Contacts of the helix formed by residues 5062 - 5069 (chain b) 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 VAL5062 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5033b TRP* 3.7 22.2 - - + -
5034b ALA 5.0 0.2 - - - +
5037b MET* 3.7 27.6 - - + -
5038b ALA* 4.5 9.9 - - - +
5041b GLU* 3.1 8.8 + - - +
5061b PHE* 1.3 83.6 - - + +
5063b LEU* 1.3 69.3 + - - +
5064b PRO 3.2 2.5 - - - -
5065b PHE* 3.0 14.6 + - - -
5066b MET* 3.4 12.7 + - + +
5514b CLA 5.3 0.9 - - + -
5515b CLA 3.2 53.1 - - - +
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Residues in contact with LEU5063 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5038b ALA 5.9 0.4 - - - +
5041b GLU* 2.9 21.4 + - + +
5042b LEU* 4.4 14.1 - - + -
5045b PHE* 3.7 38.1 - - + -
5055b MET* 3.7 26.7 - - + -
5060b MET* 4.1 9.9 - - + -
5062b VAL* 1.3 75.8 - - - +
5064b PRO* 1.3 68.5 - - + +
5066b MET* 3.0 24.3 + - + +
5067b ALA* 3.2 10.9 + - - +
5078b TRP* 5.4 0.2 - - + -
5080b ILE* 4.1 5.6 - - + -
5093b PHE* 3.5 39.0 - - + -
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Residues in contact with PRO5064 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5055b MET* 3.8 14.6 - - - -
5060b MET* 3.7 17.5 - - + +
5061b PHE* 3.2 26.2 - - + +
5062b VAL 3.3 0.7 - - - -
5063b LEU* 1.3 94.8 - - + +
5065b PHE* 1.3 62.6 + - + +
5067b ALA* 3.2 5.5 + - + +
5068b ARG* 3.2 22.7 + - - +
5267b LEU* 3.3 36.9 - - + +
5268b PHE* 4.0 17.4 - - + -
5447b PRO* 5.5 1.1 - - + -
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Residues in contact with PHE5065 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5061b PHE* 3.1 30.7 - + - -
5062b VAL* 3.0 9.9 + - - +
5064b PRO* 1.3 79.5 - - + +
5066b MET* 1.3 60.9 + - - +
5067b ALA 3.6 0.2 + - - -
5068b ARG* 3.4 33.3 + - - +
5069b LEU* 4.0 4.5 + - - +
5256b MET* 4.4 3.1 - - + -
5268b PHE* 3.5 32.5 - + - -
5451b PHE* 3.7 27.8 - + - -
5514b CLA 3.5 59.5 - + + -
5515b CLA 3.6 37.3 - - + +
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Residues in contact with MET5066 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5038b ALA* 4.2 14.4 - - + -
5041b GLU* 5.2 0.2 - - - +
5042b LEU* 6.1 0.7 - - + -
5062b VAL* 3.4 30.9 + - + +
5063b LEU* 3.0 18.1 + - + +
5065b PHE* 1.3 76.2 - - - +
5067b ALA* 1.3 62.4 + - - +
5069b LEU* 3.8 3.4 + - - +
5070b GLY 3.6 2.8 + - - -
5071b VAL* 3.0 37.4 + - + +
5093b PHE* 3.8 36.6 - - + +
5096b VAL* 3.7 35.0 - - + -
5515b CLA 3.3 31.4 - - + +
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Residues in contact with ALA5067 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5055b MET* 4.3 9.4 - - + -
5063b LEU 3.2 10.0 + - - +
5064b PRO* 3.4 6.7 - - + +
5065b PHE 3.2 0.2 - - - -
5066b MET* 1.3 78.7 - - - +
5068b ARG* 1.3 66.7 + - - +
5070b GLY 3.1 11.6 + - - -
5071b VAL 3.3 12.5 + - - +
5072b THR* 3.9 5.1 - - + +
5080b ILE* 4.9 4.3 - - + -
5093b PHE* 5.2 1.3 - - + -
5167b TRP* 4.1 6.2 - - + -
5178b VAL* 3.6 15.9 - - - +
5267b LEU* 3.4 29.4 - - + -
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Residues in contact with ARG5068 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5064b PRO 3.2 11.4 + - - +
5065b PHE* 3.4 23.4 + - - +
5067b ALA* 1.3 80.1 - - - +
5069b LEU* 1.3 61.2 + - + +
5166b MET* 3.1 12.9 - - + +
5167b TRP* 2.8 40.2 + - + +
5256b MET* 6.1 1.0 - - - +
5261b ALA 5.7 0.2 - - - +
5262b THR* 3.0 49.8 + - - +
5264b PRO* 4.5 5.4 - - + -
5267b LEU* 3.9 9.6 - - + +
5268b PHE* 4.7 5.1 - - + -
5513b CLA 3.2 30.7 + - - +
5514b CLA 2.9 31.0 - - - -
5515b CLA 2.8 28.3 + - - -
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Residues in contact with LEU5069 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5065b PHE 4.0 6.9 + - - +
5066b MET 3.8 1.9 + - - +
5067b ALA 3.1 1.2 - - - -
5068b ARG* 1.3 83.1 - - + +
5070b GLY* 1.3 57.2 + - - +
5071b VAL 3.8 1.3 - - - -
5153b PHE* 4.2 12.1 - - + -
5157b HIS* 3.0 27.9 + - + -
5158b LEU* 4.8 1.8 - - + -
5164b PRO* 3.1 7.3 - - - +
5165b GLY 3.9 6.7 - - - +
5513b CLA 3.2 50.9 - - + +
5515b CLA 3.6 39.5 - - + +
5516b CLA 3.4 35.6 - - + +
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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