Contacts of the strand formed by residues 452 - 458 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B LYS* 5.1 0.3 + - - -
340B ALA* 4.8 2.6 + - - -
341B PHE* 4.1 0.6 - - - -
351B CYS 5.1 0.2 - - - +
352B SER* 3.9 19.9 - - - +
400B ILE* 4.2 12.8 - - + -
403B TRP* 5.2 5.2 - - + +
404B LEU* 4.1 24.5 - - + -
432B CYS* 3.4 4.0 - - + +
434B VAL* 4.4 14.8 - - + -
443B ILE* 4.2 17.3 - - + -
448B ILE* 3.6 45.3 - - + +
450B GLY 2.9 10.6 + - - +
451B PRO* 1.3 79.8 - - + +
453B LEU* 1.3 64.5 + - - +
454B SER* 4.0 1.7 + - - +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR* 3.6 26.0 - - + +
337B LEU* 5.3 0.2 - - + -
340B ALA* 4.0 17.3 - - + -
341B PHE* 4.1 7.6 - - + -
351B CYS* 4.0 22.9 - - - +
352B SER* 3.8 20.4 - - - +
353B ARG 4.0 0.4 - - - +
354B LEU* 4.2 7.2 - - + -
368B LEU* 4.8 7.4 - - + -
432B CYS 2.8 14.3 + - - +
433B ILE* 4.3 16.8 - - + +
434B VAL* 2.8 30.0 + - - +
451B PRO 4.2 0.6 - - - -
452B VAL* 1.3 74.0 - - - +
454B SER* 1.3 73.5 + - - +
455B VAL* 4.4 13.0 - - + -
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Residues in contact with SER 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 4.8 1.0 + - - -
352B SER 2.9 15.8 + - - -
353B ARG* 3.4 1.7 - - - +
354B LEU* 2.8 27.2 + - - +
434B VAL* 3.2 7.6 - - - +
436B SER* 5.4 1.1 - - - -
443B ILE* 3.1 43.2 + - - +
444B MET* 3.7 24.2 - - - -
452B VAL* 4.8 2.3 + - - +
453B LEU* 1.3 76.1 - - - +
455B VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.2 31.2 - - + +
356B VAL* 3.9 14.8 - - + -
361B TRP* 3.7 34.5 - - + -
368B LEU* 4.9 0.9 - - + -
416B LEU* 5.5 0.2 - - + -
433B ILE* 4.1 22.2 - - + -
434B VAL 2.8 15.9 + - - +
435B GLU* 3.5 9.4 - - + +
436B SER* 2.8 30.1 + - - +
444B MET* 4.7 2.7 - - - -
453B LEU* 4.4 5.6 - - + -
454B SER* 1.3 80.0 - - - +
456B TYR* 1.3 64.9 + - - +
457B VAL* 4.4 3.4 - - + -
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU 2.7 9.7 + - - -
355B TYR* 3.3 27.0 - + + -
356B VAL 2.9 24.3 + - - +
436B SER* 3.4 15.9 - - - +
437B LYS* 3.6 12.5 + - - -
438B ASP 4.3 0.2 - - - -
439B PRO* 3.5 47.7 - - + +
444B MET* 4.0 23.0 - - + +
454B SER 4.3 0.2 - - - -
455B VAL* 1.3 74.0 - - - +
457B VAL* 1.3 72.7 + - - +
458B TYR* 3.6 24.8 + - + -
459B PRO* 4.6 9.5 - - - +
466B THR* 4.8 1.3 - - + -
469B LEU* 4.4 10.0 - - + +
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 3.1 14.4 - - + +
358B HIS* 3.5 40.6 - - + -
361B TRP* 3.6 41.7 - - + -
435B GLU* 3.4 24.9 - - - +
436B SER 4.5 2.8 + - - -
455B VAL* 4.2 3.3 + - + -
456B TYR* 1.3 88.8 + - - +
458B TYR* 1.3 62.8 + - - +
459B PRO* 4.3 2.1 - - - +
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Residues in contact with TYR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PHE* 3.6 20.4 - + - -
323B VAL 2.7 26.0 + - - -
324B HIS* 3.9 6.9 - - - -
325B ARG 4.6 0.3 + - - -
355B TYR* 3.8 6.5 - - + -
356B VAL 2.8 47.2 + - - -
357B PRO* 3.3 19.5 - - + +
358B HIS* 2.7 33.7 + - - -
456B TYR* 3.7 15.9 - - + -
457B VAL* 1.3 74.8 - - - +
459B PRO* 1.3 87.7 - - + +
460B ASP* 4.6 2.0 - - - -
463B TYR* 3.6 28.3 - - + +
466B THR* 3.4 34.8 - - + +
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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
------------------------------------------------------------
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