Contacts of the strand formed by residues 341 - 343 (chain C) in PDB entry 2AXT
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 LEU 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LEU* 3.9 23.8 - - + -
328C VAL* 4.4 26.4 + - + +
329C GLY* 4.5 12.9 - - - +
331C ALA 5.1 1.2 + - - +
337C LEU 3.5 13.3 - - - +
338C GLY* 3.8 7.4 - - - +
339C LYS 3.7 0.2 - - - -
340C TYR* 1.3 88.3 - - + +
342C MET* 1.3 61.4 + - - +
349C ILE* 4.4 14.8 - - + -
350C ILE 3.4 14.4 - - - +
351C PHE* 4.2 0.2 - - + -
352C GLY 4.1 0.7 - - - +
375C LEU* 3.6 28.5 - - + +
377C LEU* 4.7 10.5 - - + -
380C ILE* 4.1 13.5 - - + -
127O ILE* 5.3 11.3 - - + +
129O PHE* 5.5 2.9 - - - -
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ASN* 5.7 0.9 - - - +
337C LEU* 3.6 41.1 - - + +
338C GLY 4.3 4.7 - - - +
341C LEU* 1.3 74.5 - - - +
343C ARG* 1.3 70.9 + - - +
349C ILE* 3.7 5.2 - - - +
350C ILE* 2.8 42.5 + - + +
352C GLY* 3.3 26.9 - - - -
353C GLY* 3.3 12.6 - - - +
356C MET* 3.6 42.4 - - + +
101O THR* 6.1 0.7 - - + -
127O ILE* 6.4 1.3 - - - -
130O GLN* 5.2 7.4 - - - +
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Residues in contact with ARG 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C MET* 1.3 90.9 - - - +
344C SER* 1.3 64.0 + - - +
347C GLY 2.7 34.1 + - - +
348C GLU 3.3 5.4 - - - +
349C ILE* 3.9 23.2 - - + +
350C ILE* 4.3 5.9 - - - +
373C ASN* 5.7 0.6 - - - +
42O ALA 3.5 14.8 + - - -
43O ASN* 3.8 12.5 + - - -
100O GLU 4.6 0.4 - - - -
101O THR* 3.6 34.9 + - + +
103O SER* 2.8 50.0 + - - -
105O ASP* 3.8 22.8 - - - +
127O ILE* 5.2 4.2 - - + +
130O GLN* 3.6 22.0 + - - +
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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