Contacts of the strand formed by residues 405 - 413 (chain A) in PDB entry 5FFO
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 PHE 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PRO* 3.4 18.5 - - - +
370A LYS 3.4 19.5 + - - +
371A GLY* 3.7 20.2 - - - -
372A ILE 4.1 3.6 + - - +
373A VAL* 3.7 20.9 - - + -
391A LEU* 4.1 18.2 - - + -
392A GLU 4.4 2.5 - - - -
393A GLY* 4.2 10.5 - - - -
395A TRP* 3.8 20.4 - + + -
403A PRO* 3.2 4.6 - - + -
404A SER* 1.3 73.6 - - - +
406A GLY* 1.3 57.6 + - - +
425A VAL* 3.6 21.8 - - + -
427A ALA* 3.5 15.7 - - + -
434A ILE* 3.7 24.7 - - + -
436A TYR* 3.5 31.9 - + - -
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Residues in contact with GLY 406 (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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343A ALA* 3.3 7.8 - - - +
361A ALA* 3.1 32.2 - - - +
363A PRO* 4.3 1.6 - - - -
373A VAL* 3.9 4.3 - - - -
405A PHE* 1.3 72.8 - - - +
407A TYR* 1.3 64.3 + - - +
408A SER* 3.1 8.3 + - - -
409A MET* 4.3 2.3 - - - +
425A VAL* 3.6 21.0 - - - +
426A GLY 2.8 12.3 + - - -
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Residues in contact with TYR 407 (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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21A PHE* 3.7 33.8 - + - -
278A PHE* 3.7 22.0 - + - -
342A SER* 4.5 7.8 - - - +
343A ALA* 3.3 13.8 - - - +
363A PRO* 3.9 18.5 - - + +
364A TYR* 4.3 18.6 - + - -
404A SER* 3.1 19.0 + - - +
405A PHE 3.5 0.6 - - - -
406A GLY* 1.3 76.8 - - - +
408A SER* 1.3 59.7 + - - +
426A GLY 3.5 1.7 + - - +
428A PHE* 3.5 32.5 - + + -
261B MET* 5.7 3.4 - - + -
264B LYS* 2.7 40.8 + - - +
269B VAL* 4.4 7.7 - - + +
291B GLU* 6.0 1.6 - - - -
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Residues in contact with SER 408 (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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20A GLY 2.9 25.8 + - - -
21A PHE* 2.9 23.8 + - - -
22A ALA* 3.7 9.0 + - - -
23A VAL* 3.9 7.3 + - - +
99A ARG* 5.8 3.6 - - - -
343A ALA* 4.3 2.7 - - - -
406A GLY 3.9 2.2 - - - +
407A TYR* 1.3 79.4 - - - +
409A MET* 1.3 66.0 + - - +
425A VAL* 3.9 0.5 - - - -
426A GLY 2.9 28.2 + - - +
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Residues in contact with MET 409 (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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23A VAL* 3.6 9.1 - - - +
99A ARG* 5.1 4.9 + - - +
343A ALA* 3.3 36.9 - - + +
344A ILE 5.0 2.3 - - - +
345A ALA* 3.5 21.7 - - + +
359A ALA* 3.3 38.1 - - + +
360A ILE 3.7 0.9 - - - +
361A ALA* 3.5 20.6 - - + +
373A VAL* 3.9 22.7 - - + -
406A GLY* 4.3 2.0 - - - +
408A SER* 1.3 78.6 - - - +
410A LYS* 1.3 65.7 - - - +
423A LEU* 4.2 4.5 - - + -
424A ILE 3.2 18.4 - - - +
425A VAL* 4.3 8.1 - - - -
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Residues in contact with LYS 410 (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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23A VAL* 3.8 19.2 - - + +
24A ASP* 3.5 33.3 + - - +
25A PHE* 3.3 20.8 - - + -
99A ARG* 4.7 16.2 - - - +
100A SER 5.9 1.2 + - - -
162A ASP* 6.2 0.2 - - - -
345A ALA* 3.9 3.6 - - - +
346A PRO* 5.0 16.6 - - + -
409A MET* 1.3 79.2 - - - +
411A GLY* 1.3 75.9 + - - +
412A ALA* 5.8 1.3 - - - +
413A THR* 5.6 1.6 + - - -
423A LEU* 3.5 5.9 - - - +
424A ILE* 3.3 21.9 + - + -
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Residues in contact with GLY 411 (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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25A PHE* 3.9 4.7 - - - -
345A ALA* 4.2 2.8 - - - +
346A PRO 3.3 17.9 + - - +
347A LEU* 4.3 10.3 - - - -
410A LYS* 1.3 92.2 + - - +
412A ALA* 1.3 71.4 + - - +
413A THR* 3.3 9.4 + - - -
422A ASP 3.7 11.7 - - - -
423A LEU* 4.4 0.2 - - - -
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Residues in contact with ALA 412 (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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346A PRO* 3.8 7.6 - - + +
347A LEU 3.3 22.4 + - - -
348A GLY* 3.5 22.7 - - - +
410A LYS* 5.8 2.0 - - - +
411A GLY* 1.3 74.8 - - - +
413A THR* 1.3 61.1 + - - +
421A PRO* 3.9 9.0 - - - -
422A ASP 3.8 4.0 + - - -
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Residues in contact with THR 413 (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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25A PHE* 3.5 51.3 - - + +
27A VAL* 5.5 7.0 - - + -
34A MET* 4.6 17.5 - - + -
410A LYS* 5.6 1.4 + - - -
411A GLY 3.3 3.6 + - - -
412A ALA* 1.3 82.7 + - - +
414A ASP* 1.3 67.1 + - - +
415A ILE 3.3 5.8 + - - +
421A PRO* 3.9 2.3 - - - +
422A ASP* 2.9 24.8 + - - +
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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
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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