Contacts of the strand formed by residues 452 - 458 (chain A) in PDB entry 4OE5
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 VAL 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LYS* 5.4 0.3 + - - -
340A ALA* 5.0 1.9 + - - -
341A PHE* 4.7 0.4 - - - -
351A CYS 5.1 0.3 - - - +
352A SER* 4.0 19.4 - - - +
400A ILE* 4.3 19.1 - - + +
403A TRP* 5.2 4.7 - - + +
404A LEU* 4.3 17.7 - - + -
429A VAL* 5.7 0.2 - - + -
432A CYS* 3.5 7.9 - - + +
434A VAL* 4.4 14.4 - - + -
443A ILE* 4.1 18.6 - - + -
448A ILE* 3.9 46.0 - - + +
450A GLY 3.0 7.2 + - - +
451A PRO* 1.3 81.4 - - - +
453A LEU* 1.3 63.0 + - - +
454A SER* 4.1 1.4 + - - +
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Residues in contact with LEU 453 (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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336A THR* 3.7 25.8 - - + +
337A LEU* 5.1 1.1 - - + -
340A ALA* 4.0 20.9 - - + -
341A PHE* 4.1 6.5 - - + -
351A CYS* 4.1 16.2 - - - -
352A SER* 3.8 20.4 - - - +
353A ARG 4.0 2.5 - - - +
354A LEU* 4.2 8.1 - - + -
368A LEU* 5.1 5.4 - - + -
432A CYS 2.8 14.5 + - - +
433A ILE* 3.4 22.8 - - + +
434A VAL* 2.8 33.6 + - - +
451A PRO 4.1 0.4 - - - -
452A VAL* 1.3 74.9 - - - +
454A SER* 1.3 69.0 + - - +
455A VAL* 4.3 13.2 - - + -
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Residues in contact with SER 454 (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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318A LYS* 4.9 0.7 + - - -
352A SER 2.9 15.3 + - - -
353A ARG* 3.2 3.3 - - - +
354A LEU 2.9 25.1 + - - +
434A VAL* 3.3 6.2 - - - +
436A SER* 5.6 0.9 - - - -
443A ILE* 3.4 45.0 + - - +
444A MET* 3.8 23.0 - - - +
448A ILE* 5.4 0.2 - - - +
452A VAL* 4.7 2.9 + - - +
453A LEU* 1.3 73.7 - - - +
455A VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 455 (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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354A LEU* 3.3 32.8 - - + +
356A VAL* 4.2 11.0 - - + -
361A TRP* 3.8 35.9 - - + -
368A LEU* 5.1 1.1 - - + -
416A LEU* 5.2 0.2 - - + -
433A ILE* 4.0 22.0 - - + -
434A VAL 2.7 18.2 + - - +
435A GLU* 3.4 9.4 - - + +
436A SER 2.8 30.4 + - - +
444A MET* 4.7 2.2 - - - -
453A LEU* 4.3 6.3 - - + -
454A SER* 1.3 79.8 - - - +
456A TYR* 1.3 64.0 + - - +
457A VAL* 4.7 2.0 - - + -
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Residues in contact with TYR 456 (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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354A LEU 2.8 9.7 + - - -
355A TYR* 3.4 23.8 - + + +
356A VAL* 3.0 25.0 + - - -
436A SER 3.3 17.9 - - - +
437A LYS* 3.6 12.7 + - - -
439A PRO* 3.5 47.3 - - + +
444A MET* 3.8 22.4 - - + +
454A SER 4.3 0.2 + - - -
455A VAL* 1.3 74.2 - - - +
457A VAL* 1.3 74.4 + - - +
458A TYR* 3.7 25.6 + - + +
459A PRO* 4.8 5.7 - - - +
466A THR* 4.8 6.3 - - + -
469A LEU* 4.8 5.0 - - + +
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Residues in contact with VAL 457 (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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356A VAL* 3.2 25.4 - - + +
358A HIS* 3.8 33.4 - - + -
361A TRP* 3.7 34.8 - - + -
435A GLU* 3.3 27.1 + - - +
436A SER 4.7 1.4 + - - -
455A VAL* 4.7 3.1 - - + -
456A TYR* 1.3 91.6 + - - +
458A TYR* 1.3 62.3 + - - +
459A PRO* 4.5 1.7 - - - +
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Residues in contact with TYR 458 (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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322A PHE* 3.4 24.4 - + - -
323A VAL 2.7 25.1 + - - -
324A HIS* 3.8 6.4 - - - -
325A ARG 4.6 0.3 + - - -
355A TYR* 4.1 2.7 - - + -
356A VAL 2.7 48.4 + - - -
357A PRO* 3.4 18.5 - - + +
358A HIS* 2.8 27.1 + - - -
456A TYR* 3.7 15.3 - + + -
457A VAL* 1.3 74.2 - - - +
459A PRO* 1.3 91.2 - - + +
460A ASP 4.3 1.8 - - - -
463A TYR* 3.5 27.8 - - + +
466A THR* 3.4 36.1 - - + +
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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