Contacts of the strand formed by residues 5341 - 5343 (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 LEU5341 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5318c LEU* 3.9 23.1 - - + -
5328c VAL* 4.4 23.8 + - + +
5329c GLY* 4.4 16.2 - - - +
5331c ALA 5.0 0.7 - - - +
5337c LEU 3.4 13.3 - - - +
5338c GLY* 3.7 8.8 - - - +
5339c LYS 3.7 0.4 - - - -
5340c TYR* 1.3 87.6 - - + +
5342c MET* 1.3 60.8 + - - +
5349c ILE* 4.5 14.4 - - + -
5350c ILE 3.4 14.6 - - - +
5351c PHE* 4.2 0.4 - - + -
5352c GLY 4.1 0.4 - - - +
5375c LEU* 3.5 29.2 - - + +
5377c LEU* 4.7 10.1 - - + -
5380c ILE* 4.1 13.2 - - + -
5127o ILE* 5.2 11.5 - - + +
5129o PHE* 5.5 2.9 - - - -
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Residues in contact with MET5342 (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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5338a ASN* 5.7 0.9 - - - +
5337c LEU* 3.6 38.6 - - + +
5338c GLY 4.3 4.5 - - - +
5341c LEU* 1.3 75.1 - - - +
5343c ARG* 1.3 70.8 + - - +
5349c ILE* 3.7 5.2 - - - +
5350c ILE* 2.9 41.9 + - + +
5352c GLY* 3.2 27.8 - - - -
5353c GLY 3.2 11.9 - - - +
5356c MET* 3.5 44.2 - - + +
5101o THR* 6.1 0.4 - - + -
5127o ILE* 6.4 1.6 - - - -
5130o GLN* 5.2 7.4 - - - +
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Residues in contact with ARG5343 (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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5342c MET* 1.3 91.0 - - - +
5344c SER* 1.3 64.7 + - - +
5345c PRO* 4.9 0.3 - - - +
5347c GLY 2.7 35.4 + - - +
5348c GLU 3.2 6.1 - - - +
5349c ILE* 3.9 24.0 - - + +
5350c ILE* 4.3 4.9 - - - +
5373c ASN* 5.7 0.8 - - - +
5042o ALA 3.5 14.3 + - - -
5043o ASN* 3.7 18.6 + - - -
5101o THR* 3.6 37.8 + - + +
5103o SER* 2.8 45.4 + - - -
5105o ASP* 3.8 23.4 + - - +
5127o ILE* 5.3 4.0 - - + +
5130o GLN* 3.7 17.6 + - - +
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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