Contacts of the helix formed by residues 5003 - 5023 (chain t) 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 THR5003 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5053a ILE* 6.5 0.4 - - - -
5071a LEU* 3.6 22.8 - - - +
5072a LEU* 3.8 22.4 - - + +
5075a ASN* 2.5 52.3 - - + +
5001t MET 2.3 23.4 + - - +
5002t GLU 1.3 67.4 - - - -
5004t ILE* 1.3 84.4 + - - +
5005t THR 3.1 1.6 - - - -
5006t TYR* 3.0 11.3 + - - +
5007t VAL* 3.0 19.0 + - - +
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Residues in contact with ILE5004 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 5.4 15.3 - - + -
5072a LEU* 5.5 2.0 - - + -
1046t BCR 3.8 36.8 - - + +
5001t MET* 2.4 39.9 - - - +
5003t THR* 1.3 93.4 - - - +
5005t THR* 1.3 59.5 + - - +
5007t VAL* 3.7 6.3 + - - +
5008t PHE* 3.4 20.9 + - + +
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Residues in contact with THR5005 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032l SER* 4.8 2.0 - - - +
5036l PHE* 3.5 34.5 - - + -
5008m PHE* 4.5 7.1 - - - +
5011m THR* 3.5 32.6 - - + +
5001t MET* 4.6 2.3 - - - -
5002t GLU 3.9 4.2 + - - +
5003t THR 3.1 0.4 - - - -
5004t ILE* 1.3 78.8 - - - +
5006t TYR* 1.3 63.5 + - + +
5008t PHE* 3.2 7.6 + - + +
5009t ILE* 3.0 42.8 + - + +
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Residues in contact with TYR5006 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5071a LEU* 3.0 34.5 - - + -
5075a ASN 3.6 3.7 + - - -
5076a ASN* 2.8 38.6 + - - -
5077a ILE* 3.2 25.0 - - + +
5029l LEU* 4.0 12.7 - - + +
5032l SER* 3.4 20.2 - - - -
5033l SER* 2.6 37.4 + - - -
5036l PHE* 3.9 18.5 - + - +
5002t GLU* 2.3 27.9 - - + +
5003t THR 3.0 2.5 + - - +
5005t THR* 1.3 79.6 - - + +
5007t VAL* 1.3 60.4 + - - +
5009t ILE 3.9 0.2 + - - -
5010t PHE* 3.2 24.3 + - - +
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Residues in contact with VAL5007 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5053a ILE* 3.5 43.1 - - + -
5071a LEU* 4.4 9.9 - - + -
1046t BCR 5.4 13.9 - - + -
5003t THR* 3.0 16.4 + - - +
5004t ILE* 4.3 5.4 - - - +
5006t TYR* 1.3 76.9 - - - +
5008t PHE* 1.3 58.3 + - + +
5010t PHE* 3.7 6.4 - - - +
5011t ALA* 3.1 28.4 + - + +
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Residues in contact with PHE5008 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5015m VAL* 6.1 5.4 - - + -
1046t BCR 3.8 54.3 - - + -
5004t ILE* 3.4 15.3 + - + +
5005t THR* 3.2 12.9 + - + +
5007t VAL* 1.3 74.7 - - - +
5009t ILE* 1.3 62.6 + - + +
5010t PHE 2.6 14.9 + - - -
5011t ALA* 2.9 13.2 + - - +
5012t CYS* 3.3 28.2 + - - -
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Residues in contact with ILE5009 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5025l LEU* 3.0 60.6 - - + +
5028l ALA* 3.8 15.9 - - + -
5029l LEU* 3.4 49.6 - - + +
5032l SER* 3.9 17.0 - - - +
5011m THR* 4.1 4.7 - - + +
5015m VAL* 4.7 11.0 - - + -
5005t THR* 3.0 26.7 + - + +
5008t PHE* 1.3 85.2 - - + +
5010t PHE* 1.3 58.0 + - - +
5012t CYS* 5.0 1.3 - - - -
5013t ILE* 3.3 3.6 + - - +
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Residues in contact with PHE5010 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5048a PHE* 5.2 2.5 - + - -
5049a VAL* 4.0 37.7 - - + -
5052a PHE* 4.5 28.3 - + - -
5077a ILE* 6.1 1.6 - - + -
6005d CLA 4.3 15.7 - - + -
6042d PQ9 6.0 0.7 - - + -
6062d MGE 4.2 27.1 - - + -
5029l LEU* 4.5 12.3 - - + +
5006t TYR 3.2 19.1 + - - +
5007t VAL* 3.7 7.9 - - - +
5008t PHE 2.6 5.3 + - - -
5009t ILE* 1.3 72.9 - - - +
5011t ALA* 1.3 56.2 + - - +
5012t CYS 2.7 5.4 + - - -
5013t ILE* 2.6 37.5 + - + +
5014t ILE* 3.3 19.3 + - + -
