Contacts of the strand formed by residues 348 - 355 (chain A) 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 ALA 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A LEU* 2.9 39.7 + - + +
345A SER 3.4 13.4 + - - +
346A GLY 3.0 1.2 + - - +
347A LEU* 1.3 79.3 - - - +
349A TRP* 1.3 70.3 + - - +
416A GLN* 4.3 5.8 - - - +
417A LEU 3.2 13.2 - - - +
418A GLU* 3.2 28.9 - - - +
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Residues in contact with TRP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A TYR* 3.6 24.0 - - - -
341A GLU* 4.0 8.7 - - + -
342A ARG 3.4 12.8 - - - -
343A PRO* 3.4 46.2 - - + -
344A LEU* 3.7 5.2 - - - -
347A LEU* 3.8 12.4 + - - +
348A ALA* 1.3 80.4 + - - +
350A ALA* 1.3 61.8 + - - +
351A VAL* 4.8 2.7 - - + -
373A GLY* 3.5 37.4 + - - -
374A LYS* 4.2 13.9 - - + -
376A VAL* 4.4 10.6 - - + +
377A ALA* 3.4 28.5 - - + +
416A GLN* 3.3 4.7 - - - +
417A LEU* 2.7 53.9 + - + +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ILE* 3.7 15.4 - - + +
319A ILE* 3.7 43.5 - - + -
341A GLU* 3.2 5.5 - - - +
342A ARG* 2.8 35.6 + - + +
344A LEU* 3.7 5.5 - - + +
349A TRP* 1.3 74.8 - - - +
351A VAL* 1.3 63.2 + - - +
414A LEU* 4.6 1.3 - - + -
415A LEU 3.3 5.8 - - - +
416A GLN* 4.5 0.4 - - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A VAL* 4.0 19.7 - - + -
340A TRP 3.4 9.2 - - - +
341A GLU* 4.2 11.7 - - + +
349A TRP* 4.8 3.8 - - + -
350A ALA* 1.3 79.0 - - - +
352A ALA* 1.3 66.5 + - - +
353A MET* 4.5 9.4 - - + -
367A ILE* 6.3 0.2 - - + -
372A LEU* 4.1 21.5 - - + -
373A GLY 5.7 0.2 - - - +
403A LEU* 6.0 0.2 - - + -
413A VAL 3.6 1.4 - - - +
414A LEU* 3.4 4.4 - - - +
415A LEU* 2.7 51.6 + - + +
417A LEU* 3.9 35.0 - - + -
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ALA* 5.0 0.2 - - + -
286A LEU* 4.1 12.6 - - + -
289A ILE* 3.9 24.8 - - + +
338A GLU 3.7 0.9 - - - +
339A VAL* 3.3 4.2 - - - +
340A TRP* 2.7 47.0 + - + +
351A VAL* 1.3 74.1 - - - +
353A MET* 1.3 62.3 + - - +
354A ILE* 4.1 1.3 + - + -
412A THR* 4.0 16.6 - - + -
413A VAL 3.3 4.0 - - - -
414A LEU* 4.1 6.1 - - + -
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Residues in contact with MET 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 6.2 0.4 - - + -
338A GLU 3.3 5.4 - - - +
339A VAL* 4.3 14.4 - - + -
351A VAL* 4.5 11.2 - - + -
352A ALA* 1.3 76.3 - - - +
354A ILE* 1.3 61.2 + - - +
365A TYR* 3.8 27.6 - - + +
367A ILE* 4.7 13.7 - - - -
403A LEU* 4.5 4.0 - - + +
405A SER* 3.2 36.8 - - - +
407A ILE* 3.5 19.1 - - + +
412A THR* 3.2 4.1 - - - -
413A VAL* 2.9 52.2 + - + +
415A LEU* 3.7 17.7 - - + -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TRP* 4.9 3.8 - - + -
243A LEU* 4.2 13.7 - - + -
282A THR* 4.3 10.1 - - + +
286A LEU* 3.7 31.9 - - + -
337A PHE* 3.3 10.9 - - - -
338A GLU* 2.8 51.8 + - + +
340A TRP* 3.9 23.3 - - + +
352A ALA 5.0 0.9 - - - +
353A MET* 1.3 75.5 - - - +
355A ASN* 1.3 66.3 + - - +
356A ARG* 3.8 22.0 + - + -
407A ILE* 4.4 0.7 - - - -
410A THR 5.1 0.2 - - - -
411A GLY 3.5 12.8 - - - +
412A THR* 3.5 15.0 - - + +
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Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ASN 3.8 1.8 - - - -
337A PHE* 4.2 7.6 - - + -
354A ILE* 1.3 70.3 - - - +
356A ARG* 1.3 57.9 + - - +
357A GLN* 3.1 12.1 + - - +
361A GLY 4.3 1.2 + - - -
363A ARG* 2.9 46.8 + - - +
407A ILE* 3.0 34.6 + - + +
408A ASN 3.3 12.3 - - - +
409A PRO* 3.5 21.2 - - - +
410A THR* 2.8 36.0 + - - -
411A GLY 3.1 7.7 + - - -
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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