Contacts of the helix formed by residues 5041 - 5047 (chain u) 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 ASN5041 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5385b ARG* 3.8 14.6 - - - +
5189o GLY 4.3 2.6 + - - -
5190o LEU* 3.1 40.7 + - - +
5213o VAL* 3.7 14.6 - - + +
5214o LYS 5.1 3.6 - - - +
5040u VAL* 1.3 74.5 - - - +
5042u VAL* 1.3 60.7 + - - +
5043u VAL* 2.7 20.3 + - - +
5044u ASP* 2.8 34.4 + - + +
5045u GLU* 3.1 11.1 + - - +
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Residues in contact with VAL5042 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5190o LEU* 4.0 15.5 - - + +
5214o LYS 5.6 0.2 - - - +
5215o ARG* 6.3 2.0 - - - -
5216o PHE* 5.5 5.6 - - + +
5040u VAL* 3.2 9.8 + - + +
5041u ASN* 1.3 71.5 - - - +
5043u VAL* 1.3 61.6 + - + +
5045u GLU* 3.5 17.1 + - - +
5046u LYS* 3.0 29.1 + - - +
5118u GLU* 3.7 38.0 - - - +
5120u ALA* 3.8 19.7 - - + -
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Residues in contact with VAL5043 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5385b ARG* 3.6 31.4 - - + -
5190o LEU* 4.3 11.2 - - + +
5191o ALA* 4.1 24.2 - - + -
5041u ASN* 2.7 14.8 + - - +
5042u VAL* 1.3 80.8 - - + +
5044u ASP* 1.3 64.2 + - - +
5046u LYS* 3.1 15.5 + - - +
5047u LEU* 3.2 16.4 + - + +
5051u TYR* 5.1 6.9 - - + +
5118u GLU* 5.7 0.7 - - + -
5120u ALA* 4.6 5.8 - - + -
5121u LEU* 4.4 27.1 - - + -
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Residues in contact with ASP5044 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5382b PRO* 4.9 4.2 - - - +
5385b ARG* 2.9 46.4 + - - +
5393b GLU* 2.8 39.0 - - - +
5418b LYS* 4.0 16.4 + - - +
5195o ASP* 4.2 7.4 - - - +
5041u ASN* 2.8 30.6 + - + +
5043u VAL* 1.3 73.4 - - - +
5045u GLU* 1.3 62.2 + - - +
5047u LEU* 3.2 14.9 + - - +
5048u GLY 4.1 0.2 + - - -
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Residues in contact with GLU5045 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5393b GLU* 5.6 0.7 - - - -
5040u VAL* 3.7 29.5 - - + +
5041u ASN 3.1 11.6 + - - +
5042u VAL* 3.6 18.2 - - - +
5044u ASP* 1.3 79.4 - - - +
5046u LYS* 1.3 56.6 + - - +
5047u LEU 3.1 0.2 - - - -
5048u GLY* 3.1 20.3 + - - -
5049u THR* 4.0 7.5 - - + +
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Residues in contact with LYS5046 (chain u).
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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5042u VAL 3.0 18.2 + - - +
5043u VAL* 3.1 8.5 + - - +
5045u GLU* 1.3 71.1 - - - +
5047u LEU* 1.3 55.2 + - - +
5048u GLY 2.9 7.0 + - - -
5049u THR* 2.9 37.3 + - + +
5051u TYR* 2.9 46.5 - - + +
5059u ASN* 2.8 20.2 - - - +
5115u THR* 2.9 20.9 - - + +
5116u GLU* 2.7 32.1 + - - -
5118u GLU* 3.9 16.0 - - + +
5121u LEU* 4.4 8.5 - - + -
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Residues in contact with LEU5047 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5382b PRO* 5.1 0.7 - - + -
5385b ARG* 3.9 30.7 - - + +
5388b SER* 3.8 22.9 - - - +
5391b SER* 3.9 18.8 - - - +
5393b GLU* 3.6 7.1 - - - +
5394b GLN* 3.4 37.4 + - - +
5043u VAL* 3.4 12.8 - - + +
5044u ASP* 3.2 18.3 + - - +
5045u GLU 3.1 1.6 - - - -
5046u LYS* 1.3 75.3 - - - +
5048u GLY* 1.3 56.5 + - - +
5049u THR 3.6 0.4 - - - -
5051u TYR* 3.7 33.0 - - + -
5052u GLY* 4.3 13.0 - - - -
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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