Contacts of the helix formed by residues 5142 - 5147 (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 TRP5142 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5140a ARG* 3.0 29.6 - - - -
5141a PRO* 1.3 91.3 - - + +
5143a ILE* 1.3 65.2 + - - +
5144a CYS* 3.1 6.6 - - - +
5145a VAL* 2.8 23.0 + - + +
5146a ALA* 3.3 9.2 + - - +
5567a LHG 3.3 66.3 - - + +
5442c LEU 4.8 1.8 - - - -
5443c TRP* 2.9 67.6 + + + -
5447c ARG* 3.3 32.1 - - + +
5456c GLU* 5.5 1.3 - - + -
5220d ASN* 3.3 27.4 + - - +
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Residues in contact with ILE5143 (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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5130a GLN* 3.8 19.1 - - - +
5134a SER* 6.1 0.7 - - - -
5139a MET* 4.3 15.7 - - + -
5141a PRO 2.4 23.8 + - - +
5142a TRP* 1.3 66.4 - - - +
5144a CYS* 1.3 58.8 + - - +
5146a ALA* 2.9 22.0 + - - +
5147a TYR* 3.3 9.5 + - - +
5561a PHO 4.7 2.9 - - + +
5216d ALA* 3.6 18.6 - - + +
5217d THR* 3.7 23.1 - - + +
5220d ASN* 3.1 21.7 - - + +
5252d PHE* 3.7 33.7 - - + -
5253d TRP* 3.9 25.1 - - + +
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Residues in contact with CYS5144 (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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5127a MET* 3.2 45.9 - - + +
5130a GLN* 3.5 29.4 + - - +
5131a TRP* 4.3 15.9 - - - -
5141a PRO* 5.5 0.9 - - - -
5142a TRP* 3.1 9.2 - - - -
5143a ILE* 1.3 80.8 - - - +
5145a VAL* 1.3 73.0 + - - +
5146a ALA 3.3 0.4 - - - -
5147a TYR* 3.7 2.5 + - - +
5148a SER 3.5 13.2 + - - -
5442c LEU* 4.6 17.5 - - - -
5446c GLY* 6.6 0.4 - - - -
5495c CLA 5.7 2.5 - - - -
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Residues in contact with VAL5145 (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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5142a TRP* 2.8 19.1 + - + +
5144a CYS* 1.3 83.9 - - - +
5146a ALA* 1.3 62.4 + - - +
5147a TYR 3.3 0.2 - - - -
5148a SER* 2.8 23.8 + - - +
5284a TRP* 3.5 29.2 - - + -
5567a LHG 4.0 16.8 - - + -
5439c VAL* 4.4 9.4 - - + +
5442c LEU* 3.7 33.7 - - + -
5443c TRP* 4.0 23.1 - - + +
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Residues in contact with ALA5146 (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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5142a TRP 3.3 3.4 + - - +
5143a ILE 2.9 11.0 + - - +
5145a VAL* 1.3 76.7 - - - +
5147a TYR* 1.3 60.0 + - - +
5148a SER 3.1 3.0 + - - -
5149a ALA* 3.4 19.1 + - - +
5150a PRO* 3.6 3.3 - - - +
5280a VAL* 3.6 28.4 - - + +
5561a PHO 3.7 19.2 - - + +
5567a LHG 4.2 9.4 - - + -
5212d ALA 4.5 1.3 - - - +
5216d ALA* 3.9 22.2 - - + -
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Residues in contact with TYR5147 (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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5123a ALA* 3.4 29.2 + - - +
5126a TYR* 3.4 17.9 - + - -
5127a MET* 3.7 26.5 - - + -
5130a GLN* 3.4 20.6 - - - +
5143a ILE 3.3 3.7 + - - +
5144a CYS 4.0 4.3 - - - +
5145a VAL 3.3 0.4 - - - -
5146a ALA* 1.3 75.3 - - - +
5148a SER* 1.3 57.9 + - - +
5149a ALA 3.0 6.7 + - - -
5150a PRO* 3.3 15.1 - - + +
5151a LEU* 3.4 15.7 + - + +
5558a CLA 3.6 22.8 - - + +
5561a PHO 3.1 79.5 + + + +
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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