Contacts of the strand formed by residues 346 - 352 (chain B) in PDB entry 6TX0
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 GLU 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B TRP* 4.1 19.9 - - + -
292B GLU* 4.4 13.2 - - + +
295B SER* 3.2 30.8 - - - +
299B GLU* 6.2 0.2 - - - -
342B GLU* 3.6 2.0 - - - +
343B VAL 3.0 35.7 + - - +
344B ASP 3.9 4.8 - - - +
345B ASN* 1.3 80.4 - - - +
347B LEU* 1.3 65.2 + - - +
348B ARG* 3.3 37.5 + - - +
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Residues in contact with LEU 347 (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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189B LEU* 4.4 18.8 - - + -
292B GLU 3.9 6.2 + - - +
293B ASN* 3.5 30.7 - - + +
295B SER* 2.7 28.0 + - - +
296B PHE* 3.2 18.6 + - + -
340B VAL* 3.8 14.8 - - + -
341B CYS* 3.7 3.1 - - - -
342B GLU* 4.0 30.5 - - + +
346B GLU* 1.3 71.6 - - - +
348B ARG* 1.3 59.5 - - - +
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Residues in contact with ARG 348 (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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295B SER* 5.8 0.2 - - - -
296B PHE* 4.3 0.9 - - - -
299B GLU* 3.6 10.9 + - - +
305B ARG* 3.1 51.4 - - - +
340B VAL* 3.2 8.7 - - - +
341B CYS 2.9 34.5 + - - +
343B VAL* 3.6 43.8 + - + +
344B ASP* 4.3 11.3 + - - +
346B GLU* 3.3 49.1 + - + +
347B LEU* 1.3 79.2 - - - +
349B ILE* 1.3 65.7 + - - +
350B CYS* 3.5 2.4 + - - -
531B ARG* 5.0 2.4 - - - +
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Residues in contact with ILE 349 (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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178B LEU* 4.4 12.8 - - + -
182B LEU* 4.0 24.7 - - + -
296B PHE* 3.8 28.5 - - + +
299B GLU* 2.9 34.5 + - + +
300B ILE* 4.2 13.2 - - + -
303B ASN* 6.2 0.4 - - - +
305B ARG* 3.9 15.6 + - - -
306B ASN* 5.6 1.7 + - - -
334B PHE* 5.0 12.3 - - + -
338B ALA* 4.2 17.3 - - + -
339B ARG 3.5 8.5 - - - +
340B VAL* 4.6 1.3 - - + +
348B ARG* 1.3 72.3 - - - +
350B CYS* 1.3 68.8 + - - +
518B VAL* 5.8 0.9 - - - +
519B SER 4.6 2.1 + - - +
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Residues in contact with CYS 350 (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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334B PHE* 5.6 1.3 - - - -
338B ALA* 3.3 6.4 - - - +
339B ARG 2.6 34.6 + - - +
341B CYS* 3.6 30.7 - - - -
343B VAL* 4.1 8.7 - - - -
348B ARG* 3.7 11.7 - - - -
349B ILE* 1.3 76.0 - - - +
351B ALA* 1.3 60.9 + - - +
518B VAL* 5.7 0.7 - - - -
519B SER* 3.2 37.7 - - - +
520B PHE* 4.5 1.3 - - - +
521B TYR* 4.0 15.0 - - + -
529B ALA* 4.3 2.9 - - - -
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Residues in contact with ALA 351 (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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334B PHE* 4.1 25.8 - - + -
337B PHE 3.5 8.1 - - - +
350B CYS* 1.3 76.4 - - - +
352B ARG* 1.3 70.8 + - - +
355B GLU* 4.5 9.9 - - + -
359B LEU* 4.7 6.1 - - + -
518B VAL* 5.0 2.9 - - + -
519B SER 3.2 5.9 + - - +
520B PHE* 3.1 18.3 - - + +
521B TYR* 3.0 24.3 + - - -
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Residues in contact with ARG 352 (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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337B PHE* 3.1 35.2 + - + +
351B ALA* 1.3 74.1 - - - +
353B ASP* 1.3 93.5 + - - +
354B LYS* 3.3 48.7 - - + +
355B GLU* 3.0 21.4 + - + +
520B PHE* 3.7 4.2 - - - -
521B TYR* 3.5 43.4 + - - +
523B LYS* 3.9 43.0 - - - +
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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