Contacts of the helix formed by residues 5018 - 5025 (chain k) 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 PHE5018 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5504c BCR 3.5 34.3 - - + -
5014k ALA 5.0 0.2 - - - -
5015k TYR* 2.6 19.3 + - - +
5017k ILE* 1.3 105.6 - - + +
5019k ASP* 1.3 68.8 + - - +
5020k PRO* 3.2 5.8 - - - -
5021k LEU* 2.7 27.9 + - + -
5022k VAL* 2.8 25.9 + - + -
5006z GLN* 4.9 6.5 - - + -
5009z LEU* 3.5 37.5 - - + -
5010z ALA* 4.5 14.8 - - + -
5013z VAL* 3.8 13.7 - - + -
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Residues in contact with ASP5019 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5073c ALA* 4.6 11.8 - - - +
5074c HIS* 4.8 0.2 - - - -
5011k LEU* 4.5 8.8 - - + +
5015k TYR 4.0 2.0 + - - -
5016k ALA* 4.0 13.8 + - - +
5018k PHE* 1.3 85.1 - - - +
5020k PRO* 1.4 71.5 - - + +
5022k VAL* 2.9 8.4 + - - +
5023k ASP* 2.8 41.0 + - - +
5056k CA 2.6 30.0 - - - -
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Residues in contact with PRO5020 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5016k ALA 5.2 0.7 - - - +
5017k ILE 4.4 9.2 - - - +
5018k PHE* 3.2 5.8 - - - +
5019k ASP* 1.4 98.4 - - + +
5021k LEU* 1.3 64.1 + - + +
5023k ASP* 3.4 20.7 - - + +
5024k VAL* 3.5 14.0 - - - +
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Residues in contact with LEU5021 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5504c BCR 4.4 13.7 - - + -
5018k PHE* 2.7 38.3 + - + +
5020k PRO* 1.3 72.9 - - + +
5022k VAL* 1.3 57.0 + - - +
5023k ASP 3.0 1.3 - - - -
5024k VAL* 2.7 31.6 + - + +
5025k LEU* 3.3 18.6 + - + +
5130x BCR 3.7 47.6 - - + -
5013z VAL* 5.1 4.7 - - + -
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Residues in contact with VAL5022 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5066c ALA 4.6 1.3 - - - +
5069c LEU* 3.8 42.8 - - + +
5070c PHE* 4.0 6.3 - - - +
5073c ALA* 4.0 6.5 - - + -
5504c BCR 4.5 16.6 - - + -
5011k LEU* 3.8 26.2 - - + -
5018k PHE* 2.8 35.8 + - + +
5019k ASP* 3.3 6.1 - - - +
5021k LEU* 1.3 73.5 - - + +
5023k ASP* 1.3 61.1 + - - +
5024k VAL 3.4 0.3 + - - -
5025k LEU* 3.7 21.1 + - + +
5026k PRO* 3.7 8.7 - - - +
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Residues in contact with ASP5023 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5070c PHE* 3.4 26.1 - - + -
5073c ALA* 4.5 2.9 - - - +
5074c HIS* 3.1 23.3 - - - -
5478c UNK 5.5 10.4 - - + +
5494c CLA 5.3 2.9 - - - +
5019k ASP* 2.8 40.8 + - - +
5020k PRO* 3.4 13.4 - - + +
5021k LEU 2.9 0.2 + - - -
5022k VAL* 1.3 78.4 - - - +
5024k VAL* 1.3 61.3 + - + +
5026k PRO* 3.8 3.6 - - - +
5027k VAL* 5.6 1.4 - - - +
5056k CA 2.8 18.8 - - - -
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Residues in contact with VAL5024 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5020k PRO 3.5 16.8 - - - +
5021k LEU* 2.7 17.5 + - + +
5023k ASP* 1.3 72.2 - - + +
5025k LEU* 1.3 66.0 + - + +
5026k PRO* 3.1 5.8 - - - -
5027k VAL* 3.1 27.2 + - + +
5028k ILE* 4.1 9.4 + - + +
5031k LEU* 6.5 1.1 - - + -
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Residues in contact with LEU5025 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5062c PHE* 3.6 9.6 - - + -
5066c ALA* 3.7 16.6 - - + +
5069c LEU* 5.5 3.6 - - + -
5119c LEU* 4.1 19.7 - - + -
5504c BCR 4.0 26.5 - - + -
5021k LEU* 3.3 27.2 + - + +
5022k VAL* 4.0 15.0 - - + +
5023k ASP 3.7 0.2 - - - -
5024k VAL* 1.3 77.6 - - + +
5026k PRO* 1.3 69.2 - - + +
5027k VAL 3.2 0.7 + - - -
5028k ILE* 3.3 34.3 + - + +
5130x BCR 4.0 30.5 - - + -
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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