Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 5ANC
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 ILE 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.5 45.1 - - + -
216A GLU* 3.8 17.7 - - + +
217A LEU* 1.3 77.9 - - - +
219A ASP* 1.3 75.4 + - - +
220A VAL 3.9 1.6 - - - +
281A ARG 3.7 0.3 - - - -
282A ASN 2.8 27.2 + - - -
283A LYS* 2.8 25.8 + - + +
285A ILE* 3.9 19.5 - - + -
332A LEU* 4.8 2.2 - - + -
346A LEU* 3.4 31.9 - - + -
347A ARG 3.2 19.5 - - - +
348A LYS* 4.5 2.2 - - - -
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Residues in contact with ASP 219 (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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218A ILE* 1.3 71.7 - - - +
220A VAL* 1.3 65.6 - - - +
221A ILE* 3.5 8.3 + - - +
279A VAL* 3.8 12.5 - - + +
280A GLU 3.2 4.9 - - - +
281A ARG* 3.3 19.7 + - - +
282A ASN* 2.9 18.9 + - - +
347A ARG* 2.8 61.0 + - - +
349A SER* 2.7 37.0 + - - -
350A ILE* 4.0 3.6 + - - +
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Residues in contact with VAL 220 (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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218A ILE* 4.6 1.6 - - + -
219A ASP* 1.3 74.6 - - - +
221A ILE* 1.3 65.4 + - - +
222A GLY 4.5 0.7 - - - +
278A ARG 3.8 0.9 - - - +
279A VAL* 3.5 5.4 - - - -
280A GLU* 3.0 38.9 + - + +
283A LYS* 4.1 13.5 - - + +
332A LEU* 3.9 14.8 - - + -
336A VAL* 3.8 32.5 - - + -
337A ALA* 5.1 1.6 - - + +
344A LEU* 3.8 33.2 - - + -
345A THR 4.0 2.9 - - - -
346A LEU* 3.7 21.3 - - + -
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Residues in contact with ILE 221 (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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27A GLY* 3.4 22.6 - - - -
28A LYS 3.7 22.2 - - - +
29A VAL* 4.4 8.5 - - + -
30A LYS 5.5 0.2 - - - +
31A SER* 5.2 1.8 - - - +
219A ASP 3.9 7.6 - - - +
220A VAL* 1.3 82.6 - - - +
222A GLY* 1.3 65.0 + - - +
277A HIS* 4.5 9.6 - - + -
278A ARG 3.7 11.4 - - - +
279A VAL* 4.0 21.1 - - + -
344A LEU* 3.3 4.0 - - - -
345A THR* 2.8 41.1 + - + +
347A ARG* 3.5 34.1 - - + +
3473N C 5.0 1.8 - - - +
3474N U 5.3 0.2 - - - +
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Residues in contact with GLY 222 (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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27A GLY* 4.1 4.0 - - - -
221A ILE* 1.3 75.6 - - - +
223A VAL* 1.3 64.1 + - - -
224A THR 4.2 0.2 - - - -
277A HIS* 3.4 31.4 + - - +
278A ARG 3.9 5.4 + - - -
337A ALA* 3.8 23.1 - - - +
342A ARG* 5.7 0.2 - - - -
343A ALA 3.8 13.5 - - - -
344A LEU* 4.5 3.4 - - - -
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Residues in contact with VAL 223 (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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22A ALA* 5.0 4.5 - - + +
24A ARG 3.1 27.6 - - - +
25A HIS* 4.0 18.6 - - + -
26A GLN 4.6 1.3 - - - +
222A GLY* 1.3 76.8 - - - +
224A THR* 1.3 76.9 + - - +
275A TYR* 3.5 39.9 - - + +
276A HIS 3.3 4.5 - - - +
277A HIS* 4.3 8.3 - - + +
337A ALA* 4.0 2.4 + - - +
338A GLY* 3.3 16.3 - - - -
342A ARG* 3.4 23.5 - - - +
343A ALA 4.8 0.6 + - - -
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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