Contacts of the strand formed by residues 410 - 417 (chain A) in PDB entry 4UHW
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 ILE 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 4.5 4.0 - - + -
252A LEU* 4.3 21.3 - - + -
253A LEU* 3.6 18.2 - - + -
256A LYS* 3.6 32.1 - - + -
264A VAL* 4.4 9.2 - - + -
294A LEU* 4.1 15.9 - - + -
381A LEU* 3.6 3.0 - - - -
382A LEU 3.1 34.2 + - - +
405A LEU* 4.2 4.0 - - - -
409A GLU* 1.3 80.5 - - - +
411A LEU* 1.3 69.5 + - - +
412A VAL* 3.8 21.5 - - + -
3006A FAD 3.7 17.7 - - + +
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Residues in contact with LEU 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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294A LEU* 4.4 2.1 - - - +
308A ALA* 3.1 18.0 - - + +
356A GLY* 3.9 23.1 - - - +
359A ILE* 4.3 21.5 - - + -
360A ILE* 4.0 26.5 - - + -
379A LEU* 4.0 23.8 - - + -
380A ASN 3.9 6.1 - - - +
381A LEU* 4.4 6.7 - - + -
405A LEU* 4.1 3.7 - - + +
410A ILE* 1.3 73.8 - - - +
412A VAL* 1.3 59.4 + - - +
413A SER 3.4 29.6 - - - +
414A VAL* 5.1 0.4 - - + -
3006A FAD 3.0 36.2 + - + +
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Residues in contact with VAL 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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249A LEU* 6.0 0.4 - - + -
293A GLU* 3.5 34.3 - - + +
294A LEU* 4.0 11.5 - - + -
296A VAL* 5.9 0.4 - - + -
307A GLY* 3.7 2.9 - - - -
308A ALA* 2.9 21.9 + - - +
380A ASN* 2.8 23.0 + - + +
381A LEU 4.4 0.7 - - - +
382A LEU* 3.4 41.3 - - + -
387A LYS* 5.6 3.1 - - + -
410A ILE* 3.8 12.8 - - + +
411A LEU* 1.3 72.6 - - - +
413A SER* 1.3 67.3 + - - +
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Residues in contact with SER 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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296A VAL* 4.1 13.6 - - - +
305A THR* 4.6 5.5 + - - -
306A LEU 3.2 24.5 - - - -
307A GLY* 4.0 2.7 - - - -
308A ALA* 3.9 3.8 - - - +
380A ASN* 2.8 54.3 + - - +
411A LEU* 3.4 11.1 - - - +
412A VAL* 1.3 86.5 - - - +
414A VAL* 1.3 57.4 + - - +
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Residues in contact with VAL 414 (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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304A LEU 3.9 0.7 - - - +
305A THR* 3.3 1.9 - - - -
306A LEU* 2.9 30.0 + - + +
308A ALA* 6.0 0.9 - - - +
355A LEU* 3.4 33.9 - - + -
359A ILE* 4.2 16.8 - - + -
372A LEU* 4.7 5.8 - - + -
377A CYS* 4.3 11.9 - - + -
378A THR 3.4 13.2 - - - +
379A LEU* 4.0 17.7 - - + -
380A ASN* 4.6 0.2 - - - -
392A LEU* 4.8 0.7 - - + -
411A LEU* 5.3 1.3 - - + -
413A SER* 1.3 74.9 - - - +
415A ASN* 1.3 74.3 + - - +
416A ILE* 3.9 16.8 + - + +
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Residues in contact with ASN 415 (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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302A ASN* 6.0 3.8 - - - +
304A LEU 3.5 6.5 - - - +
305A THR* 3.0 28.6 - - + +
376A ASN 4.5 0.2 - - - +
377A CYS* 3.4 12.0 - - - +
378A THR* 2.8 53.6 + - - +
380A ASN* 3.0 33.9 + - - +
389A GLN* 4.2 5.8 - - - +
414A VAL* 1.3 72.1 - - - +
416A ILE* 1.3 62.1 + - - +
417A PRO* 3.8 3.5 - - + +
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Residues in contact with ILE 416 (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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304A LEU* 3.0 27.1 + - + +
306A LEU* 4.0 26.9 - - + -
319A LEU* 5.9 0.2 - - + -
333A MET* 3.8 34.1 - - + -
334A TYR* 2.8 44.5 + - + -
337A LEU* 4.5 10.1 - - + -
355A LEU* 5.4 1.1 - - + -
372A LEU* 3.9 24.2 - - + -
377A CYS* 3.9 3.1 - - - -
414A VAL* 4.1 23.1 - - + +
415A ASN* 1.3 73.3 - - - +
417A PRO* 1.3 64.8 - - + +
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Residues in contact with PRO 417 (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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302A ASN* 3.7 20.0 - - - +
303A GLY* 4.0 2.5 - - - -
333A MET* 4.3 9.7 - - + +
334A TYR* 3.7 5.9 + - - -
375A GLY 3.4 26.7 - - - +
376A ASN* 3.7 22.4 - - + +
377A CYS* 4.3 0.4 - - - -
415A ASN* 3.8 5.8 - - + +
416A ILE* 1.3 96.5 - - + +
418A TYR* 1.3 70.9 + - - +
419A SER 3.8 0.7 + - - -
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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