Contacts of the strand formed by residues 346 - 352 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A TRP* 4.1 19.4 - - + -
292A GLU* 4.3 11.7 - - + +
295A SER* 3.1 35.3 - - - +
299A GLU* 5.6 0.3 - - - +
342A GLU* 4.3 0.6 - - - +
343A VAL 3.0 36.1 + - - +
344A ASP 3.9 5.6 - - - +
345A ASN* 1.3 80.0 - - - +
347A LEU* 1.3 64.7 + - - +
348A ARG* 3.3 38.5 + - - +
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Residues in contact with LEU 347 (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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189A LEU* 4.2 20.6 - - + -
292A GLU 3.8 2.6 + - - +
293A ASN* 3.5 34.3 - - + +
295A SER* 2.7 27.2 + - - +
296A PHE* 3.1 20.0 + - + -
340A VAL* 3.8 14.1 - - + -
341A CYS 3.7 2.5 - - - -
342A GLU* 4.0 32.1 - - + +
345A ASN 6.1 0.2 - - - -
346A GLU* 1.3 71.4 - - - +
348A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 348 (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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295A SER* 5.8 0.4 - - - -
296A PHE* 4.3 1.6 - - - -
299A GLU* 3.6 13.2 + - - +
305A ARG* 3.1 48.7 - - - +
340A VAL* 3.2 8.5 - - - +
341A CYS 3.0 34.3 + - - +
343A VAL* 3.4 40.9 + - + +
344A ASP* 3.5 18.2 + - - +
346A GLU* 3.3 46.9 + - + +
347A LEU* 1.3 79.0 - - - +
349A ILE* 1.3 64.2 + - - +
350A CYS* 3.5 2.5 + - - -
531A ARG* 4.8 2.8 - - - +
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Residues in contact with ILE 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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178A LEU* 4.4 12.3 - - + -
182A LEU* 4.0 25.6 - - + -
296A PHE* 3.8 27.4 - - + +
299A GLU* 2.9 32.5 + - + +
300A ILE* 4.3 12.1 - - + -
303A ASN* 6.1 1.1 - - - +
305A ARG* 3.9 15.9 + - - -
306A ASN* 5.6 1.9 + - - -
334A PHE* 4.9 12.8 - - + -
338A ALA* 4.2 17.3 - - + -
339A ARG 3.5 7.9 - - - +
340A VAL* 4.6 0.9 - - + +
348A ARG* 1.3 72.8 - - - +
350A CYS* 1.3 70.3 + - - +
518A VAL* 5.8 1.2 - - - +
519A SER 4.5 2.1 + - - +
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Residues in contact with CYS 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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334A PHE* 5.6 1.3 - - - -
338A ALA* 3.4 6.2 - - - +
339A ARG 2.6 37.4 + - - +
341A CYS* 3.6 31.2 - - - -
343A VAL* 4.2 9.0 - - - -
348A ARG* 3.7 10.3 - - - -
349A ILE* 1.3 75.6 - - - +
351A ALA* 1.3 59.3 + - - +
518A VAL* 5.8 0.4 - - - -
519A SER* 3.2 37.2 - - - +
520A PHE* 4.5 1.8 - - - +
521A TYR* 4.2 15.0 - - + -
529A ALA* 4.5 3.1 - - - -
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Residues in contact with ALA 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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334A PHE* 4.3 23.6 - - + -
337A PHE 3.6 7.0 - - - +
338A ALA* 4.7 0.7 - - - +
350A CYS* 1.3 76.4 - - - +
352A ARG* 1.3 71.0 + - - +
355A GLU* 4.5 7.0 - - + -
359A LEU* 4.5 7.6 - - + -
518A VAL* 4.9 2.7 - - + +
519A SER 3.2 5.9 + - - +
520A PHE* 3.1 20.6 - - + -
521A TYR* 3.0 24.7 + - - -
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Residues in contact with ARG 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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337A PHE* 3.1 32.5 + - + -
351A ALA* 1.3 75.7 - - - +
353A ASP* 1.3 93.5 + - - +
354A LYS* 3.6 48.9 - - + +
355A GLU* 3.0 22.4 + - + +
520A PHE* 3.5 4.2 - - - -
521A TYR* 3.5 44.1 + - - +
523A LYS* 3.9 45.3 - - - +
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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