Contacts of the helix formed by residues 5012 - 5022 (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 ASN5012 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5010a SER* 4.0 3.0 - - - -
5011a ALA* 1.3 90.6 - - - +
5013a LEU* 1.3 68.1 - - - +
5014a TRP* 3.1 18.8 - - - +
5015a GLU* 2.7 30.3 + - + +
5016a ARG* 3.3 2.1 + - - -
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Residues in contact with LEU5013 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5010a SER* 4.1 22.0 - - - -
5012a ASN* 1.3 79.0 - - - +
5014a TRP* 1.3 52.4 + - - +
5016a ARG* 2.8 27.7 + - + +
5017a PHE* 2.4 40.1 + - + +
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Residues in contact with TRP5014 (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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5012a ASN* 2.9 17.6 + - - +
5013a LEU* 1.3 76.0 - - - +
5015a GLU* 1.3 70.2 + - - +
5017a PHE* 3.5 17.2 - + + +
5018a CYS* 2.9 58.1 + - - -
5032a TRP* 4.3 6.3 - + - -
5018i LEU* 3.7 33.2 - - + -
5021i PHE* 3.5 37.5 - + + -
5022i GLY 3.8 9.0 - - - -
5025i SER* 3.3 16.6 + - - -
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Residues in contact with GLU5015 (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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5011a ALA* 2.6 51.4 - - - +
5012a ASN* 2.7 10.8 + - + +
5014a TRP* 1.3 85.0 - - - +
5016a ARG* 1.3 56.9 + - - +
5018a CYS* 3.4 10.2 + - - +
5019a ASN* 2.5 31.3 + - - +
5030i ARG* 5.5 0.2 + - - -
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Residues in contact with ARG5016 (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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5011a ALA* 5.3 3.6 - - + +
5012a ASN 3.3 2.2 + - - +
5013a LEU* 2.8 30.8 + - + +
5015a GLU* 1.3 80.1 + - - +
5017a PHE* 1.3 90.4 + - - +
5019a ASN* 2.6 37.4 + - + +
5020a TRP* 3.1 21.4 + - + +
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Residues in contact with PHE5017 (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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5013a LEU* 2.4 25.2 + - + +
5014a TRP* 3.5 20.0 - + + +
5016a ARG* 1.3 94.9 - - - +
5018a CYS* 1.3 66.6 + - - +
5019a ASN 2.9 0.9 + - - -
5020a TRP* 3.0 18.0 + + - +
5021a VAL* 2.9 50.2 + - + -
5032a TRP* 4.7 10.5 - + - -
5035a VAL* 5.4 0.2 - - + -
5566a BCR 4.0 31.0 - - + -
5014i PHE* 6.1 1.8 - + - -
5018i LEU* 4.6 15.9 - - + -
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Residues in contact with CYS5018 (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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5014a TRP* 2.9 67.7 + - - +
5015a GLU* 3.5 7.0 - - - +
5017a PHE* 1.3 76.7 - - - +
5019a ASN* 1.3 57.5 + - - +
5021a VAL* 4.4 0.2 - - - -
5022a THR* 2.7 29.6 + - - -
5032a TRP* 3.7 24.2 - - + -
5025i SER* 3.9 7.2 - - - -
5030i ARG* 3.1 27.4 + - - +
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Residues in contact with ASN5019 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5015a GLU* 2.5 33.4 - - - +
5016a ARG* 2.6 23.2 + - - +
5018a CYS* 1.3 72.3 - - - +
5020a TRP* 1.3 57.7 + - - +
5022a THR* 3.3 4.9 + - - -
5023a SER* 2.8 24.9 + - - -
5030i ARG* 3.8 15.2 + - - +
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Residues in contact with TRP5020 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212a SQD 3.0 51.9 + - + -
5016a ARG* 3.1 22.9 + - + +
5017a PHE* 3.0 29.0 + + - +
5019a ASN* 1.3 72.7 - - - +
5021a VAL* 1.3 90.3 + - + +
5022a THR 2.8 1.6 - - - -
5023a SER* 2.5 34.3 + - - +
5026a ASN* 3.2 27.1 + - - +
5030a VAL* 4.2 18.8 - - + -
5566a BCR 4.4 24.7 - - + -
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Residues in contact with VAL5021 (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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5017a PHE* 2.9 49.0 + - + +
5018a CYS 4.2 3.4 - - - +
5020a TRP* 1.3 92.9 - - + +
5022a THR* 1.3 59.4 + - - +
5029a TYR* 3.4 2.9 - - - -
5030a VAL* 2.4 34.1 - - + +
5031a GLY* 3.4 26.6 - - - +
5032a TRP* 3.7 33.9 - - + +
5035a VAL* 4.5 8.7 - - + -
5132a GLU* 5.4 0.2 - - - +
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Residues in contact with THR5022 (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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5018a CYS 2.7 20.5 + - - -
5019a ASN* 3.3 6.1 + - - -
5020a TRP 2.8 1.2 - - - -
5021a VAL* 1.3 80.3 - - - +
5023a SER* 1.3 67.2 + - - +
5024a THR* 3.1 8.0 + - - -
5029a TYR* 4.0 8.3 + - - +
5032a TRP* 3.8 19.1 + - - -
5136a ARG* 2.9 47.0 + - - +
5030i ARG* 4.0 21.3 + - + -
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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