Contacts of the helix formed by residues 208 - 215 (chain C) in PDB entry 4NY0
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 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C TYR* 4.7 3.6 - - - +
156C MET* 4.6 6.3 - - + -
160C ALA* 3.7 44.4 - - + +
161C ASP* 3.9 10.8 - - - +
168C ALA* 4.0 23.3 - - + +
206C PHE 4.7 0.9 - - - +
207C PHE* 1.3 94.5 - - + +
209C LYS* 1.3 64.9 + - - +
210C SER* 4.1 3.8 - - - +
211C LEU* 3.0 29.0 + - + +
212C LEU* 3.4 10.6 + - - +
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Residues in contact with LYS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ASP* 4.2 5.3 + - - +
204C LYS* 5.9 10.9 - - + +
207C PHE 3.8 1.0 + - - -
208C PRO* 1.3 72.6 - - - +
210C SER* 1.3 61.1 + - - +
211C LEU 3.1 1.2 + - - -
212C LEU* 3.4 19.0 + - + +
213C ASP* 2.8 57.2 + - - +
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ALA 5.0 0.2 - - - -
161C ASP* 3.2 48.5 + - - -
165C GLN* 4.4 10.9 + - - -
208C PRO* 4.5 4.0 - - - -
209C LYS* 1.3 79.4 - - - +
211C LEU* 1.3 58.3 + - - +
213C ASP* 4.0 4.9 + - - +
214C SER* 3.4 22.5 + - - -
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C GLN* 3.3 40.2 - - + +
168C ALA* 4.7 10.8 - - + -
169C LEU* 3.6 35.4 - - + -
207C PHE* 4.1 22.2 - - + -
208C PRO* 3.0 22.1 + - + +
210C SER* 1.3 77.7 - - - +
212C LEU* 1.3 61.7 + - - +
213C ASP 3.0 6.0 + - - -
214C SER* 3.7 0.8 + - - -
215C VAL* 3.7 25.6 + - + -
220C LEU* 3.6 18.2 - - + +
223C LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LEU* 3.9 29.6 - - + +
204C LYS* 3.7 37.7 - - + +
207C PHE* 4.6 12.8 - - + +
208C PRO 3.4 11.7 + - - +
209C LYS* 3.4 16.5 + - + +
211C LEU* 1.3 78.2 - - + +
213C ASP* 1.3 64.7 + - - +
215C VAL 3.7 11.0 - - - +
220C LEU* 3.9 21.3 - - + +
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Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LYS* 2.8 50.8 + - - +
210C SER* 4.1 5.8 - - - +
211C LEU 3.0 0.8 - - - -
212C LEU* 1.3 81.3 - - - +
214C SER* 1.3 65.0 + - - +
215C VAL 3.2 10.6 + - - +
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Residues in contact with SER 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C GLN* 3.6 20.6 + - - -
210C SER 3.4 15.9 + - - -
211C LEU 3.7 5.0 + - - -
213C ASP* 1.3 78.7 - - - +
215C VAL* 1.3 66.4 + - - +
216C LYS* 5.8 0.5 - - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C GLN* 4.6 4.9 - - - +
211C LEU* 3.7 21.5 + - + -
212C LEU 3.7 11.8 - - - +
213C ASP 3.2 9.0 - - - +
214C SER* 1.3 90.4 - - - +
216C LYS* 1.3 67.4 + - - +
217C ALA* 3.9 1.0 + - - -
219C THR* 3.3 21.1 - - - +
220C LEU* 3.5 37.0 - - + +
223C LEU* 4.3 16.4 - - + -
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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