Contacts of the strand formed by residues 212 - 216 (chain B) in PDB entry 1MOX
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 CYS 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 4.9 0.3 - - - +
198B ARG* 4.6 13.8 + - + +
208B CYS* 3.7 13.9 - - + -
209B HIS* 3.1 33.3 + - - +
210B ASN 4.4 2.8 - - - +
211B GLN* 1.3 77.9 - - - +
213B ALA* 1.3 59.7 + - - +
214B ALA 4.3 0.3 + - - -
215B GLY* 3.9 9.2 - - - +
216B CYS* 3.9 9.0 - - - -
220B ARG 4.6 2.2 - - - -
223B ASP* 4.4 0.7 - - - -
224B CYS* 2.0 58.7 - - + -
228B ARG* 4.1 6.8 - - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 4.4 11.2 - - + -
118B GLU* 3.7 8.1 - - - +
120B LEU* 4.6 2.2 - - + -
211B GLN 3.3 0.8 + - - -
212B CYS* 1.3 72.3 - - - +
214B ALA* 1.3 60.7 + - - +
215B GLY 2.6 22.6 + - - +
226B VAL* 2.6 38.8 + - + +
227B CYS 3.5 22.9 - - - +
228B ARG* 3.7 13.0 - - + +
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Residues in contact with ALA 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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81B GLN* 4.3 17.7 - - + +
82B ILE* 4.9 0.2 - - + -
117B GLN* 3.9 14.7 - - + +
118B GLU* 2.7 37.7 + - + +
187B THR* 2.8 24.8 + - - +
198B ARG* 3.2 12.6 + - - +
213B ALA* 1.3 72.7 - - - +
215B GLY* 1.3 56.3 + - - +
225B LEU* 4.2 11.0 - - + -
226B VAL* 3.6 14.8 - - + -
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Residues in contact with GLY 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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187B THR* 4.6 8.7 - - - -
198B ARG* 4.3 5.6 - - - +
208B CYS* 3.8 10.8 - - - -
212B CYS* 3.9 4.5 - - - +
213B ALA 2.6 14.2 + - - +
214B ALA* 1.3 77.4 - - - +
216B CYS* 1.3 63.9 + - - +
224B CYS* 3.7 2.3 - - - -
225B LEU* 2.8 36.6 + - - +
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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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187B THR* 5.7 0.6 - - - +
199B CYS 4.9 1.6 + - - -
200B ARG* 3.7 27.1 + - - +
208B CYS* 2.0 54.1 - - + -
212B CYS* 3.9 9.0 - - - -
215B GLY* 1.3 72.7 - - - +
217B THR* 1.3 66.0 + - - +
218B GLY 3.2 23.3 - - - +
223B ASP 3.3 13.9 - - - +
225B LEU* 3.7 9.9 - - - +
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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