Contacts of the strand formed by residues 337 - 343 (chain B) in PDB entry 3LX9
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 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B GLN* 3.4 3.7 - - - +
334B GLY 2.9 34.3 + - - +
335B ASP* 3.1 25.3 - - + -
336B ASN* 1.3 78.4 - - - +
338B GLU* 1.3 67.3 + - - +
353B MET* 6.0 0.4 - - + -
354B ILE 3.3 13.5 - - - -
355B ASN* 4.1 11.7 - - - -
356B ARG* 5.3 0.2 - - - -
363B ARG* 3.2 50.0 - - + -
364B SER 3.6 22.7 - - - -
365B TYR* 3.4 47.8 - + + -
407B ILE* 4.0 17.5 - - + -
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 5.3 1.6 - - - +
244B ASP* 4.0 4.7 - - - +
247B SER* 4.9 0.2 + - - -
330B GLN* 2.8 22.8 + - - +
332B ARG 3.5 7.0 - - - +
333B GLN* 4.1 9.0 - - + +
337B PHE* 1.3 80.1 - - - +
339B VAL* 1.3 65.5 + - - +
340B TRP* 2.8 41.9 + - + +
352B ALA 3.8 0.2 - - - +
353B MET* 3.3 5.5 - - - +
354B ILE* 2.8 45.2 + - + +
356B ARG* 2.6 46.8 + - + +
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Residues in contact with VAL 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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330B GLN* 3.6 2.1 - - - -
331B LEU* 2.7 51.9 + - + -
332B ARG* 2.9 27.5 + - + +
338B GLU* 1.3 77.6 - - - +
340B TRP* 1.3 66.0 + - - +
351B VAL* 4.1 15.5 - - + -
352B ALA 3.3 6.1 - - - +
353B MET* 4.1 7.9 - - + -
365B TYR* 3.4 41.3 - - + +
367B ILE* 4.1 11.9 - - + -
372B LEU* 4.4 0.4 - - + -
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Residues in contact with TRP 340 (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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243B LEU* 3.8 38.4 - - + -
246B THR* 4.4 9.0 - - + -
247B SER* 3.8 27.6 - - - -
250B GLN* 5.1 1.3 - - - -
286B LEU* 3.4 25.8 - - + -
289B ILE* 4.0 20.2 - - + -
290B MET* 3.9 21.1 - - + -
328B GLY 5.3 0.4 - - - -
329B TYR* 3.1 24.0 - - - -
330B GLN* 3.8 15.2 - - + +
331B LEU 4.1 0.2 - - - +
338B GLU* 2.8 37.0 + - + +
339B VAL* 1.3 81.6 - - - +
341B GLU* 1.3 65.5 + - - +
351B VAL* 3.4 5.2 - - - +
352B ALA* 2.8 35.5 + - + +
354B ILE* 4.0 9.9 - - + +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 4.1 3.6 - - - -
328B GLY* 3.0 2.2 - - - -
329B TYR* 2.6 73.6 + - + -
331B LEU* 3.7 26.6 - - + +
340B TRP* 1.3 77.2 - - - +
342B ARG* 1.3 62.5 + - - +
343B PRO* 4.7 0.2 - - - -
349B TRP* 3.8 10.0 - - + -
350B ALA 3.1 11.7 - - - +
351B VAL* 4.2 9.4 - - + +
372B LEU* 3.6 12.3 - - - +
373B GLY* 2.9 33.1 + - - -
374B LYS* 4.2 3.6 + - - +
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Residues in contact with ARG 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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262B TRP* 4.9 0.8 - - - -
288B ALA 2.9 20.5 + - - -
289B ILE* 3.4 27.1 - - + +
291B ALA* 3.6 19.0 - - - +
319B ILE* 2.8 27.7 + - - -
320B ASN* 3.3 17.4 + - - +
322B ASP* 3.9 12.3 + - - +
325B GLY* 3.5 30.7 - - - +
326B LYS 2.7 25.8 + - - +
328B GLY* 3.6 10.8 - - - +
341B GLU* 1.3 76.4 - - - +
343B PRO* 1.3 74.8 + - - +
344B LEU* 3.7 12.3 - - - +
349B TRP* 3.4 6.6 - - - -
350B ALA* 2.8 38.7 + - + +
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Residues in contact with PRO 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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322B ASP* 4.3 1.6 - - - +
324B LEU* 4.1 6.2 - - + +
326B LYS* 3.8 45.6 + - + +
327B GLN 4.3 8.7 - - - +
329B TYR* 4.4 10.8 - - + -
342B ARG* 1.3 97.7 + - + +
344B LEU* 1.3 62.2 + - - +
349B TRP* 3.5 41.6 - - + -
374B LYS* 6.2 1.3 - - - -
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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