Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 1ADI
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 PHE 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ASN* 3.6 29.8 - - - -
26B ARG* 2.9 44.0 - - + +
27B ALA* 3.9 3.1 - - - -
28B LYS* 3.0 26.2 + - + +
29B TYR 3.4 5.9 + - - -
215B GLY 4.2 4.9 - - - -
216B ASP* 1.3 72.9 - - - +
218B VAL* 1.3 59.8 + - - +
429B PHE* 3.6 44.4 - + + -
430B ASP* 5.9 2.7 - - - -
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Residues in contact with VAL 218 (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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2B ASN 2.9 9.0 + - - +
3B ASN* 3.4 21.0 - - - +
4B VAL* 2.8 27.7 + - - +
29B TYR* 3.6 20.0 - - + -
31B VAL* 3.6 28.0 - - + -
208B LEU* 4.0 13.0 - - + +
211B ALA* 4.0 25.1 - - + -
212B ARG 5.3 0.4 - - - +
216B ASP 3.5 4.0 + - - +
217B PHE* 1.3 78.4 - - - +
219B MET* 1.3 65.0 + - - +
220B PHE* 4.4 10.9 - - + -
429B PHE* 3.9 4.4 - - - -
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Residues in contact with MET 219 (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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4B VAL* 3.3 10.3 - - + +
6B VAL* 4.3 19.5 - - + -
20B VAL* 4.1 15.3 - - + +
23B LEU* 4.2 24.5 - - - -
24B THR* 3.9 17.5 - - - +
27B ALA* 4.3 9.8 - - + +
29B TYR 3.0 14.6 + - - +
30B VAL* 3.6 22.2 - - + +
31B VAL* 2.8 28.4 + - - +
218B VAL* 1.3 76.3 - - - +
220B PHE* 1.3 72.9 + - - +
221B GLU* 3.7 26.6 + - - +
429B PHE* 4.4 6.5 - - + -
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Residues in contact with PHE 220 (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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3B ASN* 4.1 18.4 - - + -
4B VAL 2.6 21.5 + - - +
5B VAL* 3.4 22.1 - - + -
6B VAL 2.9 26.4 + - - -
31B VAL* 3.6 31.6 - - + -
33B TYR* 4.2 15.0 - + + -
208B LEU* 3.9 14.1 - - + -
218B VAL* 4.4 12.6 - - + -
219B MET* 1.3 79.4 - - - +
221B GLU* 1.3 61.5 + - - +
222B GLY 4.2 0.2 - - - -
248B VAL* 3.8 17.5 - - + -
252B SER* 3.7 19.3 - - - -
254B LEU* 3.3 34.1 - - + -
259B VAL* 6.0 2.7 - - + -
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Residues in contact with GLU 221 (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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6B VAL* 3.6 5.4 - - + +
20B VAL* 4.3 29.9 - - + +
30B VAL* 3.3 27.5 - - - +
31B VAL 3.0 18.3 + - - +
32B ARG* 4.1 29.2 + - - -
33B TYR* 3.7 14.0 + - - -
34B GLN* 4.8 1.0 - - - +
41B HIS* 5.3 4.5 + - - -
56B PRO* 4.4 8.5 - - - +
57B SER* 5.2 3.5 + - - -
219B MET* 3.7 14.7 - - + +
220B PHE* 1.3 75.1 - - - +
222B GLY* 1.3 68.9 + - - +
223B ALA 3.9 0.5 + - - -
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Residues in contact with GLY 222 (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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6B VAL* 2.7 19.8 + - - +
7B LEU* 4.3 9.2 - - - -
8B GLY 6.0 0.2 - - - -
16B LYS* 3.8 17.9 - - - +
32B ARG* 5.9 0.6 - - - -
33B TYR* 3.6 22.5 - - - -
34B GLN* 4.2 2.5 - - - -
221B GLU* 1.3 83.1 - - - +
223B ALA* 1.3 62.2 + - - -
224B GLN 3.8 1.3 - - - -
243B THR 5.1 2.2 - - - -
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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