Contacts of the helix formed by residues 143 - 154 (chain B) in PDB entry 5FWW
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B LYS 3.9 8.3 - - - +
142B LEU* 1.3 87.3 - - - +
144B ILE* 1.3 64.0 + - - +
145B GLN 3.5 0.3 + - - -
146B THR* 2.6 42.1 + - + +
147B CYS* 3.4 10.7 + - - +
161B MET* 4.4 0.2 - - - +
190B CYS* 4.0 5.4 - - - -
192B GLY* 4.2 2.2 - - - -
193B ASP* 3.8 21.8 - - + +
196B GLN* 3.5 4.7 - - - -
198B CYS* 4.0 6.9 - - - -
232B ASP* 2.9 39.7 + - - +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA* 3.6 31.0 - - + -
143B THR* 1.3 76.5 - - - +
145B GLN* 1.3 58.6 + - - +
148B ILE* 3.1 51.2 + - + +
161B MET* 3.5 12.2 - - + +
190B CYS* 4.0 3.6 - - - -
196B GLN* 3.0 23.5 + - + +
197B PRO* 3.4 29.8 - - + +
198B CYS* 4.0 2.4 - - - -
207B PHE* 3.6 35.7 - - + -
231B PRO* 3.7 14.1 - - + -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B THR* 3.3 1.8 + - - -
144B ILE* 1.3 78.0 - - - +
146B THR* 1.3 57.3 + - + +
148B ILE* 3.1 6.0 + - - +
149B SER* 2.6 39.8 + - - -
152B ARG* 2.9 28.4 + - - -
211B VAL 3.4 19.0 + - - -
212B GLY* 3.5 7.9 - - - +
229B ASP* 3.6 38.3 - - + +
230B PHE 2.7 28.9 + - - +
231B PRO* 3.9 5.2 - - + +
232B ASP* 3.6 17.0 - - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS* 4.8 7.3 + - - -
139B SER* 6.1 0.4 - - - -
141B LYS 4.6 8.7 - - - +
142B LEU* 3.6 10.4 - - - +
143B THR* 2.6 48.4 + - + +
145B GLN* 1.3 77.1 - - + +
147B CYS* 1.3 55.5 + - - +
149B SER* 4.1 6.3 - - - -
150B PHE* 3.2 25.8 + - - +
232B ASP* 4.5 5.2 - - - +
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS* 5.9 0.2 - - - +
142B LEU* 4.1 6.0 - - + +
143B THR 3.4 14.0 + - - +
144B ILE 3.8 3.8 - - - +
145B GLN 3.2 0.2 - - - -
146B THR* 1.3 79.2 + - - +
148B ILE* 1.3 59.2 + - - +
150B PHE* 3.4 1.9 + - - +
151B CYS* 3.0 34.0 + - - -
159B ALA* 4.2 1.6 - - - -
160B GLY 3.6 19.3 - - - -
161B MET* 3.7 21.5 - - + -
167B CYS* 2.0 57.7 - - + -
168B PHE 3.9 0.4 - - - -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 3.1 41.3 + - + +
145B GLN* 3.1 13.4 + - - +
147B CYS* 1.3 76.4 - - - +
149B SER* 1.3 51.7 + - - +
151B CYS* 3.3 1.7 + - - +
152B ARG* 2.8 59.1 + - - +
159B ALA* 3.7 21.5 - - + -
161B MET* 3.9 3.8 - - + -
207B PHE* 3.6 22.7 - - + -
208B ASP 4.7 1.1 - - - +
209B THR* 3.7 16.4 - - - +
211B VAL* 3.5 25.1 - - + +
230B PHE 5.0 0.4 - - - +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 2.6 33.0 + - - -
146B THR* 4.1 7.0 - - - -
148B ILE* 1.3 70.8 - - - +
150B PHE* 1.3 56.5 + - - +
152B ARG* 3.7 17.8 + - - +
153B SER* 2.7 41.8 + - - -
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Residues in contact with PHE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B THR* 3.9 23.6 - - + -
136B SER* 4.2 2.0 - - - -
137B LYS* 3.4 57.0 - - + +
146B THR 3.2 19.7 + - - +
147B CYS* 3.5 4.3 - - - +
148B ILE 3.3 0.2 - - - -
149B SER* 1.3 76.6 - - - +
151B CYS* 1.3 59.1 + - - +
153B SER* 3.4 6.5 + - - -
154B GLN* 3.2 43.8 + - + +
167B CYS* 3.9 6.3 - - - -
169B CYS* 3.5 32.3 - - - -
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Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B CYS 3.0 22.2 + - - +
148B ILE 3.9 0.9 - - - +
150B PHE* 1.3 72.8 - - - +
152B ARG* 1.3 63.9 + - - +
154B GLN* 3.4 2.4 + - - -
155B ARG 3.4 5.0 + - - -
156B PHE* 2.9 31.1 + - + +
158B PHE 3.8 7.0 - - - +
159B ALA* 3.5 20.9 - - + -
167B CYS* 3.7 4.5 - - - -
168B PHE 3.5 10.1 - - - -
169B CYS* 2.0 58.8 - - + -
209B THR* 4.0 2.2 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 2.9 23.2 + - - -
148B ILE* 2.8 36.1 + - - +
149B SER* 3.7 21.0 + - - +
151B CYS* 1.3 72.0 - - - +
153B SER* 1.3 62.6 + - - +
155B ARG* 3.2 35.4 + - - +
156B PHE 4.2 8.5 - - - -
209B THR* 2.8 41.0 + - - +
210B LEU* 5.6 0.2 - - - +
211B VAL 3.5 1.4 + - - -
212B GLY 3.6 6.9 + - - -
213B ALA* 3.3 38.9 - - - +
214B CYS 4.9 2.0 - - - +
229B ASP* 5.8 0.2 + - - -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B SER* 2.7 27.4 + - - -
150B PHE* 3.5 9.4 - - - -
151B CYS 3.3 0.2 - - - -
152B ARG* 1.3 78.3 - - - +
154B GLN* 1.3 65.1 + - - +
155B ARG* 3.3 5.6 + - - +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B THR* 4.3 14.6 + - + +
150B PHE* 3.2 42.2 + - + +
151B CYS 3.4 0.6 + - - +
152B ARG 3.3 0.4 - - - -
153B SER* 1.3 81.0 - - - +
155B ARG* 1.3 69.8 + - - +
156B PHE* 3.6 30.3 - - + -
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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