Contacts of the strand formed by residues 338 - 343 (chain B) in PDB entry 2W8D
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 THR 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ASN 3.5 4.2 + - - -
337B TYR* 1.3 73.1 - - - +
339B SER* 1.3 68.3 + - - +
362B ASP* 3.7 16.2 - - + +
363B LYS* 4.7 14.6 - - + -
398B LEU* 4.7 8.7 - - + +
399B PRO* 3.3 46.9 + - + +
401B PRO 3.0 5.3 + - - -
402B PHE* 3.1 9.9 - - - +
403B TYR 2.9 22.6 + - - -
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PRO* 3.8 24.1 - - - +
333B LYS* 4.0 1.7 + - - -
337B TYR 4.0 1.3 + - - -
338B THR* 1.3 76.3 - - - +
340B ALA* 1.3 61.6 + - - +
360B GLY 3.2 7.6 + - - -
361B ILE* 3.2 12.8 - - - -
362B ASP* 3.0 39.2 + - - +
363B LYS* 2.9 25.1 + - - +
403B TYR* 3.1 18.2 - - - -
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 6.0 0.2 - - + -
339B SER* 1.3 77.2 - - - +
341B THR* 1.3 61.3 + - - +
342B PHE* 4.0 6.6 - - + -
361B ILE* 3.8 3.9 - - - +
363B LYS* 3.0 15.7 - - + +
365B PHE* 3.8 26.5 - - + -
398B LEU* 3.9 20.9 - - + -
403B TYR 3.2 5.1 + - - +
404B THR* 3.2 7.8 - - + +
405B LYS* 3.1 23.8 + - - +
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Residues in contact with THR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 1.3 73.2 - - - +
342B PHE* 1.3 65.5 + - - +
343B HIS* 4.8 1.1 - - + -
352B ARG* 5.9 0.2 - - - -
356B TYR* 3.3 45.8 - - + +
361B ILE* 3.7 10.6 - - - +
363B LYS 2.8 8.2 + - - -
364B PHE* 3.5 10.8 - - + -
365B PHE* 2.7 36.1 + - - +
405B LYS* 3.5 28.5 - - + +
407B ILE* 3.9 17.3 - - + -
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 4.0 10.5 - - + -
341B THR* 1.3 74.1 - - - +
343B HIS* 1.3 62.4 + - - +
365B PHE* 3.2 40.6 - + + -
370B TYR* 3.3 22.9 - - - +
387B PHE* 3.5 6.2 - - + -
391B SER* 4.0 13.2 - - - -
394B LEU* 3.8 19.1 - - + -
395B LEU* 4.1 18.4 - - + -
398B LEU* 4.5 1.6 - - + -
404B THR* 3.8 18.6 - - + -
405B LYS 2.9 12.3 + - - +
406B PHE* 3.5 48.5 - + + -
407B ILE 3.1 25.3 + - - -
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Residues in contact with HIS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TPO 6.2 0.4 - - - -
341B THR* 4.8 1.1 - - + -
342B PHE* 1.3 74.0 - - - +
344B GLY* 1.3 58.7 + - - +
345B ASN* 3.1 40.2 + - + +
346B THR 4.6 3.8 - - - -
352B ARG* 2.9 33.7 + - - +
364B PHE* 4.1 18.2 - + + -
365B PHE 2.9 7.3 + - - +
366B ASP* 3.2 23.9 - - - -
370B TYR* 3.8 1.8 - - - -
387B PHE* 3.7 9.6 - - - -
407B ILE* 3.0 44.8 + - + +
408B THR 4.7 0.2 - - - -
409B LEU* 3.5 33.0 - - + +
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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