Contacts of the strand formed by residues 454 - 459 (chain B) in PDB entry 5EEQ
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 LEU 454 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B ILE* 3.6 39.2 - - + +
448B GLN* 3.7 45.1 - - + +
451B VAL* 3.1 29.9 + - + +
452B ASP 3.3 1.4 + - - -
453B GLY* 1.3 77.1 - - - +
455B PHE* 1.3 60.8 + - - +
471B LEU* 3.5 0.5 - - - -
472B CYS* 2.8 33.0 + - + +
525B HIS* 3.3 28.0 - - + +
526B CYS 3.8 10.3 - - - +
527B CYS* 4.0 7.4 - - + -
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Residues in contact with PHE 455 (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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431B TRP* 3.7 22.5 - + + +
445B ILE* 5.0 2.0 - - - -
453B GLY 3.7 5.6 - - - -
454B LEU* 1.3 77.0 - - - +
456B LEU* 1.3 67.4 + - - +
457B VAL* 4.6 0.7 - - + -
469B LEU* 3.8 19.1 - - + -
470B SER 3.2 12.1 - - - +
471B LEU* 4.1 3.1 - - + -
509B VAL* 3.8 32.8 - - + -
513B GLN* 4.2 6.5 - - - -
523B LEU* 3.7 41.7 - - + -
524B ARG 4.8 0.2 - - - -
525B HIS 2.9 42.3 + - - -
526B CYS* 3.7 22.1 - - - -
527B CYS* 2.9 29.8 + - - +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B TRP 3.4 13.0 - - - +
433B HIS* 3.7 22.9 - - + +
436B ILE* 4.1 8.7 - - + -
441B SER* 4.0 24.7 - - - +
444B LEU* 4.3 3.6 - - + -
445B ILE* 4.2 9.0 - - + -
455B PHE* 1.3 78.9 - - - +
457B VAL* 1.3 80.8 + - - +
458B ARG* 4.0 24.9 - - + -
469B LEU* 3.6 2.9 - - - +
470B SER* 2.9 41.7 + - - +
527B CYS* 4.0 22.2 - - + -
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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
----------------------------------------------------------
431B TRP* 2.8 35.7 + - + -
432B PHE* 3.4 8.1 - - + -
433B HIS* 2.9 28.1 + - - +
455B PHE* 4.6 1.6 - - + -
456B LEU* 1.3 79.7 - - - +
458B ARG* 1.3 69.3 + - - +
467B PHE* 4.2 7.2 - - + -
468B VAL 3.4 10.3 - - - +
469B LEU* 4.0 20.0 - - + -
482B ILE* 4.5 8.1 - - + -
505B LEU* 3.9 28.7 - - + -
508B LEU* 6.0 0.7 - - + -
509B VAL* 4.0 11.4 - - + -
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Residues in contact with ARG 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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432B PHE* 4.3 4.0 - - - -
434B GLY 3.4 14.1 - - - +
436B ILE* 3.5 37.4 + - + -
437B SER 4.0 0.2 - - - -
438B ARG* 3.5 20.8 - - - +
441B SER* 3.7 16.2 + - - -
456B LEU* 4.0 4.9 - - + -
457B VAL* 1.3 77.5 - - - +
459B GLU* 1.3 68.8 + - - +
467B PHE* 3.2 11.5 - - - +
468B VAL* 2.7 48.5 + - + +
470B SER* 3.1 14.7 + - - -
479B HIS* 3.3 22.4 + - - -
601B PO4 2.6 45.6 + - - -
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Residues in contact with GLU 459 (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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432B PHE* 4.2 8.0 - - + -
434B GLY* 2.8 23.1 + - - +
435B ARG* 3.9 29.8 + - + +
436B ILE 3.7 8.0 + - - +
458B ARG* 1.3 91.6 + - - +
460B SER* 1.3 66.6 + - - +
461B GLN 3.7 0.3 + - - -
464B PRO* 5.4 6.8 - - + +
466B GLY 3.8 7.9 - - - +
467B PHE* 4.0 20.5 - - + -
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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