
140F ARG* 2.9 29.0 + - - -
163F PHE 2.8 21.5 + - - +
164F GLN* 3.6 8.4 - - - +
165F PHE 3.2 0.2 - - - -
166F THR* 1.3 77.9 + - - +
168F LYS* 1.3 62.5 + - + +
170F GLY 4.9 0.5 + - - -
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Residues in contact with LYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F GLN 3.6 13.9 - - - +
165F PHE 3.1 0.8 + - - -
166F THR 3.0 0.4 - - - -
167F ASP* 1.3 84.1 - - + +
169F HIS* 1.3 99.4 + - + +
170F GLY 3.6 0.7 - - - -
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Residues in contact with HIS 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F PHE* 2.7 79.5 + + + +
168F LYS* 1.3 111.7 + - + +
170F GLY* 1.3 61.3 + - - +
171F GLU 4.5 3.1 - - - +
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Residues in contact with GLY 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E PRO* 4.7 1.6 - - - -
165F PHE* 4.7 0.7 - - - -
166F THR* 3.1 35.3 + - - +
167F ASP 4.9 0.4 + - - -
168F LYS 3.6 1.8 - - - -
169F HIS* 1.3 83.4 - - - +
171F GLU* 1.3 76.8 + - - -
172F VAL* 4.3 2.9 - - - +
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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
------------------------------------------------------------
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