Contacts of the helix formed by residues 5159 - 5166 (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 LEU5159 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5117a PHE* 5.1 6.7 - - + -
5120a LEU* 3.7 17.3 - - + -
5155a PHE* 2.8 43.4 + - + +
5156a ALA 3.7 0.4 + - - -
5158a PHE* 1.3 75.5 - - - +
5160a ILE* 1.3 65.0 + - + +
5162a PRO* 3.1 10.5 - - - +
5163a ILE* 3.0 48.6 + - + +
5168a PHE* 4.2 14.6 - - + -
5507c DGD 3.9 40.2 - - + -
5201i MGE 4.4 10.8 - - + -
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Residues in contact with ILE5160 (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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5155a PHE* 3.0 13.4 + - + +
5156a ALA* 3.6 15.3 - - - +
5159a LEU* 1.3 76.9 - - + +
5161a TYR* 1.3 67.4 + - - +
5163a ILE* 3.1 10.1 + - + +
5164a GLY* 3.1 19.4 + - - -
5291a SER* 3.7 34.3 - - - +
5294a ALA* 4.1 4.6 - - + +
5295a PHE* 4.6 8.1 - - + -
5431c PHE* 3.2 38.8 - - + -
5507c DGD 3.6 33.0 - - + -
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Residues in contact with TYR5161 (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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5156a ALA 2.8 19.0 + - - +
5157a VAL* 4.5 5.8 - - - +
5160a ILE* 1.3 73.3 - - - +
5162a PRO* 1.3 63.0 - - + +
5164a GLY* 3.4 1.2 + - - -
5165a GLN* 3.0 51.0 + - + +
5170a ASP* 4.4 7.2 - - + -
5171a GLY 4.0 14.1 - - - -
5182a PHE* 3.8 24.2 - + - -
5186a PHE* 3.3 32.0 - + - -
5189a GLU* 4.2 10.4 + - - -
5190a HIS* 2.8 31.3 + - - -
5290a ILE* 4.0 12.1 + - + -
5293a MET 3.8 10.8 - - - -
5294a ALA* 3.7 20.7 - - + +
5565a OEC 5.1 0.4 - - - -
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Residues in contact with PRO5162 (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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5091a LEU* 3.6 3.3 - - + +
5112a TYR* 5.9 0.7 - - + +
5156a ALA 4.1 0.2 - - - +
5157a VAL 4.3 0.7 - - - +
5158a PHE 3.7 17.3 - - - +
5159a LEU* 3.1 21.8 - - - +
5161a TYR* 1.3 92.2 - - + +
5163a ILE* 1.3 55.8 + - - +
5164a GLY 2.9 1.8 - - - -
5165a GLN* 4.3 2.7 - - + +
5166a GLY* 2.7 33.1 + - - -
5167a SER 3.3 25.1 + - - +
5168a PHE* 3.7 22.4 - - + -
5170a ASP 3.8 17.9 - - - +
5171a GLY* 4.1 7.0 - - - -
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Residues in contact with ILE5163 (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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5091a LEU* 3.9 14.3 - - + +
5159a LEU* 3.0 42.4 - - + +
5160a ILE* 3.1 11.6 + - + +
5162a PRO* 1.3 77.8 - - + +
5164a GLY* 1.3 60.6 + - - +
5166a GLY 4.0 1.9 + - - -
5168a PHE* 5.5 0.2 - - + -
5295a PHE* 5.3 8.3 - - + -
5288c CYS* 4.3 9.9 - - - -
5291c TRP* 4.4 0.2 - - - -
5292c PHE* 3.2 32.9 - - + -
5507c DGD 3.1 64.2 - - + +
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Residues in contact with GLY5164 (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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5160a ILE 3.1 11.2 + - - -
5161a TYR 3.8 1.6 - - - -
5162a PRO 2.9 0.8 - - - -
5163a ILE* 1.3 80.2 - - - +
5165a GLN* 1.3 62.8 + - - +
5166a GLY* 3.2 1.6 + - - -
5294a ALA 3.4 23.1 - - - -
5295a PHE* 4.1 9.4 - - - -
5291c TRP* 3.3 29.1 + - - -
5292c PHE* 5.3 0.9 - - - -
5307c PRO* 6.0 1.0 - - - +
5358c PHE* 5.4 1.6 - - - -
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Residues in contact with GLN5165 (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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5161a TYR* 3.0 55.7 + - + +
5162a PRO* 4.1 2.0 - - + +
5164a GLY* 1.3 75.5 - - - +
5166a GLY* 1.3 58.1 + - - +
5167a SER 3.5 0.9 - - - +
5170a ASP* 3.7 21.3 - - + +
5189a GLU* 5.2 1.0 + - - -
5190a HIS* 4.1 1.2 + - - -
5294a ALA 3.6 11.7 - - - +
5296a ASN* 3.3 29.6 + - - +
5344a ALA* 3.3 26.9 + - - +
5565a OEC 4.2 4.8 - - - -
5357c ARG* 2.8 21.0 + - - +
5358c PHE* 3.4 15.4 - - - -
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Residues in contact with GLY5166 (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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5090a GLY* 3.6 2.8 - - - -
5091a LEU* 3.3 33.3 + - - +
5162a PRO 2.7 13.7 + - - -
5163a ILE 4.0 1.5 + - - -
5164a GLY 3.2 4.7 + - - -
5165a GLN* 1.3 75.4 - - - +
5167a SER* 1.3 60.7 + - - -
5292c PHE* 5.7 3.6 - - - -
5357c ARG* 4.1 13.3 - - - +
5358c PHE* 3.8 15.0 - - - -
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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