Contacts of the strand formed by residues 411 - 417 (chain A) in PDB entry 3EDY
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 GLY 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ALA* 5.6 0.4 - - - -
374A PHE* 5.9 2.2 - - - -
376A PRO* 5.5 1.1 - - - -
410A GLY* 1.3 75.0 - - - -
412A PHE* 1.3 73.4 + - - -
448A ALA* 3.1 5.5 - - - +
449A TYR* 2.8 43.3 + - - -
536A PHE* 3.8 14.6 - - - -
544A PRO* 3.7 2.4 + - - -
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Residues in contact with PHE 412 (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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374A PHE* 6.2 1.0 - - - +
376A PRO* 3.3 25.3 - - - +
411A GLY* 1.3 77.0 - - - -
413A SER* 1.3 65.0 + - - +
414A ASN* 4.5 3.3 + - - -
426A VAL* 3.9 20.2 - - + -
429A PHE* 4.5 8.3 - + - -
430A LEU* 4.1 19.1 - - + -
442A PHE* 3.9 9.1 - + + +
443A ASN* 3.1 37.7 + - - +
444A ALA* 4.2 12.3 - - - -
446A GLY 3.5 15.7 - - - +
447A ARG 3.4 3.6 - - - +
448A ALA* 3.6 19.1 - - + -
449A TYR* 4.4 0.8 - - - -
536A PHE* 3.4 36.8 - + - -
542A TRP* 4.6 0.7 - + - -
544A PRO* 4.1 14.8 - - + -
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Residues in contact with SER 413 (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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329A GLU* 2.7 27.7 + - - -
376A PRO* 4.4 3.8 - - - +
381A SER* 4.0 12.3 - - - -
412A PHE* 1.3 74.9 - - - +
414A ASN* 1.3 57.4 + - - +
415A VAL* 2.9 13.3 + - - +
416A PHE* 2.9 27.4 + - - -
443A ASN* 3.5 10.4 - - - +
446A GLY* 3.3 17.2 - - - -
447A ARG* 2.8 22.1 + - - +
449A TYR* 5.0 1.0 - - - -
567A NAG 3.9 0.3 - - - +
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Residues in contact with ASN 414 (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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329A GLU* 2.9 12.4 + - - +
366A TRP* 3.9 26.6 - - + -
374A PHE 5.0 1.0 + - - -
376A PRO* 4.0 20.6 - - - +
412A PHE 3.6 1.8 + - - -
413A SER* 1.3 73.2 - - - +
415A VAL* 1.3 62.4 + - + +
443A ASN* 3.0 22.4 + - - +
567A NAG 3.2 41.5 + - - +
703A EDO 2.8 37.2 + - - -
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Residues in contact with VAL 415 (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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329A GLU* 3.5 25.1 - - + +
337A ILE* 4.1 9.6 - - + -
338A GLN* 3.6 27.3 + - - +
413A SER* 2.9 5.1 + - - +
414A ASN* 1.3 86.2 - - + +
416A PHE* 1.3 80.2 + - + +
417A PRO* 3.8 6.4 - - - +
567A NAG 3.9 11.5 + - - -
702A EDO 3.6 34.3 - - - +
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Residues in contact with PHE 416 (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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337A ILE* 3.8 21.1 - - + -
338A GLN* 3.7 23.8 - - - -
341A ASN* 3.5 42.6 - - + -
378A PHE* 3.5 27.8 - + - -
381A SER* 3.9 13.9 - - - -
382A SER* 4.5 2.0 - - - -
383A PRO* 3.8 20.9 - - + -
413A SER* 2.9 16.3 + - - +
415A VAL* 1.3 89.0 - - + +
417A PRO* 1.3 63.4 - - + +
446A GLY* 3.5 5.2 - - - -
447A ARG* 2.8 35.7 + - + -
567A NAG 4.0 2.4 - - - -
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Residues in contact with PRO 417 (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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383A PRO* 5.2 2.3 - - - +
415A VAL 3.8 6.5 - - - +
416A PHE* 1.3 92.8 - - + +
418A ARG* 1.3 70.4 + - - +
419A PRO* 2.9 9.2 - - - +
445A SER 3.6 1.8 - - - +
447A ARG* 3.8 1.5 + - - +
567A NAG 3.2 22.1 - - - +
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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