Contacts of the helix formed by residues 209 - 215 (chain C) in PDB entry 1D5Z
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 ASP 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.2 2.6 - - - +
57A GLN* 2.5 29.3 + - - +
92C GLN* 5.6 1.9 - - - +
207C LYS* 4.0 21.9 + - - +
208C PHE* 1.3 75.9 - - - +
210C GLN* 1.3 63.1 + - - +
211C SER* 3.3 7.4 + - - -
212C LYS* 2.9 36.9 + - + +
213C TYR* 2.9 22.9 + - - +
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Residues in contact with GLN 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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23C ASN* 2.9 43.6 + - + +
26C VAL* 3.3 21.0 - - - +
27C LEU* 3.8 19.4 - - + +
89C TYR* 4.3 14.5 - - + +
90C TYR 4.9 1.2 + - - -
91C TYR* 4.2 22.5 + - - +
208C PHE* 3.4 22.9 + - + +
209C ASP* 1.3 71.0 + - - +
211C SER* 1.3 64.8 + - - +
213C TYR* 3.1 2.4 + - - +
214C LEU* 2.9 30.2 + - - +
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Residues in contact with SER 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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39A LYS* 3.1 15.2 + - - +
57A GLN* 3.2 23.1 + - - -
89C TYR* 3.1 32.9 + - - -
91C TYR 4.6 4.2 + - - -
92C GLN* 4.8 0.6 + - - -
115C TYR* 2.6 49.9 + - - -
209C ASP* 3.3 2.8 + - - -
210C GLN* 1.3 77.6 - - - +
212C LYS* 1.3 57.8 + - - +
215C MET* 3.1 9.5 + - - +
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Residues in contact with LYS 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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38A LYS* 2.5 30.1 + - - +
39A LYS* 3.2 22.1 + - + +
40A GLU* 4.4 8.7 + - - +
57A GLN* 3.2 13.7 - - - +
209C ASP* 2.9 39.9 + - + +
211C SER* 1.3 72.6 - - - +
213C TYR* 1.3 66.3 + - - +
215C MET* 3.3 28.4 - - + +
216C MET 4.3 1.0 + - - -
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Residues in contact with TYR 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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12C HIS* 5.7 4.0 - + - -
24C MET* 3.7 17.7 - - + -
27C LEU* 4.3 7.9 - - + -
28C TYR* 3.4 22.9 - - - -
165C ARG* 2.6 31.6 + - - -
199C ASP* 2.6 28.5 + - + -
200C MET* 3.6 1.0 - - - -
201C MET 4.3 9.0 - - - -
202C PRO* 5.3 0.9 - - + -
203C ALA 5.9 0.7 - - - -
208C PHE* 3.5 38.6 - + + -
209C ASP 2.9 11.7 + - - +
210C GLN 3.5 2.0 - - - +
212C LYS* 1.3 78.3 - - - +
214C LEU* 1.3 66.5 + - + +
215C MET 3.1 1.4 + - - -
216C MET* 3.2 43.3 + - - +
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Residues in contact with LEU 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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27C LEU* 3.9 34.8 - - + -
28C TYR* 4.3 7.4 - - - +
87C ALA* 3.5 36.3 - - + +
89C TYR* 3.7 25.4 - - + -
115C TYR* 3.2 24.7 - - + -
210C GLN 2.9 16.9 + - - +
213C TYR* 1.3 74.7 - - + +
215C MET* 1.3 60.1 + - - +
216C MET 3.0 6.1 - - - -
217C TYR* 3.0 49.3 + - + +
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Residues in contact with MET 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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37A ALA 3.4 25.6 - - - +
38A LYS* 3.8 17.7 - - - +
39A LYS* 3.5 22.2 - - + -
115C TYR* 3.5 35.2 - - + +
211C SER 3.1 8.4 + - - +
212C LYS* 3.3 27.6 - - + +
213C TYR 3.0 0.8 - - - -
214C LEU* 1.3 76.4 - - - +
216C MET* 1.3 54.5 + - - +
217C TYR 3.0 1.1 - - - -
218C ASN* 2.8 51.0 + - - +
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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