Contacts of the strand formed by residues 408 - 414 (chain L) in PDB entry 1DZG
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 408 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391I ALA* 4.0 17.9 - - + -
392I GLY* 3.5 35.0 - - - -
283L LEU* 3.5 34.5 - - + -
284L ILE 3.4 13.2 - - - +
285L LEU* 4.0 17.3 - - + -
292L LEU* 4.1 0.9 - - - -
320L MET* 4.0 10.3 - - + -
321L PRO* 4.0 14.4 - - + -
323L PHE* 4.6 1.6 - + - -
406L ARG 4.6 0.4 - - - -
407L PRO* 1.3 77.2 - - + +
409L LEU* 1.3 68.1 + - - +
410L VAL* 3.7 4.8 + - + +
425L ARG* 4.3 0.4 - - - -
426L VAL* 2.8 76.6 + - + -
429L PRO* 6.0 0.2 - - + -
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Residues in contact with LEU 409 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L TYR* 3.5 26.0 - - + +
282L VAL 4.4 0.2 - - - -
283L LEU* 3.6 4.9 - - - -
284L ILE* 2.9 53.0 + - + +
292L LEU* 3.5 36.8 - - + +
295L VAL* 5.5 4.0 - - + -
296L GLU* 4.1 13.2 - - + +
299L LEU* 4.2 26.9 - - + -
307L TRP* 5.9 1.3 - - + -
408L PHE* 1.3 75.5 - - - +
410L VAL* 1.3 60.9 + - - +
411L PHE* 4.5 14.6 - - + -
424L GLY 3.4 5.6 - - - +
425L ARG* 4.1 7.0 - - + -
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Residues in contact with VAL 410 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L PHE* 5.2 2.9 - - + -
281L MET* 3.5 37.2 - - + -
282L VAL 3.6 3.4 - - - -
283L LEU* 4.1 12.8 - - + -
320L MET* 5.9 0.2 - - + -
323L PHE* 5.1 1.6 - - + -
373L LEU* 4.5 17.3 - - + -
408L PHE* 4.0 4.7 - - + +
409L LEU* 1.3 77.4 - - - +
411L PHE* 1.3 75.9 + - - +
412L ILE* 4.8 4.0 - - + -
423L MET* 3.5 1.7 - - - +
424L GLY* 2.7 38.8 + - - +
426L VAL* 3.4 33.7 - - + -
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Residues in contact with PHE 411 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L THR* 6.0 0.4 - - - -
280L THR 3.7 1.2 - - - +
281L MET* 3.4 1.7 - - - -
282L VAL* 2.8 49.2 + - + +
284L ILE* 3.9 18.4 - - + -
299L LEU* 3.9 24.2 - - + -
304L LEU* 3.5 46.4 - - + -
307L TRP* 5.9 0.2 - + - -
409L LEU* 4.5 15.3 - - + -
410L VAL* 1.3 82.8 - - - +
412L ILE* 1.3 65.3 + - - +
413L ARG* 3.8 7.6 + - + +
420L ILE* 4.2 16.6 - - + -
422L PHE 3.8 4.9 - - - +
423L MET* 3.9 33.2 - - + +
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Residues in contact with ILE 412 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 4.9 1.1 - - + -
221L PHE* 4.3 13.9 - - + -
274L PHE* 4.2 8.7 - - + -
279L ILE* 3.5 28.3 - - + -
280L THR 3.8 4.7 - - - +
281L MET* 4.0 30.5 - - + -
373L LEU* 4.1 11.4 - - + -
380L SER* 4.2 4.5 - - - +
382L ALA* 4.0 28.0 - - + -
410L VAL* 4.8 3.8 - - + -
411L PHE* 1.3 74.9 - - - +
413L ARG* 1.3 58.9 + - - +
420L ILE* 3.8 1.0 - - - -
421L ILE* 3.0 27.1 + - + -
422L PHE* 3.1 33.0 + - + +
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Residues in contact with ARG 413 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L ARG* 5.0 5.3 - - - +
271L GLU* 2.6 32.5 + - - -
279L ILE* 3.2 8.8 - - - +
280L THR* 3.1 47.8 + - - +
282L VAL* 4.3 13.5 - - - -
304L LEU* 6.4 1.1 - - - -
305L GLN* 4.9 6.5 + - - +
308L LEU* 3.4 43.0 - - - +
411L PHE* 3.8 8.0 + - + +
412L ILE* 1.3 74.8 - - - +
414L GLU* 1.3 60.0 + - - +
415L VAL* 3.6 39.6 + - - +
418L ASN* 5.9 4.0 - - - +
419L THR 3.4 12.8 - - - +
420L ILE* 4.6 8.3 - - + -
421L ILE* 4.4 2.5 - - - +
901L GOL 4.9 8.6 + - - +
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Residues in contact with GLU 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L LEU* 4.3 10.7 - - + +
133L LYS* 2.7 34.6 + - - +
140L LEU* 5.1 1.6 - - + -
278L ASP* 3.4 9.8 - - - +
279L ILE* 3.8 16.8 - - + -
413L ARG* 1.3 72.4 - - - +
415L VAL* 1.3 64.8 + - - +
416L PRO* 3.2 16.0 - - - +
417L LEU* 3.0 44.9 + - - +
418L ASN* 3.0 19.2 + - - -
419L THR* 2.8 29.4 + - - +
421L ILE* 4.2 11.1 - - + +
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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