Contacts of the strand formed by residues 363 - 368 (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 ARG 363 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 5.6 0.2 - - - -
335B ASP* 2.9 42.2 + - - -
336B ASN* 3.0 26.1 + - - +
337B PHE* 3.2 32.6 - - + -
355B ASN* 3.1 30.2 + - - +
357B GLN* 3.3 40.1 + - - +
361B GLY 3.3 5.4 + - - +
362B PRO* 1.3 73.0 - - - +
364B SER* 1.3 65.7 + - - +
365B TYR 3.7 0.5 + - - -
406B HIS* 3.5 2.1 - - - -
407B ILE* 2.9 32.8 + - - +
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 4.3 8.9 + - - -
337B PHE* 3.6 13.4 - - - -
363B ARG* 1.3 78.2 - - - +
365B TYR* 1.3 59.0 + - - +
366B THR* 4.3 1.4 + - - -
404B ARG* 3.9 24.9 + - - -
405B SER 3.2 7.4 - - - -
406B HIS* 3.6 28.6 - - - -
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Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 3.4 26.6 + - - +
334B GLY 5.1 2.0 - - - -
337B PHE* 3.4 47.2 - + + +
339B VAL* 3.4 33.5 - - + +
353B MET* 3.8 23.1 - - + +
364B SER* 1.3 74.5 - - - +
366B THR* 1.3 72.0 + - - +
367B ILE* 3.9 17.7 - - + -
403B LEU 3.6 1.9 - - - +
404B ARG* 3.3 1.3 - - - -
405B SER* 2.7 36.5 + - - +
407B ILE* 3.9 20.6 - - + -
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Residues in contact with THR 366 (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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332B ARG* 5.1 2.1 + - - -
364B SER* 4.3 2.1 + - - -
365B TYR* 1.3 85.8 + - - +
367B ILE* 1.3 62.8 + - - +
402B ARG* 4.0 30.1 - - + -
403B LEU 3.2 11.0 - - - +
404B ARG* 3.6 31.0 + - + +
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Residues in contact with ILE 367 (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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331B LEU* 4.7 2.0 - - + -
332B ARG* 3.4 32.8 - - - +
339B VAL* 4.1 24.2 - - + -
351B VAL* 6.1 0.7 - - + -
353B MET* 4.4 19.1 - - - -
365B TYR* 3.9 6.9 - - + -
366B THR* 1.3 75.0 - - - +
368B ALA* 1.3 73.2 + - - +
369B VAL 3.5 0.5 + - - -
371B SER* 4.4 4.5 - - - -
372B LEU* 3.8 33.9 - - + -
402B ARG* 3.5 4.2 - - - -
403B LEU* 2.8 55.0 + - + +
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Residues in contact with ALA 368 (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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332B ARG* 5.3 0.6 - - - +
367B ILE* 1.3 78.2 - - - +
369B VAL* 1.3 60.6 + - - +
370B ALA* 4.3 9.9 - - + +
371B SER* 2.9 38.1 + - - +
372B LEU 4.0 0.7 + - - -
400B THR 5.6 2.0 - - - +
401B SER 3.7 9.0 - - - +
402B ARG* 3.8 20.5 - - + +
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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