Contacts of the strand formed by residues 319 - 324 (chain A) in PDB entry 1E3Q
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 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.7 29.6 - - + -
222A ALA* 3.4 16.8 - - + +
224A LEU* 4.7 6.3 - - + -
317A THR* 4.9 1.6 - - + -
318A GLN* 1.3 78.8 - - - +
320A LEU* 1.3 62.2 + - - +
321A LEU* 4.1 25.8 - - + -
407A PHE* 4.2 8.7 - - + -
408A VAL* 5.1 1.1 - - + -
411A TYR* 3.3 44.9 - - + +
417A GLY 3.0 7.9 + - - +
418A THR* 3.4 12.3 - - + +
419A TYR* 2.9 26.2 + - - +
476A PHE* 3.7 3.8 - - - -
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Residues in contact with LEU 320 (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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222A ALA 3.2 4.8 + - - -
223A ILE* 2.9 51.8 - - + +
224A LEU 3.1 0.5 + - - -
319A ILE* 1.3 75.5 - - - +
321A LEU* 1.3 62.4 + - - +
419A TYR* 3.3 10.5 - - + +
421A TYR* 4.1 8.1 - - + -
472A TYR 4.7 0.7 - - - +
473A TRP* 4.0 30.5 - - + -
476A PHE* 3.8 43.3 - - + -
482A PRO* 4.1 10.1 - - + -
492A TRP* 3.8 28.9 - - + -
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Residues in contact with LEU 321 (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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224A LEU* 2.9 29.8 - - + +
319A ILE* 4.1 11.4 - - + -
320A LEU* 1.3 76.1 - - - +
322A GLY* 1.3 60.0 + - - +
404A LEU* 4.1 18.8 - - + -
407A PHE* 3.9 26.7 - - + -
408A VAL* 3.3 36.3 - - + -
418A THR* 4.3 12.6 - - + -
419A TYR 3.0 13.7 + - - +
420A LEU* 3.0 23.3 - - + +
421A TYR* 3.1 20.4 + - - -
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Residues in contact with GLY 322 (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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224A LEU 3.1 7.3 + - - -
226A SER 3.0 21.7 + - - -
321A LEU* 1.3 77.6 - - - +
323A VAL* 1.3 61.0 + - - -
404A LEU* 3.3 13.3 - - - +
420A LEU* 3.8 4.0 - - - -
421A TYR* 3.1 34.5 - - - -
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Residues in contact with VAL 323 (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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226A SER* 4.1 2.0 - - - -
322A GLY* 1.3 78.1 - - - +
324A ASN* 1.3 67.1 + - - +
327A GLU* 3.7 14.1 - - - +
400A VAL* 3.9 10.3 - - + -
401A ILE* 3.5 51.8 - - + -
404A LEU* 4.1 13.7 - - + -
420A LEU* 5.8 0.4 - - + -
421A TYR* 3.4 6.3 + - - +
422A PHE* 3.5 22.0 - - + -
423A PHE* 2.9 24.6 + - - +
516A LEU* 4.4 14.1 - - + -
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Residues in contact with ASN 324 (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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226A SER* 4.0 6.2 + - - -
323A VAL* 1.3 85.5 - - - +
325A LYS* 1.3 67.5 + - - +
327A GLU* 3.1 34.9 + - - +
401A ILE* 4.4 2.9 - - - +
421A TYR* 4.5 2.4 - - - -
422A PHE* 4.4 1.1 - - - -
423A PHE* 3.4 35.3 - - - +
438A VAL* 4.2 6.2 - - + +
439A ILE 3.0 27.0 + - - +
441A GLY 4.1 2.4 - - - +
442A TYR 3.9 3.0 - - - +
443A GLU* 2.8 33.3 + - - +
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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