Contacts of the helix formed by residues 5222 - 5229 (chain b) 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 PRO5222 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5220b ARG 3.5 8.7 - - - +
5221b PRO* 1.3 81.6 - - + +
5223b GLN* 1.3 69.8 + - - +
5224b ARG 3.1 0.2 - - - -
5225b LEU* 2.8 21.7 + - + +
5226b TYR 3.0 7.4 + - - -
5519b CLA 3.7 22.7 - - - +
5022h ALA* 4.1 7.2 - - + +
5024h GLY 3.6 3.1 - - - +
5025h TRP* 3.6 2.0 - - - -
5026h GLY* 3.3 19.7 - - - +
5027h THR* 3.0 32.1 - - - +
5028h THR* 3.3 24.9 - - - +
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Residues in contact with GLN5223 (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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5222b PRO* 1.3 70.3 - - - +
5224b ARG* 1.3 68.7 + - - +
5226b TYR* 3.2 3.1 + - - +
5227b LYS* 3.0 74.7 + - - +
5021h VAL* 3.1 20.5 - - + +
5022h ALA 2.8 16.8 + - - +
5023h PRO* 3.7 2.9 - - + -
5024h GLY* 3.1 29.8 + - - +
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Residues in contact with ARG5224 (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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5222b PRO* 5.0 0.7 - - + -
5223b GLN* 1.3 80.5 + - - +
5225b LEU* 1.3 60.5 + - + +
5227b LYS* 3.2 10.1 + - - +
5228b ALA* 2.9 27.8 + - - +
5024h GLY* 2.8 25.0 + - - +
5025h TRP* 4.0 29.2 - - + +
5028h THR* 5.3 0.4 - - - +
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Residues in contact with LEU5225 (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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5222b PRO* 2.8 16.5 + - + +
5224b ARG* 1.3 73.6 - - + +
5226b TYR* 1.3 65.9 + - - +
5227b LYS 2.9 2.9 + - - -
5228b ALA* 3.0 12.3 + - + -
5229b LEU* 3.0 26.5 + - + +
5231b MET* 3.7 10.4 - - + +
5519b CLA 3.9 43.7 - - + +
5028h THR* 3.3 30.7 - - + +
5031h MET* 3.8 34.1 - - + -
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Residues in contact with TYR5226 (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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5136b PRO* 4.6 10.1 - - + -
5221b PRO* 3.6 26.7 - - + -
5222b PRO 3.0 10.2 + - - +
5223b GLN 3.7 7.9 - - - +
5225b LEU* 1.3 76.2 - - - +
5227b LYS* 1.3 65.1 + - + +
5230b ARG* 3.9 1.2 - - - -
5231b MET* 3.1 60.3 + - + +
5232b GLY* 3.7 16.9 - - - -
5018h TYR* 4.1 18.3 + - - -
5019h GLY* 4.0 28.8 - - - -
5020h LYS 4.4 4.0 - - - -
5021h VAL* 4.3 18.4 - - + -
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Residues in contact with LYS5227 (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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5223b GLN* 3.0 45.4 + - - +
5224b ARG* 3.2 10.5 + - - +
5225b LEU 2.9 0.4 - - - -
5226b TYR* 1.3 82.6 - - + +
5228b ALA* 1.3 71.6 + - - +
5230b ARG* 3.1 21.5 + - - -
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Residues in contact with ALA5228 (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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5224b ARG 2.9 15.0 + - - +
5225b LEU* 3.0 18.8 + - + +
5227b LYS* 1.3 73.3 - - - +
5229b LEU* 1.3 59.4 + - + +
5230b ARG* 2.4 39.8 + - - +
5474b LEU* 3.9 0.2 - - - +
5482c UNK 3.8 20.5 - - + +
5490c UNK 4.9 9.0 - - + -
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Residues in contact with LEU5229 (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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5225b LEU* 3.0 16.2 + - + +
5226b TYR 4.2 1.1 - - - -
5228b ALA* 1.3 77.1 - - + +
5230b ARG* 1.3 54.1 + - - +
5231b MET* 2.4 30.1 + - - +
5236b THR* 3.6 18.0 + - - +
5474b LEU* 4.8 3.6 - - - -
5518b CLA 4.3 16.4 - - - +
5519b CLA 2.9 64.4 - - + +
5520b CLA 4.0 26.0 - - + -
5482c UNK 3.9 23.6 - - + -
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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