Contacts of the strand formed by residues 318 - 323 (chain D) in PDB entry 6DBU
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 318 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.4 9.0 - - + -
16D GLN 4.1 4.7 - - - -
17D PRO* 3.5 44.0 - - + +
19D PHE* 3.6 24.2 - + - -
260D SER* 5.5 7.2 - - - +
262D ILE* 3.8 8.5 - - - -
276D GLY* 6.4 0.2 - - - -
277D TYR* 6.0 0.4 - - + -
316D THR* 5.0 4.9 - - + -
317D TRP* 1.3 85.5 - - - +
319D GLY* 1.3 73.1 + - - +
329D VAL* 3.2 9.2 - - - +
330D ALA* 2.9 46.3 + - + -
332D PRO* 4.8 5.4 - - + -
343D TYR* 3.3 43.3 - + - -
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Residues in contact with GLY 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.6 27.6 - - - +
262D ILE* 3.5 20.0 - - - +
318D PHE* 1.3 83.6 - - - +
320D GLY* 1.3 58.3 + - - -
328D LEU 3.3 10.5 - - - -
329D VAL* 4.1 2.0 - - - -
330D ALA* 4.6 1.3 - - - -
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Residues in contact with GLY 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.7 7.3 - - - -
20D SER* 6.4 0.9 - - - -
21D LEU* 3.7 23.0 - - - +
262D ILE* 3.5 10.2 - - - +
319D GLY* 1.3 74.1 - - - -
321D SER* 1.3 60.8 + - - -
327D ALA* 3.5 3.8 - - - +
328D LEU 2.8 31.0 + - - +
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Residues in contact with SER 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.1 21.9 + - - +
23D ASP* 4.6 7.3 - - - +
28D VAL* 5.3 0.5 - - - +
262D ILE* 3.7 5.9 - - - +
263D ALA 3.2 31.6 + - - -
264D SER* 4.1 9.4 - - - -
265D PRO* 4.8 4.1 - - - +
320D GLY* 1.3 69.8 - - - -
322D LEU* 1.3 60.8 + - - +
323D GLY* 3.0 10.2 + - - -
327D ALA* 3.9 6.7 - - - -
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Residues in contact with LEU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.7 11.0 - - + -
23D ASP* 2.5 19.6 - - - +
28D VAL* 3.7 40.6 - - + +
48D VAL* 5.2 3.8 - - + -
50D ILE* 3.6 34.1 - - + -
320D GLY 3.7 0.8 + - - -
321D SER* 1.3 70.5 - - - +
323D GLY* 1.3 55.1 + - - +
324D LYS* 5.3 0.3 - - - +
326D THR* 3.0 25.9 + - - +
327D ALA* 3.4 7.7 - - - +
328D LEU* 4.1 16.8 - - + +
347D GLN* 3.7 26.7 - - + +
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Residues in contact with GLY 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 3.0 14.4 - - - -
264D SER* 4.4 4.9 - - - -
265D PRO* 4.8 11.7 - - - -
321D SER* 3.0 9.1 + - - +
322D LEU* 1.3 78.1 - - - +
324D LYS* 1.3 67.7 + - - +
325D GLY 3.4 2.7 - - - -
326D THR* 2.3 35.6 + - - -
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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