Contacts of the strand formed by residues 204 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ALA* 4.3 14.7 - - + +
172A VAL* 3.9 23.1 - - + -
202A GLN 4.1 8.3 - - - +
203A VAL* 1.3 79.5 - - - +
205A TRP* 1.3 70.8 + - - +
206A ASN* 3.3 29.1 + - - +
250A ALA* 4.6 1.1 - - - -
251A LEU* 2.8 50.6 + - + +
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 5.2 6.5 - - + +
204A THR* 1.3 78.6 + - - +
206A ASN* 1.3 73.8 + - - +
246A VAL* 3.6 5.6 - - + +
247A ALA* 2.9 47.2 + - - +
248A PRO 3.9 7.6 - - - -
249A GLU* 3.5 16.2 - - - -
250A ALA* 3.1 46.6 - - + +
251A LEU* 5.4 0.7 - - - -
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 3.5 28.0 - - + +
169A PRO* 6.1 0.2 - - - +
171A ALA* 5.8 0.5 - - - +
172A VAL* 4.6 2.6 - - - +
204A THR* 3.3 25.5 + - - +
205A TRP* 1.3 94.8 + - - +
207A ILE* 1.3 63.1 + - - +
208A ILE* 3.9 23.9 + - + +
244A ALA* 5.2 1.1 - - + -
245A ILE 3.5 3.8 - - - +
246A VAL* 3.9 26.3 - - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 4.5 11.9 - - + -
198A VAL* 5.0 10.5 - - + -
206A ASN* 1.3 71.5 - - - +
208A ILE* 1.3 64.2 + - - +
209A LEU* 4.1 4.4 + - + -
221A PHE* 3.7 31.6 - - + -
243A ILE 3.7 0.3 - - - +
244A ALA* 3.3 3.8 - - - -
245A ILE* 2.8 52.7 + - + +
247A ALA* 5.6 1.1 - - + -
251A LEU* 3.7 28.0 - - + -
259A LEU* 4.3 25.1 - - + -
306A PHE* 3.8 28.9 - - + -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.3 4.5 - - + -
162A PRO* 4.1 8.1 - - + +
163A TRP* 4.0 24.9 - - + -
168A LEU* 3.9 18.0 - - + +
169A PRO* 3.7 33.9 - - + +
172A VAL* 6.1 0.4 - - - +
206A ASN* 3.9 20.5 + - + +
207A ILE* 1.3 73.0 - - - +
209A LEU* 1.3 65.8 + - - +
242A GLN* 3.9 22.7 - - - +
243A ILE 3.5 6.1 - - - +
244A ALA* 3.7 24.0 - - + -
306A PHE* 3.4 22.6 - - - -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.3 5.2 - - - -
196A ILE* 4.3 7.6 - - + -
207A ILE* 4.7 4.9 - - + +
208A ILE* 1.3 77.6 - - - +
210A HIS* 1.3 71.6 + - - +
242A GLN* 3.2 11.1 - - - +
243A ILE* 2.9 41.2 + - + +
245A ILE* 4.0 11.7 - - + -
259A LEU* 3.9 27.4 - - + -
261A ILE* 4.3 8.3 - - + -
304A PRO* 4.6 2.2 - - + -
305A CYS* 3.2 34.1 - - - +
306A PHE* 3.3 32.3 - - + +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 4.5 5.3 + - - +
168A LEU* 3.4 36.1 - - + +
209A LEU* 1.3 73.8 - - - +
211A SER* 1.3 65.5 + - - +
240A HIS 3.7 8.1 + - - -
241A GLY 3.2 12.3 - - - +
242A GLN* 3.8 15.5 + - + +
243A ILE* 4.4 1.1 - - - -
300A ARG* 3.4 55.5 + - + +
303A PHE 4.2 1.2 - - - +
304A PRO* 3.2 3.3 - - - +
305A CYS 2.8 40.4 + - - +
307A ASP* 3.1 27.5 + - + +
308A GLU* 4.3 6.3 - - + -
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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