Contacts of the helix formed by residues 182 - 187 (chain A) in PDB entry 5FWU
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 ALA 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLU* 3.9 20.0 - - + +
122A CYS* 3.4 10.9 - - - -
180A GLU* 5.4 0.9 - - - -
181A ALA* 1.3 75.5 - - - +
183A SER* 1.3 66.0 + - - +
184A THR* 3.3 11.9 - - - +
185A GLU* 3.2 26.7 + - + +
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Residues in contact with SER 183 (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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109A CYS 5.2 0.7 + - - -
110A GLU* 2.7 26.9 + - - +
111A ILE 4.2 15.2 + - - -
114A CYS 5.9 2.0 - - - -
122A CYS* 4.5 7.9 - - - +
181A ALA 3.7 1.2 + - - -
182A ALA* 1.3 70.8 - - - +
184A THR* 1.3 61.3 + - - +
186A CYS* 2.9 23.7 + - - +
187A ASN* 3.3 12.5 - - - +
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Residues in contact with THR 184 (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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108A TYR* 4.5 11.2 - - + +
109A CYS 4.2 7.0 - - - +
110A GLU* 3.3 42.7 - - + +
182A ALA* 4.2 7.6 - - - +
183A SER* 1.3 78.1 - - - +
185A GLU* 1.3 68.7 + - - +
187A ASN* 3.1 37.5 + - - +
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Residues in contact with GLU 185 (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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124A LYS* 5.6 1.1 - - - -
181A ALA* 3.6 9.6 - - - +
182A ALA* 3.2 23.1 + - + +
183A SER 3.1 1.0 - - - -
184A THR* 1.3 88.8 + - - +
186A CYS* 1.3 57.3 + - - +
187A ASN 3.3 1.7 + - - -
188A SER 5.0 0.2 + - - -
200A GLY* 3.3 20.3 + - - -
203A ARG* 1.8 67.6 + - + +
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Residues in contact with CYS 186 (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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122A CYS* 2.0 55.6 - - + -
183A SER 2.9 10.9 + - - +
185A GLU* 1.3 75.4 - - - +
187A ASN* 1.3 56.5 + - - +
188A SER 3.3 4.3 - - - -
197A PRO* 3.5 7.4 - - - +
199A GLY* 2.5 39.4 + - - -
203A ARG* 3.8 17.3 - - - -
204A ILE 3.7 12.6 - - - -
205A ILE* 4.2 12.7 - - + +
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Residues in contact with ASN 187 (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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91A VAL* 3.6 31.4 - - + +
92A SER* 3.9 16.8 + - - -
108A TYR* 3.7 36.5 + - + +
183A SER 3.3 11.6 - - - +
184A THR* 3.1 32.9 + - - +
185A GLU 3.3 2.0 + - - -
186A CYS* 1.3 75.0 - - - +
188A SER* 1.3 69.0 + - - +
189A VAL* 3.1 5.2 + - - +
197A PRO* 3.9 11.3 - - - +
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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