Contacts of the strand formed by residues 204 - 210 (chain B) in PDB entry 5MJ6
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 THR 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B ALA* 4.0 22.8 - - + +
172B VAL* 4.1 12.3 - - + -
202B GLN* 3.8 12.1 - - - +
203B VAL* 1.3 82.1 - - - +
205B TRP* 1.3 73.1 + - - +
206B ASN* 3.0 28.2 + - - +
250B ALA* 3.7 1.1 - - - -
251B LEU* 2.8 45.0 + - + +
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Residues in contact with TRP 205 (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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203B VAL* 5.6 4.8 - - + +
204B THR* 1.3 79.2 + - - +
206B ASN* 1.3 78.8 + - - +
247B ALA* 3.2 44.1 + - - +
248B PRO 3.8 6.7 - - - -
249B GLU* 3.5 17.3 - - - -
250B ALA* 3.2 43.7 - - + +
251B LEU* 4.4 2.0 - - - -
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Residues in contact with ASN 206 (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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162B PRO* 3.5 34.7 + - + +
171B ALA* 5.9 0.2 - - - +
172B VAL* 4.3 3.8 - - - +
204B THR* 3.0 24.8 + - - +
205B TRP* 1.3 97.1 - - - +
207B ILE* 1.3 67.4 + - - +
208B ILE* 4.2 18.9 - - + +
245B ILE 3.5 13.1 - - - +
246B VAL* 3.6 16.3 - - - +
251B LEU* 5.0 0.2 - - - -
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Residues in contact with ILE 207 (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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172B VAL* 4.4 15.5 - - + -
198B VAL* 5.7 4.5 - - + -
206B ASN* 1.3 78.8 - - - +
208B ILE* 1.3 66.0 + - - +
209B LEU* 4.1 2.2 + - + -
221B PHE* 4.0 28.0 - - + -
243B ILE 3.8 0.5 - - - +
244B ALA* 3.4 3.5 - - - -
245B ILE* 2.8 66.7 + - + +
247B ALA* 4.5 2.7 - - + -
251B LEU* 4.1 21.1 - - + -
259B LEU* 4.5 15.9 - - + -
306B PHE* 3.9 29.2 - - + -
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Residues in contact with ILE 208 (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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161B PHE* 4.6 2.2 - - + -
162B PRO* 4.2 12.1 - - + +
163B TRP* 3.9 26.7 - - + -
168B LEU* 3.9 14.4 - - + +
169B PRO* 3.7 32.9 - - + +
206B ASN* 4.4 10.5 - - + +
207B ILE* 1.3 82.6 - - - +
209B LEU* 1.3 62.6 + - - +
242B GLN* 3.7 32.5 - - + +
243B ILE 3.5 7.0 - - - +
244B ALA* 3.8 20.6 - - + -
306B PHE* 3.6 22.7 - - - -
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Residues in contact with LEU 209 (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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168B LEU* 4.5 5.2 - - - -
196B ILE* 4.1 8.7 - - + -
207B ILE* 4.5 5.6 - - + +
208B ILE* 1.3 73.5 - - - +
210B HIS* 1.3 64.0 + - - +
242B GLN* 3.1 10.2 - - - +
243B ILE* 2.9 44.8 + - + +
245B ILE* 4.9 3.8 - - + -
259B LEU* 3.6 27.8 - - + -
261B ILE* 4.0 19.3 - - + -
304B PRO* 4.3 7.0 - - + -
305B CYS* 3.7 14.1 - - - -
306B PHE* 3.3 48.0 - - + -
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Residues in contact with HIS 210 (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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166B ILE 4.3 5.9 + - - -
168B LEU* 3.4 34.8 - - + +
209B LEU* 1.3 72.5 - - - +
211B SER* 1.3 64.0 + - - +
240B HIS 4.1 3.2 + - - -
241B GLY 3.2 13.7 - - - -
242B GLN* 4.0 18.2 + - + -
300B ARG* 3.5 55.4 + - + +
304B PRO* 3.2 3.6 - - - +
305B CYS 2.9 39.3 + - - +
307B ASP* 3.2 29.7 + - + +
308B GLU* 3.9 10.5 - - + -
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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