Contacts of the helix formed by residues 182 - 187 (chain K) in PDB entry 5FWP
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180K TYR 4.2 0.2 + - - -
181K ARG* 1.3 75.5 - - - +
183K PRO* 1.3 65.7 - - + +
184K GLU* 3.4 17.0 - - - +
185K VAL* 2.8 25.9 + - - +
186K LEU* 3.0 9.6 + - - +
195K VAL* 3.5 42.7 + - + +
198K TRP* 3.5 14.5 - - + -
199K SER* 4.7 1.2 - - - +
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Residues in contact with PRO 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K ARG 4.0 1.3 - - - +
182K ALA* 1.3 85.8 - - + +
184K GLU* 1.3 55.0 + - - +
186K LEU* 2.7 15.3 + - + +
187K LEU* 2.5 41.7 + - - +
198K TRP* 3.4 35.2 - - + +
223K LEU* 3.7 15.9 - - + -
226K ILE* 4.5 3.6 - - + -
278K PHE* 3.6 35.9 - - + -
283K ARG* 3.5 13.5 - - - +
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Residues in contact with GLU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K ALA* 3.1 5.6 - - + +
183K PRO* 1.3 74.7 - - - +
185K VAL* 1.3 57.7 + - - +
187K LEU* 3.7 15.3 - - + +
188K GLN 3.3 1.2 + - - -
189K SER* 2.7 48.7 + - - +
190K THR 4.0 3.2 + - - +
195K VAL* 3.7 23.3 - - + -
239K PRO* 5.4 2.5 - - + -
278K PHE 3.1 11.0 - - - +
280K PRO* 3.1 41.0 - - + +
283K ARG* 2.8 32.7 + - - -
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Residues in contact with VAL 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ARG* 4.2 20.8 + - + +
174K VAL* 6.5 0.2 - - + -
178K LEU* 4.7 9.2 - - + -
181K ARG* 3.5 54.3 - - + +
182K ALA 2.8 23.3 + - - +
184K GLU* 1.3 72.7 - - - +
186K LEU* 1.3 59.7 + - - +
188K GLN* 2.9 34.5 + - - +
189K SER 4.9 0.2 - - - +
190K THR 5.1 0.2 - - - +
195K VAL* 4.0 21.1 - - + -
219K GLU* 3.6 0.6 - - - +
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Residues in contact with LEU 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K LEU* 4.0 31.4 - - + -
181K ARG* 4.0 9.4 - - + +
182K ALA 3.5 8.1 - - - +
183K PRO* 2.7 10.3 + - + +
185K VAL* 1.3 77.2 - - - +
187K LEU* 1.3 55.2 + - - +
188K GLN 3.2 0.9 - - - -
219K GLU* 3.2 53.0 - - + +
222K GLN* 3.6 17.5 - - + -
223K LEU* 3.7 13.9 - - + -
226K ILE* 3.6 31.2 - - + -
243K SER* 4.1 0.5 + - - -
244K LEU* 3.1 23.9 - - + +
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Residues in contact with LEU 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K PRO* 2.5 32.7 + - + +
184K GLU* 3.9 17.0 - - + +
185K VAL 3.1 0.2 - - - -
186K LEU* 1.3 71.4 - - - +
188K GLN* 1.3 68.0 + - - +
223K LEU* 4.2 1.1 - - + -
238K TRP* 3.7 29.2 - - + -
239K PRO* 3.5 31.4 - - + -
241K ASP 3.3 15.1 - - - +
242K VAL* 3.7 16.3 - - + -
243K SER* 3.0 27.1 + - - +
244K LEU* 4.1 13.0 - - + -
278K PHE* 3.6 17.9 - - + -
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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
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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