Contacts of the helix formed by residues 5070 - 5074 (chain a) 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 SER5070 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5051a ALA 3.4 22.9 - - - -
5052a PHE 3.2 11.2 - - - -
5053a ILE 3.6 4.4 + - - -
5055a ALA* 3.0 32.7 + - - +
5069a GLY* 1.3 77.5 - - - +
5071a LEU* 1.3 63.6 + - - +
5073a TYR* 3.2 27.7 + - - +
5075a ASN* 2.8 21.4 + - - +
5081a ALA 3.8 2.5 + - - -
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Residues in contact with LEU5071 (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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5052a PHE* 3.0 46.3 + - + +
5053a ILE* 3.1 10.5 + - + +
5070a SER* 1.3 70.4 - - - +
5072a LEU* 1.3 56.3 + - - +
5073a TYR 2.7 15.7 + - - -
5074a GLY* 3.0 12.3 + - - -
5075a ASN* 3.4 18.7 + - + +
5076a ASN* 3.9 27.1 - - - +
5077a ILE* 4.1 3.4 - - + +
5080a GLY* 5.2 0.2 - - - -
5474c UNK 5.8 3.8 - - + -
5003t THR* 4.1 22.3 + - + +
5006t TYR* 4.1 27.1 - - + -
5007t VAL* 4.2 20.2 - - + -
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Residues in contact with LEU5072 (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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5053a ILE* 2.9 22.3 + - + +
5054a ALA* 3.7 22.7 - - + -
5071a LEU* 1.3 74.1 - - - +
5073a TYR* 1.3 67.0 + - + +
5074a GLY 3.5 1.1 + - - -
5568a LMT 3.4 63.3 + - + +
5003t THR* 3.1 33.7 - - + +
5217t LMT 2.7 44.4 + - - +
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Residues in contact with TYR5073 (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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5054a ALA* 4.9 2.2 - - + -
5055a ALA* 3.6 23.3 - - - -
5056a PRO* 4.0 17.5 - - + +
5057a PRO* 3.9 26.0 - - + -
5068a SER* 3.3 28.8 + - - -
5070a SER* 3.2 28.7 + - - +
5071a LEU 2.7 7.3 + - - -
5072a LEU* 1.3 84.3 - - + +
5074a GLY* 1.3 55.7 + - - +
5075a ASN 3.8 1.1 - - - -
5568a LMT 3.2 78.9 + - - -
5489c UNK 4.5 7.6 - - + +
5304d ARG* 4.1 8.2 + - - -
5311d PHE* 3.6 8.3 - - - -
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Residues in contact with GLY5074 (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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5071a LEU 3.0 4.4 + - - -
5072a LEU 3.5 1.6 + - - -
5073a TYR* 1.3 79.2 - - - +
5075a ASN* 1.3 62.2 + - - +
5301d GLN* 2.8 24.4 + - - +
5304d ARG* 4.6 3.3 - - - +
5311d PHE* 3.3 17.1 - - - -
5001m MET* 3.1 24.5 - - - +
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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