Contacts of the strand formed by residues 319 - 324 (chain G) in PDB entry 5DK3
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 TYR 319 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G LEU* 3.4 11.3 - - - +
259G VAL* 4.1 13.7 - - + -
277G TRP* 4.8 5.2 - - + -
278G TYR 3.5 2.5 - - - -
279G VAL* 3.8 37.2 - - + +
306G LEU* 4.0 11.2 - - + -
307G THR 5.2 0.2 - - - -
308G VAL* 3.3 35.1 - - + +
312G ASP* 3.1 34.7 + - - +
313G TRP* 3.6 31.4 - + - -
316G GLY 4.4 1.1 - - - -
317G LYS* 3.3 26.8 - - + +
318G GLU* 1.3 69.0 - - - +
320G LYS* 1.3 59.3 + - - +
335G THR* 4.2 0.7 - - - -
336G ILE* 2.8 42.0 + - + +
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Residues in contact with LYS 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276G ASN 3.9 0.3 - - - +
277G TRP* 3.4 10.8 - - - -
278G TYR* 2.9 72.9 + - + +
281G GLY* 6.1 3.4 - - - +
318G GLU* 3.8 1.7 + - + +
319G TYR* 1.3 72.9 - - - +
321G CYS* 1.3 64.9 + - - +
322G LYS* 4.1 2.0 - - - -
333G GLU* 3.9 29.3 - - + +
334G LYS 3.4 7.4 - - - +
335G THR* 3.6 24.7 - - + +
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Residues in contact with CYS 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G VAL* 5.0 1.0 - - - +
242G LEU* 4.0 9.0 - - + -
261G CYS* 2.0 53.6 - - + -
275G PHE* 3.9 17.7 - - - -
276G ASN 3.7 3.1 - - - -
277G TRP* 3.9 18.6 - - + -
319G TYR 4.1 0.6 + - - -
320G LYS* 1.3 74.1 - - - +
322G LYS* 1.4 59.0 + - - +
323G VAL* 3.9 5.7 + - - +
332G ILE 3.9 1.2 - - - +
333G GLU* 3.4 2.8 - - - -
334G LYS* 2.8 36.1 + - + +
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Residues in contact with LYS 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G GLN 3.9 0.5 - - - +
275G PHE* 3.6 4.0 - - - -
276G ASN* 2.7 54.9 + - + +
278G TYR* 4.0 16.1 - - + +
320G LYS* 4.1 2.6 - - - -
321G CYS* 1.4 73.0 - - - +
323G VAL* 1.3 61.7 + - - +
324G SER* 5.4 2.0 - - - +
331G SER* 5.8 4.9 - - - +
332G ILE 3.5 6.5 - - - +
333G GLU* 4.3 11.4 - - + +
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Residues in contact with VAL 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G PRO* 6.2 0.2 - - + -
240G VAL* 3.9 25.6 - - + -
261G CYS* 4.0 3.1 - - - -
263G VAL* 4.1 30.3 - - + -
274G GLN 3.6 7.9 - - - +
275G PHE* 3.9 25.8 - - + -
321G CYS* 3.9 13.2 - - - +
322G LYS* 1.3 78.0 - - - +
324G SER* 1.3 69.6 + - - +
325G ASN* 5.5 3.4 - - + -
328G LEU* 4.1 8.3 - - + +
331G SER* 3.5 7.5 - - - -
332G ILE* 2.8 35.1 + - + +
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Residues in contact with SER 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G GLU* 3.9 5.9 - - - +
274G GLN* 3.0 44.6 + - - +
276G ASN* 5.1 8.2 + - - -
322G LYS* 5.4 2.1 - - - +
323G VAL* 1.3 79.2 + - - +
325G ASN* 1.3 63.9 + - - +
328G LEU* 4.6 1.1 - - - -
330G SER 5.6 0.9 - - - -
331G SER* 3.9 14.6 - - - -
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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