Contacts of the strand formed by residues 412 - 421 (chain B) in PDB entry 1FVU
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 HIS 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B SER 3.7 0.3 - - - +
408B SER* 3.4 4.9 - - - -
409B TYR 2.9 27.6 + - - +
410B GLU* 3.3 13.6 + - + +
411B GLY* 1.3 80.3 - - - +
413B CYS* 1.3 60.7 + - - +
414B TYR* 3.4 25.5 - - + +
447B GLU* 5.1 0.2 - - - -
522B GLU* 3.0 29.2 - - + +
523B PHE 3.6 7.6 - - - +
524B GLN* 3.5 48.0 + - + +
1001B MG 4.6 1.3 - - - -
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Residues in contact with CYS 413 (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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401B ASP 5.1 0.4 - - - -
402B CYS* 2.0 52.3 - - + -
406B TRP* 3.7 5.8 - - + -
407B SER 3.3 3.8 - - - -
411B GLY 4.7 5.6 - - - -
412B HIS* 1.3 74.9 - - - +
414B TYR* 1.3 65.1 + - - +
522B GLU* 3.2 6.4 - - - +
523B PHE* 3.0 65.6 + - + +
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Residues in contact with TYR 414 (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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405B ASP 4.6 0.2 - - - +
406B TRP* 3.3 6.4 - - - -
407B SER* 2.8 42.0 + - - +
409B TYR* 3.7 27.3 + + + -
412B HIS* 3.4 27.6 - - + +
413B CYS* 1.3 75.8 - - - +
415B ARG* 1.3 65.4 + - - +
440B VAL* 3.9 10.8 - - + -
447B GLU* 2.6 31.7 + - + +
450B PHE* 4.0 11.2 - + + -
451B VAL* 4.0 22.0 - - + -
454B LEU* 3.8 19.7 - - + +
520B VAL* 4.5 2.5 - - + -
521B CYS 3.4 7.6 - - - +
522B GLU* 3.2 37.6 + - + -
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Residues in contact with ARG 415 (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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404B PRO 4.1 5.2 + - - -
405B ASP* 4.1 39.6 + - - +
406B TRP* 3.4 41.6 - - + +
414B TYR* 1.3 79.5 - - - +
416B PHE* 1.3 71.9 + - - +
417B PHE* 3.3 41.9 - - + -
433B GLN* 5.3 3.6 + - - +
454B LEU* 4.8 2.5 - - - -
520B VAL* 3.4 4.8 - - - +
521B CYS 3.0 31.0 + - - -
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Residues in contact with PHE 416 (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 ARG* 1.3 84.0 + - - +
417B PHE* 1.3 61.9 + - - +
418B LYS* 3.9 22.5 + - + -
454B LEU* 3.3 39.4 - - + +
455B THR* 3.6 20.9 - - + -
457B GLU* 4.2 19.5 - - + -
458B MET* 3.9 13.7 - - + -
464B VAL* 3.8 15.9 - - + -
518B ASN* 3.6 41.3 - - + -
519B PHE 3.6 11.9 - - - -
520B VAL* 4.0 9.6 - - + +
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Residues in contact with PHE 417 (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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406B TRP* 4.2 5.2 - + - -
415B ARG* 3.3 62.1 - - + -
416B PHE* 1.3 78.7 - - - +
418B LYS* 1.3 57.9 + - - +
419B GLU* 3.0 22.3 + - - +
429B PHE* 3.6 26.0 - + - -
433B GLN* 4.1 13.7 - - + -
518B ASN* 3.5 5.5 - - - +
519B PHE* 2.8 56.0 + + + +
521B CYS* 3.4 34.1 - - + -
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Residues in contact with LYS 418 (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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416B PHE* 3.9 13.6 + - + -
417B PHE* 1.3 69.2 - - - +
419B GLU* 1.3 64.2 + - - +
420B TRP* 3.2 40.4 - - + -
457B GLU* 3.1 39.6 + - + +
458B MET* 5.0 1.3 - - - +
459B LEU 5.6 0.4 - - - +
518B ASN* 3.4 16.4 - - - +
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Residues in contact with GLU 419 (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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417B PHE* 3.0 16.1 + - + -
418B LYS* 1.3 85.2 - - - +
420B TRP* 1.3 62.4 + - - +
421B MET* 3.4 29.8 - - + +
429B PHE* 3.4 28.8 - - - -
517B LYS 3.1 10.2 - - - +
518B ASN* 2.9 16.5 + - - -
519B PHE* 3.7 11.3 - - + -
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Residues in contact with TRP 420 (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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418B LYS* 3.2 49.4 - - + -
419B GLU* 1.3 73.2 - - - +
421B MET* 1.3 63.6 + - - +
459B LEU* 5.7 10.6 - - + +
462B ASP* 4.8 10.3 + - - -
516B PHE* 3.6 38.8 - - + -
517B LYS* 3.6 7.2 - - - -
518B ASN* 3.4 21.1 - - - +
692D LEU* 3.8 35.0 - - + +
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Residues in contact with MET 421 (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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419B GLU* 3.4 34.7 + - + +
420B TRP* 1.3 79.9 - - - +
422B HIS* 1.3 68.0 + - - +
425B ASP* 3.7 32.5 - - + +
426B ALA* 3.9 5.8 - - + +
429B PHE* 3.4 32.1 - - + -
465B TRP* 2.9 22.5 + - - -
516B PHE* 3.8 9.0 - - - -
517B LYS 3.0 15.3 + - - +
519B PHE* 3.9 16.2 - - + -
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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