Contacts of the helix formed by residues 207 - 212 (chain H) in PDB entry 5YWB
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 PRO 207 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65H TRP* 3.3 23.3 - - + +
66H LEU* 4.9 3.4 - - - -
67H HIS* 5.4 10.1 - - + +
204H VAL* 6.2 2.4 - - + -
205H LYS 4.1 2.2 - - - +
206H PRO* 1.3 81.9 - - + +
208H GLU* 1.3 61.8 + - - +
209H ASP* 4.5 7.4 - - + +
210H LEU* 5.2 6.7 - - + +
211H GLN* 2.8 32.6 + - + +
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Residues in contact with GLU 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H LYS 4.9 0.2 + - - -
206H PRO 3.2 6.1 + - - +
207H PRO* 1.3 71.7 - - - +
209H ASP* 1.3 65.8 + - - +
210H LEU 3.3 0.2 - - - -
211H GLN* 3.8 2.2 - - - -
212H ASP* 3.1 32.9 + - + +
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Residues in contact with ASP 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H PRO* 3.3 6.4 - - + -
208H GLU* 1.3 80.3 - - - +
210H LEU* 1.3 60.8 + - + +
212H ASP* 4.4 5.7 - - - +
215H VAL* 5.2 4.5 - - - +
254H PRO* 4.6 3.1 - - - +
255H ILE* 3.4 41.2 + - + +
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Residues in contact with LEU 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H PRO* 4.1 7.3 + - + +
209H ASP* 1.3 77.9 - - + +
211H GLN* 1.3 59.6 + - - +
212H ASP 3.4 2.5 - - - -
215H VAL* 4.7 19.5 - - - +
217H PHE 5.6 0.8 - - - +
218H LEU* 5.5 2.1 - - - +
220H PRO* 4.8 12.6 - - + -
221H PHE* 3.5 36.1 - - + +
254H PRO* 5.4 8.3 - - + -
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Residues in contact with GLN 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G LYS* 3.2 19.9 + - - +
63H SER* 4.6 15.8 + - - +
64H THR* 4.9 14.6 - - + -
65H TRP* 5.0 8.3 - - + +
206H PRO* 5.1 2.5 - - + +
207H PRO* 2.8 27.5 + - + +
208H GLU* 4.0 2.2 - - - -
210H LEU* 1.3 78.0 - - - +
212H ASP* 1.3 65.4 + - - +
213H LEU* 4.4 0.3 - - - -
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Residues in contact with ASP 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G LYS* 4.9 2.5 - - - +
208H GLU* 3.1 24.0 + - + +
209H ASP 4.4 6.1 - - - +
210H LEU 3.4 1.6 - - - -
211H GLN* 1.3 79.6 - - - +
213H LEU* 1.3 69.0 + - - +
214H GLY 3.4 2.1 + - - -
215H VAL* 3.7 23.2 + - + +
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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