Contacts of the helix formed by residues 210 - 216 (chain B) in PDB entry 2WP9
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 MET 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B SER* 3.0 22.0 - - - +
209B ILE* 1.3 78.6 - - - +
211B ASN* 1.3 62.3 + - - +
212B CYS* 3.4 7.8 - - - -
213B VAL* 4.3 8.5 + - + +
214B SER* 4.0 7.6 + - - -
223B THR* 4.0 32.1 + - + +
23C THR* 3.4 21.5 + - + +
90C ARG* 4.7 2.9 - - - -
94C MET* 4.1 19.5 - - - +
101C GLU* 3.3 28.5 - - - +
102C THR 3.4 18.8 - - - +
103C PHE* 4.1 17.6 - - + +
106C GLY* 4.1 20.0 - - - -
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Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 2.7 47.4 + - - +
159B CYS* 4.7 3.1 - - - +
160B PRO* 4.4 4.6 - - - +
163B TRP* 5.4 0.2 - - - -
209B ILE* 3.4 8.9 - - + +
210B MET* 1.3 75.0 - - - +
212B CYS* 1.3 66.7 - - - +
213B VAL 3.4 0.4 - - - -
214B SER* 3.3 14.5 + - - -
215B VAL* 3.4 11.1 - - - +
18C ILE* 5.8 1.4 - - - +
19C ARG 5.0 2.4 + - - -
20C PHE* 4.0 24.9 - - - -
21C PRO* 2.9 34.9 - - - +
24C ALA* 3.9 8.9 - - - +
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Residues in contact with CYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B CYS* 3.9 17.2 + - + +
158B SER* 4.2 0.8 + - - -
159B CYS* 5.8 6.1 - - + +
172B PRO* 3.8 29.4 - - + -
206B CYS* 6.0 4.0 - - - -
210B MET* 4.1 4.7 - - - -
211B ASN* 1.3 84.4 - - - +
213B VAL* 1.3 65.2 + - - +
215B VAL* 3.2 18.2 + - - +
216B CYS* 3.4 9.0 + - - +
222B PRO* 3.8 21.8 - - + -
223B THR* 3.4 27.6 - - - -
226B ILE* 5.5 2.9 - - - -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 4.3 17.3 - - + +
211B ASN 3.4 0.8 - - - -
212B CYS* 1.3 77.4 - - - +
214B SER* 1.3 63.3 + - - +
215B VAL 3.1 1.2 + - - -
216B CYS* 3.4 14.2 + - - +
219B GLY* 5.6 1.7 - - - -
220B LEU 4.0 18.7 - - - +
221B ASN* 3.5 28.5 - - + +
222B PRO* 4.4 2.2 - - + -
223B THR* 3.3 29.4 - - - +
103C PHE* 3.9 28.3 - - + +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS* 3.2 27.8 + - - -
210B MET 4.0 2.5 + - - -
211B ASN* 3.3 18.7 + - - -
213B VAL* 1.3 77.7 - - - +
215B VAL* 1.3 61.6 + - - +
216B CYS 5.0 1.1 - - - +
21C PRO* 4.2 9.0 - - - +
103C PHE* 3.6 44.5 - - - -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS* 3.9 25.4 - - + +
71B ASN* 4.1 29.8 - - + +
72B GLY* 4.7 2.1 - - - -
154B CYS* 3.6 30.1 - - + +
155B CYS* 3.7 10.1 - - - -
158B SER* 3.7 10.5 - - - +
211B ASN* 3.4 17.0 - - + +
212B CYS 3.2 14.8 - - - +
213B VAL 3.1 0.2 + - - -
214B SER* 1.3 82.0 - - - +
216B CYS* 1.3 67.6 + - - +
217B PRO* 2.9 10.3 - - - +
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Residues in contact with CYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B CYS* 5.1 0.9 - - - -
155B CYS* 5.5 6.1 - - + +
212B CYS 3.4 9.7 + - - +
213B VAL 3.4 9.3 + - - +
214B SER 5.0 1.2 - - - +
215B VAL* 1.3 78.6 - - - +
217B PRO* 1.3 73.1 - - - +
218B LYS* 3.4 14.6 - - - -
219B GLY* 3.1 11.8 + - - -
220B LEU* 3.3 57.7 - - - +
222B PRO* 5.2 4.3 - - + -
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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