Contacts of the strand formed by residues 281 - 287 (chain A) in PDB entry 4D88
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 GLN 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TRP* 5.6 2.8 - - + -
191A VAL* 6.0 0.2 - - - +
275A MET* 4.3 2.4 - - - +
276A GLY* 2.8 25.0 + - - -
278A VAL* 3.0 42.1 + - + +
279A THR 3.0 7.0 + - - +
280A ASN* 1.3 83.5 + - - +
282A SER* 1.3 63.1 + - - +
360A PRO* 4.0 25.2 - - + +
361A PHE 3.1 9.0 - - - +
362A VAL* 4.5 16.9 - - + +
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Residues in contact with SER 282 (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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176A TRP* 5.0 1.7 - - - -
191A VAL* 3.7 23.1 - - - +
273A TYR* 4.0 9.4 - - - -
274A LEU 3.1 17.9 - - - -
275A MET* 4.6 0.2 - - - -
276A GLY* 3.8 3.6 - - - +
281A GLN* 1.3 76.5 - - - +
283A PHE* 1.3 65.2 + - - +
360A PRO* 3.4 8.3 - - - +
361A PHE* 2.8 47.8 + - - +
363A THR* 4.7 6.9 + - - -
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Residues in contact with PHE 283 (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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176A TRP* 3.5 56.8 - + + -
177A TYR 3.4 27.8 - - - -
178A THR* 3.8 14.4 - - - -
272A LEU 3.9 0.2 - - - +
273A TYR* 3.2 6.1 - - - -
274A LEU* 2.7 62.9 + - + -
275A MET 4.0 5.2 - - - -
276A GLY* 4.7 3.1 - - - -
282A SER* 1.3 76.7 - - - +
284A ARG* 1.3 65.5 + - - +
285A ILE* 4.2 3.1 - - + -
341A PHE* 4.0 17.3 - + + -
357A VAL* 3.9 10.3 - - + -
358A GLU 3.2 15.5 - - - +
359A GLY* 4.2 0.2 - - - -
361A PHE* 4.2 2.5 - - - -
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Residues in contact with ARG 284 (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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194A GLU* 3.8 8.7 + - - -
197A GLY* 6.2 0.2 - - - -
271A SER* 4.1 12.2 + - - -
272A LEU 3.2 9.2 - - - +
273A TYR* 3.0 48.7 + - + -
283A PHE* 1.3 76.0 - - - +
285A ILE* 1.3 65.3 + - - +
286A THR* 3.9 15.8 - - + +
356A ALA 3.8 0.3 - - - +
357A VAL* 3.3 6.2 - - - +
358A GLU* 2.7 65.5 + - + +
361A PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 285 (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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270A ILE 3.7 0.9 - - - +
271A SER* 3.5 1.9 - - - -
272A LEU* 2.9 49.2 + - + +
274A LEU* 4.6 5.2 - - + -
283A PHE* 4.2 10.3 - - + -
284A ARG* 1.3 78.4 - - - +
286A THR* 1.3 63.7 + - - +
287A ILE* 4.4 8.3 - - + +
320A MET* 3.7 30.1 - - + -
324A ILE* 4.1 15.5 - - + -
328A PHE* 4.0 13.5 - - + -
341A PHE* 4.1 30.1 - - + -
356A ALA 3.3 3.8 - - - -
357A VAL* 4.0 18.8 - - + -
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Residues in contact with THR 286 (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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269A VAL* 3.7 15.5 - - + -
270A ILE 3.3 2.5 - - - -
271A SER* 3.2 22.7 - - - +
284A ARG* 3.9 26.0 - - + +
285A ILE* 1.3 76.1 - - - +
287A ILE* 1.3 62.4 + - - +
288A LEU* 4.6 0.9 - - - -
291A GLN* 3.9 0.2 - - - +
328A PHE* 3.6 15.9 - - - -
354A THR 3.8 5.9 + - - -
355A ALA* 3.6 14.0 - - - +
356A ALA* 2.9 39.9 + - + +
358A GLU* 4.8 3.6 - - - +
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Residues in contact with ILE 287 (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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221A LEU* 6.0 0.2 - - + -
269A VAL* 3.2 5.2 - - - +
270A ILE* 2.7 54.3 + - + +
272A LEU* 4.7 8.7 - - + -
285A ILE* 4.4 10.8 - - + +
286A THR* 1.3 81.4 - - - +
288A LEU* 1.3 67.0 + - - +
291A GLN* 3.4 29.4 - - + +
292A TYR* 4.2 15.2 - - + +
323A VAL* 6.3 0.2 - - + -
324A ILE* 3.9 38.1 - - + -
328A PHE* 3.7 24.7 - - + -
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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