Contacts of the helix formed by residues 168 - 175 (chain B) in PDB entry 2FBW
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 CYS 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B CYS 3.9 7.6 - - - +
165B SER 3.0 12.8 + - - +
166B THR 3.5 0.6 - - - -
167B SER* 1.3 78.8 + - - +
169B PRO* 1.3 70.9 - - - +
170B SER* 3.4 23.3 - - - -
171B TYR* 2.9 24.8 + - + +
172B TRP* 3.0 13.9 + - - -
178B TYR* 3.8 17.3 - - - -
181B PRO* 4.3 10.5 - - + -
215B CYS* 6.0 1.1 - - - -
218B ILE* 5.3 6.1 - - - -
220B ASN* 4.8 2.9 - - + -
221B CYS* 5.5 4.0 - - + +
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Residues in contact with PRO 169 (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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167B SER 3.3 10.5 - - - +
168B CYS* 1.3 83.1 - - + +
170B SER* 1.3 61.2 + - - +
172B TRP* 3.0 29.0 + - + +
173B TRP* 3.0 42.6 + - + +
218B ILE* 3.7 36.8 - - + -
220B ASN* 4.1 12.3 - - - +
36C MET* 4.7 9.9 - - + -
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Residues in contact with SER 170 (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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168B CYS* 3.2 13.9 - - - -
169B PRO* 1.3 79.1 - - - +
171B TYR* 1.3 57.2 + - - +
173B TRP* 3.7 7.1 - - - -
174B ASN* 2.8 37.4 + - - +
178B TYR* 3.9 13.2 - - - -
214B ARG* 2.7 33.1 + - - +
215B CYS* 5.0 0.7 - - - -
216B HIS* 3.6 15.0 + - - -
218B ILE* 4.5 7.3 - - - +
57D ASP* 4.8 4.0 + - - -
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Residues in contact with TYR 171 (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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104B HIS* 5.1 0.9 + - - -
105B MET* 4.8 13.6 - - + +
117B ASN* 4.0 7.5 + - - -
118B PHE* 4.0 18.0 + + - +
121B GLN* 2.6 27.5 + - - -
165B SER* 3.3 44.6 - - - +
166B THR* 4.5 13.5 - - + -
168B CYS* 2.9 12.9 + - + +
170B SER* 1.3 77.4 - - - +
172B TRP* 1.3 63.1 + + - +
175B GLY* 2.8 37.6 + - - +
178B TYR* 3.4 33.8 - + + -
179B LEU 3.6 8.1 - - - -
180B GLY* 3.7 14.6 - - - -
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Residues in contact with TRP 172 (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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103B PRO* 4.1 13.1 + - + -
104B HIS* 2.9 51.5 + - + -
166B THR* 2.8 35.1 + - - -
167B SER 4.1 13.2 - - - -
168B CYS 3.0 16.9 + - - -
169B PRO* 3.2 26.7 - - + +
171B TYR* 1.3 81.0 - + - +
173B TRP* 1.3 89.1 + + + +
175B GLY 4.3 1.2 + - - -
220B ASN* 5.6 0.9 - - - -
26C HIS* 4.0 22.9 - - + -
27C ILE* 3.8 24.0 - - + -
30C TYR* 4.0 32.5 - + + -
36C MET* 5.8 4.3 - - - -
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Residues in contact with TRP 173 (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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104B HIS* 4.2 7.4 - - - -
169B PRO* 3.0 33.3 + - + +
170B SER* 4.2 3.4 - - - +
172B TRP* 1.3 100.9 - + + +
174B ASN* 1.3 72.4 + - - +
175B GLY 3.8 0.2 - - - -
176B ASP* 4.9 0.5 - - - +
26C HIS* 4.0 21.1 - + - -
27C ILE* 3.8 27.4 - - + -
57D ASP* 3.8 12.3 - - + +
58D TYR* 3.5 34.2 + + + -
60D HIS* 3.2 27.0 + - + +
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Residues in contact with ASN 174 (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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170B SER* 2.8 23.5 + - - +
173B TRP* 1.3 80.4 - - - +
175B GLY* 1.3 58.0 + - - +
176B ASP* 2.8 21.6 + - - +
177B LYS* 2.9 3.3 + - - -
178B TYR* 2.9 29.0 + - + -
210B PHE* 4.0 12.7 - - + -
214B ARG* 4.3 14.3 - - + +
56D THR 3.8 8.0 - - - +
57D ASP* 3.0 36.9 + - - +
60D HIS* 3.0 26.3 + - - -
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Residues in contact with GLY 175 (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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117B ASN* 3.2 12.6 + - - -
121B GLN* 2.9 25.3 + - - +
171B TYR* 2.8 43.1 + - - -
172B TRP 4.3 1.4 + - - -
173B TRP 3.8 1.0 - - - -
174B ASN* 1.3 75.1 - - - +
176B ASP* 1.3 57.1 + - - +
177B LYS 3.3 0.2 - - - -
178B TYR 4.2 0.9 - - - -
13C TRP* 4.6 4.0 - - - -
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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