Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 5PMJ
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 LYS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TYR* 3.2 14.1 + - - -
181A TYR* 5.1 1.6 + - - +
189A PHE* 3.9 17.9 - - + -
202A ASN* 4.2 2.7 - - - -
204A LEU* 4.1 10.1 - - + +
209A PRO* 1.3 74.7 - - - +
211A THR* 1.3 58.9 + - - +
212A TRP* 3.4 23.7 - - + +
265A THR* 4.4 1.1 - - - -
266A GLN* 2.8 61.3 + - - +
283A PHE 3.5 5.2 - - - +
284A ASN* 2.9 28.8 + - - +
288A ASN* 4.5 3.4 + - - +
290A ALA* 3.9 25.5 - - - +
404A OGA 2.9 29.0 + - - +
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Residues in contact with THR 211 (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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122A GLU* 4.8 0.2 - - - +
189A PHE* 4.0 2.9 - - - -
210A LYS* 1.3 71.7 - - - +
212A TRP* 1.3 65.2 + - - +
213A TYR* 3.9 19.3 - - + +
264A ILE 3.6 9.0 - - - +
265A THR* 2.8 13.6 + - - -
282A GLY* 3.1 5.9 - - - -
283A PHE* 2.9 62.9 + - + +
285A HIS* 2.7 25.8 + - - -
409A EDO 4.0 20.9 + - - +
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Residues in contact with TRP 212 (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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48A LEU* 3.7 34.7 - - + +
189A PHE* 3.8 16.6 - + - -
202A ASN* 3.8 19.7 - - + -
210A LYS* 3.4 31.6 - - + +
211A THR* 1.3 76.4 - - - +
213A TYR* 1.3 62.4 + - - +
263A ARG* 3.2 8.1 - - - +
264A ILE 2.8 38.1 + - - +
266A GLN* 2.9 37.2 + - + +
272A MET* 3.8 20.4 - - + +
274A THR* 3.8 15.5 - - + -
280A HIS* 3.7 30.3 - + + -
281A ALA 3.5 4.9 - - - -
404A OGA 3.7 24.9 - - - -
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Residues in contact with TYR 213 (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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122A GLU* 2.6 35.2 + - - +
126A TRP* 2.9 41.1 + + - -
191A TRP* 3.6 24.6 - + + -
211A THR* 3.9 17.1 - - + +
212A TRP* 1.3 73.0 - - - +
214A VAL* 1.3 60.4 + - - +
251A PRO* 3.7 17.3 - - + -
254A LEU* 6.0 0.4 - - + -
261A PHE* 4.3 16.2 - + + -
262A ASN 3.3 7.0 - - - +
263A ARG* 3.7 23.6 - - + -
280A HIS* 3.1 9.7 - - - +
281A ALA* 2.8 45.5 + - + +
282A GLY* 4.2 2.5 - - - -
283A PHE* 3.6 14.7 - + - -
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Residues in contact with VAL 214 (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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18A ILE* 3.8 31.0 - - + -
46A ALA 3.4 25.1 - - - +
47A GLY* 3.7 23.1 - - - +
48A LEU* 3.9 16.8 - - + -
191A TRP* 4.0 1.5 - - - -
213A TYR* 1.3 76.3 - - - +
215A VAL* 1.3 67.1 + - - +
216A PRO* 4.1 1.0 - - - +
261A PHE* 3.2 5.6 - - - +
262A ASN* 2.9 34.3 + - + +
278A GLY 4.6 1.8 - - - -
279A TYR 3.2 15.3 - - - +
280A HIS* 4.6 4.7 - - + -
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Residues in contact with VAL 215 (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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46A ALA 4.0 2.0 - - - -
191A TRP* 4.0 20.2 - - + -
214A VAL* 1.3 79.4 - - - +
216A PRO* 1.4 81.4 - - + +
217A PRO* 3.4 4.3 - - - +
219A HIS* 3.7 25.1 - - + +
220A GLY* 4.2 5.3 - - - +
223A LEU* 4.2 18.4 - - + -
254A LEU* 5.2 0.9 - - + -
259A ILE* 4.3 11.7 - - + -
260A PRO 3.5 19.5 - - - +
261A PHE* 4.1 5.2 - - + -
279A TYR* 2.9 31.2 + - + -
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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