Contacts of the helix formed by residues 215 - 220 (chain H) in PDB entry 5PRC
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 SER 215 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159H ALA* 2.9 18.7 - - - +
161H ASP* 2.7 30.3 + - - -
163H VAL* 3.7 21.8 - - - +
164H GLU 4.6 0.2 - - - -
165H ALA* 3.8 21.4 - - - +
187H VAL* 5.7 1.2 - - - +
214H LEU* 1.3 71.4 - - - +
216H GLU* 1.3 77.4 + - - +
217H GLN 3.0 1.4 + - - -
218H PHE* 3.3 18.2 + - - +
219H ALA 4.6 0.5 + - - -
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Residues in contact with GLU 216 (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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161H ASP* 3.1 17.5 - - - +
163H VAL* 5.4 1.9 - - - +
214H LEU* 3.4 21.0 - - - +
215H SER* 1.3 97.0 + - - +
217H GLN* 1.3 67.9 + - + +
218H PHE 3.4 1.2 + - - -
219H ALA* 3.6 18.9 + - - +
220H ASN* 5.1 1.9 - - - +
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Residues in contact with GLN 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LEU* 4.0 16.3 - - + +
213H ILE* 3.2 23.6 - - + +
214H LEU* 2.9 40.2 + - + +
216H GLU* 1.3 78.4 - - + +
218H PHE* 1.3 63.7 + - - +
219H ALA 3.1 3.5 + - - -
220H ASN* 3.4 7.3 + - - +
241H TYR* 2.7 33.7 + - - +
248H TYR 4.5 1.6 + - - -
249H ALA* 3.0 37.6 + - - +
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Residues in contact with PHE 218 (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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157H VAL* 3.7 21.5 - - + -
159H ALA* 4.4 9.4 - - + -
165H ALA* 3.9 23.1 - - + -
185H LEU* 3.4 42.2 - - + -
187H VAL* 4.1 18.5 - - + +
192H ARG* 4.1 8.5 + - - -
194H ALA* 4.3 5.8 - - + -
196H ILE* 4.4 3.8 - - + -
210H VAL* 4.1 19.5 - - + -
213H ILE* 3.6 23.3 - - + -
214H LEU 3.8 9.6 - - - -
215H SER 3.3 9.2 + - - +
217H GLN* 1.3 75.6 - - - +
219H ALA* 1.3 65.0 + - - +
220H ASN 3.2 0.2 - - - -
221H VAL* 3.0 22.3 + - + +
242H TYR* 4.0 18.6 - + - -
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H VAL* 4.6 6.8 - - + +
190H SER* 4.7 10.8 - - - +
192H ARG* 2.6 39.6 + - - +
215H SER 4.6 0.4 + - - -
216H GLU 3.6 14.9 + - - +
217H GLN 3.1 0.4 - - - -
218H PHE* 1.3 79.2 - - - +
220H ASN* 1.3 65.5 + - - +
221H VAL 3.3 0.2 - - - -
223H ARG* 4.6 3.5 + - - -
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Residues in contact with ASN 220 (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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106H ASN* 4.8 4.0 + - - -
109H VAL* 3.9 25.8 - - + +
192H ARG* 4.3 0.2 - - - +
216H GLU 5.1 2.4 - - - +
217H GLN* 3.4 5.2 + - - +
218H PHE 3.2 0.4 - - - -
219H ALA* 1.3 87.0 + - - +
221H VAL* 1.3 68.0 + - - +
222H PRO* 3.3 3.6 - - - +
241H TYR* 3.3 28.3 + - - +
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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