Contacts of the strand formed by residues 376 - 381 (chain B) in PDB entry 3A3K
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 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER 5.0 2.0 - - - -
132B LYS* 3.6 20.6 - - + -
133B LEU* 3.5 44.6 - - + -
136B PHE* 3.8 35.8 - + + -
243B VAL* 4.6 4.3 - - + -
280B ILE* 4.2 5.2 - - + -
281B THR 3.4 18.4 - - - +
282B TYR* 3.6 34.8 - + - -
283B LYS* 3.8 4.3 - - - +
374B THR* 3.5 27.6 - - + -
375B ASP* 1.3 75.4 - - - +
377B SER* 1.3 63.7 + - - +
392B LEU 4.1 0.2 - - - +
393B ASN* 3.5 3.3 - - - +
394B TYR* 2.8 38.3 + + - +
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.9 2.2 - - - -
279B ILE 3.7 0.7 - - - +
280B ILE* 3.6 6.9 - - - +
281B THR* 2.9 44.4 + - - +
282B TYR 4.4 0.4 - - - -
283B LYS* 3.5 18.3 - - - +
284B GLU 4.5 1.6 + - - -
376B PHE* 1.3 73.0 - - - +
378B LEU* 1.3 60.3 + - - +
379B TRP* 4.0 9.2 - - - -
390B VAL* 3.8 18.1 - - - +
392B LEU 3.4 4.9 - - - -
393B ASN* 2.9 19.5 + - - -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.3 11.9 - - + -
140B LEU* 4.4 12.3 - - + -
239B PHE* 3.8 24.2 - - + -
278B LYS* 3.9 23.8 - - + -
279B ILE 3.6 8.5 - - - +
280B ILE* 4.0 13.5 - - + -
377B SER* 1.3 72.2 - - - +
379B TRP* 1.3 64.4 + - - +
390B VAL* 3.5 1.9 - - - -
391B VAL* 2.9 29.8 + - + +
392B LEU* 2.8 42.8 + - + -
409B LEU* 4.3 23.6 - - + -
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Residues in contact with TRP 379 (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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248B LEU* 3.7 27.6 - - + -
257B GLN* 3.8 27.1 - - + -
278B LYS* 3.4 11.6 - - - +
279B ILE* 2.9 49.5 + - + +
281B THR* 3.0 34.8 + - + +
284B GLU* 6.4 2.2 - - + -
313B LEU* 6.1 3.4 - - + -
377B SER* 4.0 6.4 - - - -
378B LEU* 1.3 76.7 - - - +
380B ASP* 1.3 59.4 + - - +
388B PHE* 3.8 21.0 - - + -
389B ARG* 3.4 26.7 - - + -
390B VAL* 3.5 25.5 - - + +
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Residues in contact with ASP 380 (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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277B ALA 4.4 1.4 - - - +
278B LYS* 2.7 34.7 + - + +
378B LEU* 5.6 0.2 - - + -
379B TRP* 1.3 73.4 - - - +
381B MET* 1.3 67.8 + - - +
388B PHE* 3.2 12.1 - - - -
389B ARG* 2.9 36.7 + - - +
391B VAL* 3.6 25.4 - - + -
408B LYS 5.3 0.4 - - - -
409B LEU* 3.3 15.9 - - - +
410B TYR* 2.7 36.1 + - - +
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Residues in contact with MET 381 (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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260B TRP* 4.1 4.7 - - - +
271B ARG* 3.6 24.5 - - + +
274B PHE* 4.0 13.7 - - + +
275B GLN* 3.5 32.5 - - - +
277B ALA 5.2 0.9 - - - +
380B ASP* 1.3 80.8 + - - +
382B ASP* 1.3 75.7 + - - +
383B PRO* 3.6 10.0 - - + +
386B GLY* 3.4 30.7 - - - +
387B ALA 3.5 4.9 - - - -
388B PHE* 3.7 26.3 - - + -
389B ARG* 3.3 8.9 + - - -
410B TYR* 3.5 34.1 - - + +
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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