Contacts of the helix formed by residues 5059 - 5067 (chain b) in PDB entry 3A0B
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 VAL5059 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5030b TRP* 3.4 22.2 - - + -
5031b ALA 4.4 0.2 - - - +
5034b MET* 3.2 33.4 - - + -
5035b ALA* 3.6 21.8 - - + +
5038b GLU* 2.5 24.5 + - + +
5058b PHE* 1.3 77.1 - - + +
5060b LEU* 1.3 60.5 + - - +
5061b PRO* 3.5 0.2 - - - -
5062b PHE* 3.6 14.8 - - + +
5063b MET* 3.5 11.3 - - - +
6012b CLA 5.8 3.6 - - + -
6013b CLA 3.0 35.1 - - + +
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Residues in contact with LEU5060 (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 GLU* 2.8 22.0 + - + +
5039b LEU* 4.0 19.7 - - + +
5042b PHE* 4.3 23.1 - - + -
5052b MET* 3.5 42.3 - - + +
5057b MET* 4.0 12.8 - - + -
5059b VAL* 1.3 69.3 - - - +
5061b PRO* 1.3 64.5 - - + +
5062b PHE 3.1 1.8 - - - -
5063b MET* 2.8 39.3 + - + +
5064b ALA 3.4 3.6 + - - -
5075b TRP* 5.3 0.9 - - + -
5077b ILE* 5.2 1.1 - - + -
5090b PHE* 3.1 39.4 - - + -
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Residues in contact with PRO5061 (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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5052b MET* 3.1 17.4 - - + -
5057b MET 3.4 20.2 - - - +
5058b PHE 3.2 20.0 - - - +
5060b LEU* 1.3 95.5 - - + +
5062b PHE* 1.3 72.0 + - + +
5064b ALA* 3.4 5.4 - - - +
5065b ARG* 3.4 0.9 + - - +
5264b LEU* 3.1 53.2 - - + +
5265b PHE* 3.3 22.2 - - + -
5444b PRO* 5.6 2.0 - - + -
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Residues in contact with PHE5062 (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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5058b PHE* 2.9 41.1 - + - -
5059b VAL* 3.6 10.1 - - - +
5060b LEU 3.0 0.6 + - - -
5061b PRO* 1.3 79.1 - - + +
5063b MET* 1.3 68.5 + - - +
5065b ARG* 2.9 39.7 - - - +
5066b LEU* 3.8 1.9 + - - +
5253b MET* 4.8 0.9 - - + -
5265b PHE* 4.1 23.8 - + - -
5448b PHE* 3.1 33.9 - + - -
6012b CLA 3.4 50.0 - - + -
6013b CLA 4.3 22.1 - - + +
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Residues in contact with MET5063 (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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5035b ALA* 3.8 24.9 - - + +
5039b LEU* 5.5 0.9 - - + -
5059b VAL* 3.5 3.1 - - + +
5060b LEU* 2.8 32.9 + - + +
5062b PHE* 1.3 71.1 - - - +
5064b ALA* 1.3 68.4 + - - +
5066b LEU* 2.8 19.6 + - - +
5067b GLY 3.3 5.9 + - - -
5068b VAL* 3.0 27.4 + - + +
5090b PHE* 3.8 37.2 - - + +
5093b VAL* 3.6 20.2 - - - -
6013b CLA 2.9 42.2 - - - +
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Residues in contact with ALA5064 (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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5052b MET* 3.9 13.0 - - + -
5060b LEU 3.4 2.0 + - - -
5061b PRO 3.4 4.7 - - - +
5063b MET* 1.3 77.3 - - - +
5065b ARG* 1.3 65.5 + - - +
5067b GLY* 2.8 13.0 + - - -
5068b VAL 3.5 3.0 + - - +
5069b THR* 3.4 24.7 - - + -
5077b ILE* 4.7 1.8 - - + -
5090b PHE* 5.3 0.6 - - + -
5164b TRP* 3.8 4.7 - - + -
5175b VAL* 3.1 18.0 - - - +
5264b LEU* 3.3 31.6 - - + -
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Residues in contact with ARG5065 (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 PRO 3.4 0.8 + - - -
5062b PHE* 2.9 43.5 - - - +
5063b MET 2.9 3.2 + - - -
5064b ALA* 1.3 75.5 - - - +
5066b LEU* 1.3 79.8 + - + +
5163b MET* 2.7 12.1 - - - +
5164b TRP* 2.4 42.4 + - + +
5259b THR* 2.9 46.3 + - - +
5260b THR* 5.1 1.8 - - - +
5261b PRO* 5.3 0.2 - - + -
5264b LEU* 3.4 16.0 - - + +
5265b PHE* 4.7 5.2 - - - -
6011b CLA 2.9 49.3 + - - +
6012b CLA 3.6 27.5 + - - -
6013b CLA 5.0 0.6 + - - -
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Residues in contact with LEU5066 (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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5062b PHE 4.4 0.7 - - - +
5063b MET* 2.8 12.2 + - - +
5065b ARG* 1.3 89.6 - - + +
5067b GLY* 1.3 55.0 + - - +
5068b VAL* 4.0 1.1 - - + -
5150b PHE* 3.2 29.6 - - + -
5154b HIS* 3.1 38.5 + - + -
5155b LEU* 4.5 4.7 - - + -
5161b PRO* 3.3 5.0 - - - +
5163b MET* 4.4 5.8 - - + +
6011b CLA 3.2 39.9 - - + +
6013b CLA 2.9 33.4 - - + +
6014b CLA 4.4 18.6 - - + -
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Residues in contact with GLY5067 (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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5063b MET 3.3 0.8 + - - -
5064b ALA 2.8 13.6 + - - -
5065b ARG 3.2 0.6 + - - -
5066b LEU* 1.3 79.9 - - - +
5068b VAL* 1.3 60.0 + - - +
5069b THR* 2.9 20.3 + - - +
5085b PRO* 6.0 0.2 - - - +
5161b PRO* 3.8 22.1 - - - +
5175b VAL* 3.9 13.8 - - - +
6014b CLA 4.7 3.1 - - - -
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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