Contacts of the helix formed by residues 5166 - 5170 (chain d) 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 SER5166 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5082d ALA 4.6 1.1 - - - -
5083d ASN* 3.1 32.3 + - - -
5086d GLY* 3.3 13.5 - - - -
5087d HIS* 3.1 15.9 - - - -
5161d PRO* 3.6 20.4 - - - +
5164d GLN* 4.8 0.2 - - - +
5165d SER* 1.3 81.9 + - - +
5167d TRP* 1.3 63.7 + - - +
5168d PHE* 2.9 29.7 + - - +
5169d PHE* 4.0 7.9 + - - +
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Residues in contact with TRP5167 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5080d THR* 3.5 7.4 - - - +
5081d PRO* 3.7 24.4 - - + +
5085d MET* 5.8 0.4 - - + -
5086d GLY 3.1 22.4 + - - -
5087d HIS* 2.8 24.2 - + + -
5088d SER* 2.7 28.2 + - - -
5089d LEU* 5.2 6.7 - - + -
5111d TRP* 3.3 35.9 - + + -
5112d THR* 4.1 13.2 - - + -
5116d LEU* 6.0 4.0 - - + -
5157d PHE 4.0 6.1 - - - -
5158d LEU* 3.9 37.5 - - + -
5161d PRO* 3.9 13.5 - - + -
5162d LEU* 3.8 24.5 - - + -
5166d SER* 1.3 74.7 - - - +
5168d PHE* 1.3 54.5 + - - +
5169d PHE 2.7 18.1 + - - -
5170d ALA* 2.8 20.4 + - - +
5208h DGD 5.1 10.8 - - + -
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Residues in contact with PHE5168 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5060d THR 3.9 9.2 - - - -
5061d HIS* 3.4 44.2 + + - -
5080d THR* 3.2 20.7 + - - +
5081d PRO* 3.4 24.0 + - - +
5082d ALA 4.3 0.2 - - - -
5083d ASN* 3.9 20.4 - - + +
5166d SER* 2.9 16.4 + - - +
5167d TRP* 1.3 75.6 - - - +
5169d PHE* 1.3 80.9 + + + +
5170d ALA 3.4 2.5 + - - +
5180d ARG* 5.0 6.1 + - - -
5333d ASP* 3.4 29.6 - - - -
5335d PRO* 4.2 15.3 - - + -
5336d HIS* 3.9 17.5 - + - -
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Residues in contact with PHE5169 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5272b ARG* 6.3 0.2 - - - -
5362b PHE* 4.0 34.3 - + + -
5083d ASN* 3.6 12.3 - - - -
5160d TYR* 3.3 29.4 - - + +
5161d PRO* 4.4 4.0 - - + -
5164d GLN* 4.5 14.1 - - + -
5165d SER* 3.0 28.9 - - - -
5166d SER* 4.0 8.0 + - - +
5167d TRP 2.7 6.7 + - - -
5168d PHE* 1.3 95.1 - + - +
5170d ALA* 1.3 59.4 + - - -
5180d ARG* 4.3 20.5 + - - +
5181d PHE* 3.5 7.0 - - - -
5184d PHE* 4.8 4.9 - + + -
5334d GLN* 3.8 28.5 - - + -
5336d HIS* 4.0 15.0 - + - -
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Residues in contact with ALA5170 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5080d THR* 3.3 9.9 - - - +
5111d TRP* 3.5 26.0 - - + -
5157d PHE 4.5 1.8 - - - +
5161d PRO* 3.1 28.7 - - + +
5167d TRP 2.8 17.3 + - - +
5168d PHE 4.2 1.9 - - - +
5169d PHE* 1.3 76.7 - - - +
5171d PRO* 1.3 77.3 - - + +
5172d SER* 3.6 2.1 + - - -
5180d ARG* 5.0 3.5 + - - -
5181d PHE* 3.8 3.9 - - - -
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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