Contacts of the strand formed by residues 338 - 345 (chain B) in PDB entry 5DVX
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 GLN 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B ALA* 5.0 3.4 - - + +
158B GLY* 3.2 12.5 - - - -
160B PHE* 2.8 53.8 + - + +
161B GLN* 3.0 29.5 + - - +
267B GLY* 3.2 31.9 + - - +
268B ARG 4.0 0.3 + - - +
329B GLY 3.4 5.4 - - - +
330B SER* 3.9 0.9 - - - -
336B CYS 4.2 0.4 - - - +
337B ALA* 1.3 73.8 - - - +
339B GLY* 1.3 64.9 + - - +
340B VAL* 3.3 5.0 + - - +
405B CL 3.6 20.0 - - - +
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B GLY 4.9 0.9 - - - -
268B ARG 3.5 14.1 - - - +
269B PRO* 3.9 5.6 - - - -
270B GLY* 2.7 29.5 + - - -
271B GLY 4.0 1.2 + - - -
272B LEU 5.4 0.4 - - - -
328B GLU* 3.5 25.7 + - - +
329B GLY 3.1 4.4 + - - -
338B GLN* 1.3 77.0 - - - +
340B VAL* 1.3 63.4 + - - +
341B ILE* 4.1 1.2 - - - +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.5 26.7 - - + +
274B VAL* 3.8 23.3 - - + -
328B GLU* 3.4 3.1 - - - -
329B GLY 2.8 36.2 + - - +
330B SER 4.5 0.9 - - - +
331B LEU* 3.7 22.7 - - + +
337B ALA* 3.4 24.0 - - + +
338B GLN 4.3 2.7 - - - +
339B GLY* 1.3 77.9 - - - +
341B ILE* 1.3 66.5 + - - +
342B TRP* 3.5 26.5 + - + +
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 3.8 22.7 - - + -
218B ARG* 4.2 6.7 - - - +
220B TYR* 3.8 18.6 - - - +
270B GLY* 3.8 12.3 - - - -
272B LEU 3.0 8.8 + - - +
273B ALA* 3.2 9.1 - - + +
274B VAL 3.0 25.3 + - - +
326B GLN* 4.0 23.3 - - + +
327B TYR 3.8 4.3 - - - +
328B GLU* 4.2 14.1 - - + +
339B GLY 4.1 2.5 - - - +
340B VAL* 1.3 75.2 - - - +
342B TRP* 1.3 61.2 + - - +
343B THR* 4.0 1.9 + - - +
403B GOL 3.8 37.5 - - - +
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Residues in contact with TRP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B SER* 3.1 17.9 + - - -
239B HIS* 3.6 17.7 - + - -
251B HIS* 3.6 36.3 - + - -
274B VAL* 3.4 49.6 - - + -
276B ALA* 4.1 9.4 - - + -
326B GLN* 3.1 9.4 - - - +
327B TYR* 2.8 61.9 + - + +
329B GLY 4.0 5.8 - - - -
330B SER 2.8 30.7 + - - +
331B LEU* 4.8 1.6 - - - -
332B THR* 3.7 19.5 - - + -
340B VAL* 3.5 23.8 - - + +
341B ILE* 1.3 72.4 - - - +
343B THR* 1.3 61.1 - - - +
344B VAL* 4.2 2.7 - - + -
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.1 11.9 - - + -
212B MET* 6.2 0.7 - - - -
214B LEU* 3.7 14.6 - - - +
274B VAL 3.0 10.4 + - - +
275B LEU* 3.6 24.3 - - + +
276B ALA* 2.8 27.4 + - - +
324B TYR* 3.6 36.8 - - + -
325B PHE 3.3 3.4 - - - -
326B GLN* 2.9 22.2 + - - +
341B ILE* 4.6 0.9 + - - +
342B TRP* 1.3 72.5 - - - +
344B VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 3.9 31.6 - - + -
239B HIS* 4.2 21.3 - - + +
276B ALA* 3.3 23.6 - - + +
277B ALA* 5.3 0.7 - - - -
278B PHE* 4.1 21.1 - - + -
324B TYR* 3.3 3.4 - - - -
325B PHE* 2.8 46.4 + - + +
327B TYR* 4.7 9.4 - - + -
342B TRP* 5.0 1.1 - - + -
343B THR* 1.3 78.8 - - - +
345B PHE* 1.3 72.6 + - - +
346B ASN 3.6 0.2 + - - -
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Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.0 14.4 - - + -
182B LEU* 5.8 0.2 - - + -
275B LEU* 3.4 43.5 - - + -
276B ALA 2.9 29.0 + - - +
277B ALA* 3.8 6.7 - - + -
278B PHE* 4.7 10.0 + - - -
317B LEU* 4.4 10.8 - - + -
318B PRO* 3.7 31.4 - - + -
320B ASP 3.4 26.5 - - - -
321B PHE* 3.7 28.9 - + - -
323B ARG 4.0 5.2 - - - -
324B TYR* 4.2 3.8 - - + -
325B PHE* 4.9 1.4 - - - -
344B VAL* 1.3 83.3 - - - +
346B ASN* 1.3 62.5 + - - +
347B GLN 3.4 18.2 - - - +
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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