Contacts of the strand formed by residues 434 - 442 (chain B) in PDB entry 1FO4
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 434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLN 3.1 25.1 + - - +
432B ALA* 4.2 1.5 - - - +
433B LYS* 1.3 86.7 - - - +
435B THR* 1.3 65.0 + - - +
456B TYR* 4.0 20.4 - - + -
457B GLY 3.6 8.5 - - - +
459B MET* 3.9 10.5 - - + -
508B ARG* 3.6 39.9 - - + +
511B LEU* 3.8 17.5 - - + -
512B THR* 4.2 8.5 - - + -
515B PHE* 3.4 25.3 - - + -
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Residues in contact with THR 435 (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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333B GLN* 3.1 22.9 + - - -
358B ILE 4.3 2.2 - - - +
359B SER 3.3 26.7 - - - +
360B ASP* 2.8 27.3 + - - +
363B PRO* 4.2 3.5 - - + +
421B PHE 3.3 6.8 + - - -
422B LYS* 3.9 1.7 - - - +
432B ALA* 3.7 10.8 - - + -
434B VAL* 1.3 77.4 - - - +
436B CYS* 1.3 62.8 + - - +
456B TYR* 3.3 2.8 - - - +
457B GLY* 2.7 44.0 + - - +
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Residues in contact with CYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN* 3.4 11.2 + - - -
363B PRO* 4.0 8.3 - - - -
364B VAL* 4.0 1.8 - - - +
420B ALA* 3.3 21.4 - - - +
421B PHE* 2.8 32.3 + - - -
435B THR* 1.3 77.5 + - - +
437B GLY* 1.3 60.5 + - - +
438B MET* 3.7 25.8 - - + -
455B CYS 3.1 14.4 - - - +
456B TYR* 3.8 15.9 - - + -
515B PHE* 3.6 24.5 - - - -
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Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PRO* 3.8 17.9 - - - +
364B VAL* 4.2 3.1 - - - -
367B ALA* 3.1 15.7 - - - +
418B PHE* 4.1 8.1 - - - -
419B SER 3.6 5.4 - - - -
436B CYS* 1.3 74.8 - - - +
438B MET* 1.3 60.6 + - - +
455B CYS 2.9 32.2 + - - -
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Residues in contact with MET 438 (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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367B ALA* 4.0 0.2 - - - +
418B PHE* 3.2 9.4 - - - -
419B SER 2.8 39.4 + - - +
421B PHE* 4.6 2.9 - - - -
436B CYS* 3.7 24.2 - - + -
437B GLY* 1.3 79.1 - - - +
439B ARG* 1.3 60.4 + - - +
453B ALA 3.2 3.6 - - - -
454B LEU* 3.6 24.7 - - + -
456B TYR* 3.0 40.2 - - + +
515B PHE 3.9 4.5 - - - +
516B PHE* 3.7 20.6 - - + +
519B PHE* 3.5 43.3 - - + -
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 5.4 4.0 - - - -
367B ALA 2.8 31.8 + - - +
368B SER* 4.1 17.5 - - - +
369B GLY* 5.7 0.4 - - - +
413B ARG* 3.8 3.2 - - - +
416B GLU* 2.9 35.6 + - + +
417B PHE 3.4 11.9 - - - +
418B PHE* 3.5 15.9 - - + -
437B GLY 4.4 0.2 - - - -
438B MET* 1.3 74.7 - - - +
440B VAL* 1.3 63.7 + - - +
441B LEU* 3.9 13.7 - - - +
451B GLU* 3.0 39.0 + - - +
452B LEU* 3.4 8.4 - - - +
453B ALA* 2.8 43.0 + - + +
519B PHE* 3.8 2.9 - - - -
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Residues in contact with VAL 440 (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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415B ASP 3.7 0.7 - - - +
416B GLU* 3.3 5.0 - - - +
417B PHE* 3.0 37.4 + - + +
439B ARG* 1.3 81.3 - - - +
441B LEU* 1.3 65.4 + - - +
442B PHE* 3.6 41.3 - - + -
449B VAL* 4.4 5.8 - - + -
451B GLU 3.3 12.8 - - - +
452B LEU* 3.9 6.3 - - + -
478B TRP* 3.8 14.6 - - + -
519B PHE* 3.9 19.7 - - + -
523B VAL* 4.1 7.0 - - + -
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Residues in contact with LEU 441 (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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413B ARG* 3.4 35.4 - - + +
414B GLU 3.8 15.5 - - - +
415B ASP 3.5 11.9 - - - +
416B GLU* 4.0 11.7 - - + -
439B ARG* 3.9 8.1 - - - +
440B VAL* 1.3 74.5 - - - +
442B PHE* 1.3 65.0 + - - +
449B VAL* 3.7 0.7 - - - -
450B LYS* 2.6 52.3 + - + +
451B GLU* 2.8 45.7 + - + +
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Residues in contact with PHE 442 (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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415B ASP* 3.1 32.9 + - + +
417B PHE* 4.1 6.3 - + - -
440B VAL* 3.6 23.6 - - + -
441B LEU* 1.3 84.6 - - - +
443B GLN* 1.3 66.5 + - - +
444B PRO* 3.7 1.6 - - - +
446B SER 3.4 17.3 - - - +
447B MET* 3.3 31.4 - - - -
448B GLN 3.0 14.6 - - - +
449B VAL* 3.6 9.4 - - + -
450B LYS* 4.1 5.2 - - - +
478B TRP* 3.5 45.5 - + + -
523B VAL* 3.7 15.3 - - + -
527B LEU* 3.8 18.6 - - + -
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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