Contacts of the strand formed by residues 329 - 334 (chain A) in PDB entry 4LG8
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 TYR 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A HIS* 3.3 9.2 - - + -
325A SER 3.3 23.9 + - - -
327A ASP* 2.9 36.2 + - - +
328A GLN* 1.3 82.5 - - + +
330A TRP* 1.3 64.0 + - - +
343A LYS* 3.8 33.4 - - + -
344A VAL 3.3 26.7 - - - -
345A THR* 3.5 29.8 - - + +
353A LEU* 3.6 6.4 - - - +
609A UNX 4.0 12.6 - - - -
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Residues in contact with TRP 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 4.2 1.3 - - - -
322A LEU* 4.0 13.2 - - + -
323A SER 3.1 15.0 - - - +
329A TYR* 1.3 74.4 - - - +
331A ALA* 1.3 69.7 + - - +
332A PHE* 4.4 7.6 - - + -
342A THR* 4.0 24.7 - - + -
343A LYS* 3.3 5.0 - - - +
344A VAL* 2.9 72.4 + - + +
345A THR* 5.2 0.7 - - - -
353A LEU* 4.1 15.0 - - + -
365A PHE* 3.6 35.2 - + - -
367A THR* 4.4 6.3 - - + -
377A TRP* 3.4 52.5 - + + -
379A LEU* 4.5 6.3 - - + -
382A ARG* 4.4 18.2 - - + -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 3.8 23.3 - - + -
305A HIS* 3.9 4.9 - - + +
321A LEU 3.5 0.7 - - - +
322A LEU* 3.3 8.1 - - - +
323A SER* 2.9 44.6 + - - +
330A TRP* 1.3 81.6 - - - +
332A PHE* 1.3 60.5 + - - +
333A SER* 4.2 3.1 - - - +
340A VAL* 4.4 4.3 - - + -
342A THR 3.2 11.9 - - - +
343A LYS* 4.2 7.9 - - + -
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Residues in contact with PHE 332 (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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315A HIS* 4.3 4.9 - + - -
320A TYR* 3.3 53.8 - + + -
321A LEU 3.4 6.3 - - - -
322A LEU* 4.8 2.7 - - + -
330A TRP* 4.4 7.4 - - + -
331A ALA* 1.3 72.9 - - - +
333A SER* 1.3 60.7 + - - +
340A VAL* 4.1 0.2 - - - -
341A LEU* 2.8 44.8 + - + +
342A THR* 3.0 28.8 + - + +
358A PHE* 3.6 29.2 - + - -
379A LEU* 3.8 34.8 - - + -
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 5.0 6.4 - - - +
302A VAL* 3.6 31.1 - - - +
304A ALA* 4.4 5.4 - - - +
320A TYR* 3.2 11.1 - - - +
321A LEU* 2.9 42.8 + - - +
323A SER* 5.2 0.2 + - - -
331A ALA* 4.6 1.7 - - - +
332A PHE* 1.3 78.4 + - - +
334A ASP* 1.3 63.7 + - - +
335A ILE 3.5 0.5 + - - -
339A ARG 3.2 9.9 - - - -
340A VAL* 3.8 12.8 - - - +
341A LEU* 4.6 0.4 - - - -
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 5.2 0.9 - - - +
319A ASP* 3.8 7.1 - - - +
320A TYR* 3.6 19.6 + - - -
333A SER* 1.3 71.5 - - - +
335A ILE* 1.3 61.1 + - - +
336A GLN* 3.4 9.2 + - - +
337A THR* 2.7 45.8 + - - +
338A GLY* 2.8 31.4 + - - -
339A ARG 2.7 14.1 + - - +
341A LEU* 4.1 20.0 - - + +
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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