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Residues in contact with ALA5011 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046t BCR 3.6 47.1 - - + +
5007t VAL* 3.1 17.8 + - + +
5008t PHE* 2.9 6.7 + - - +
5010t PHE* 1.3 81.2 - - - +
5012t CYS* 1.3 57.6 + - - +
5013t ILE 3.5 0.2 - - - -
5014t ILE* 3.7 11.1 - - - +
5015t ALA* 3.5 13.7 + - - +
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Residues in contact with CYS5012 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5025l LEU* 3.2 32.7 - - + +
1046t BCR 3.6 23.8 - - - -
5008t PHE* 3.3 35.4 + - - +
5009t ILE* 5.0 0.4 - - - -
5010t PHE 2.7 2.8 + - - -
5011t ALA* 1.3 74.4 - - - +
5013t ILE* 1.3 54.9 + - - +
5014t ILE 3.0 5.4 - - - -
5015t ALA* 3.5 8.9 - - + +
5016t LEU* 2.7 35.7 + - - +
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Residues in contact with ILE5013 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6062d MGE 3.1 35.4 - - + -
5022l LEU* 4.9 8.7 - - + +
5025l LEU* 3.1 27.8 - - + -
5026l VAL* 3.5 35.7 - - + +
5029l LEU* 5.1 3.6 - - + -
5009t ILE 3.3 9.9 - - - +
5010t PHE* 2.6 14.4 + - + +
5012t CYS* 1.3 78.1 - - - +
5014t ILE* 1.3 50.7 + - + +
5016t LEU* 3.9 6.2 - - + -
5017t PHE* 2.7 63.9 + - + -
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Residues in contact with ILE5014 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B BCR 4.6 3.8 - - + -
1046t BCR 3.3 73.6 - - + +
5010t PHE* 3.3 21.4 + - + +
5011t ALA* 3.7 12.3 - - + +
5012t CYS 3.0 0.2 - - - -
5013t ILE* 1.3 79.5 - - + +
5015t ALA* 1.3 65.7 + - - +
5017t PHE* 3.3 9.6 + - + +
5018t PHE* 3.0 22.3 + - - +
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Residues in contact with ALA5015 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046t BCR 4.7 12.3 - - + -
5011t ALA 3.5 11.9 + - - +
5012t CYS* 3.2 12.3 + - + +
5014t ILE* 1.3 79.5 - - - +
5016t LEU* 1.3 51.5 + - - +
5017t PHE 2.8 14.6 + - - -
5018t PHE* 2.9 8.6 + - - +
5019t PHE* 2.8 41.6 + - + +
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Residues in contact with LEU5016 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6062d MGE 4.4 4.6 - - + +
5018l TYR* 3.7 25.9 - - + +
5021l LEU* 3.4 37.5 - - + +
5022l LEU* 3.7 42.0 - - + -
5025l LEU* 5.3 7.4 - - + -
5012t CYS 2.7 21.4 + - - +
5013t ILE* 4.0 10.5 - - + +
5015t ALA* 1.3 71.3 - - - +
5017t PHE* 1.3 65.1 + - + +
5019t PHE* 4.1 10.1 - - + +
5020t ALA* 3.6 16.8 + - - +
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Residues in contact with PHE5017 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6003a CLA 3.8 19.3 - - + -
6005d CLA 5.5 2.5 - - + -
6062d MGE 3.2 70.7 - - + -
5022l LEU* 4.0 16.8 - - + -
1046t BCR 4.2 8.7 - - + -
5013t ILE* 2.7 45.2 + - + +
5014t ILE* 3.4 17.9 - - + +
5015t ALA 2.8 1.2 + - - -
5016t LEU* 1.3 80.8 - - + +
5018t PHE* 1.3 62.5 + - - +
5019t PHE 3.1 0.9 - - - -
5020t ALA 3.2 5.5 + - - -
5021t ILE* 2.7 40.8 - - + +
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Residues in contact with PHE5018 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 3.4 38.1 - + - -
109B LEU* 4.6 6.1 - - + -
112B CYS* 3.6 21.3 - - - -
1045B BCR 6.3 1.1 - - + -
1048B BCR 5.1 9.2 - - + -
1046t BCR 3.5 40.7 - - + +
5014t ILE 3.0 7.6 + - - +
5015t ALA* 2.9 9.4 + - - +
5017t PHE* 1.3 80.8 - - - +
5019t PHE* 1.3 94.4 + + - +
5021t ILE* 3.2 0.4 + - - -
5022t PHE* 3.1 61.3 + + + +
5023t PHE* 4.2 16.8 - + - -
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Residues in contact with PHE5019 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 5.3 6.1 - + - -
1022B CLA 4.4 28.5 - - + -
1045B BCR 4.6 17.9 - - + -
5018l TYR* 3.0 37.7 - + + +
5015t ALA* 2.8 26.3 + - + +
5016t LEU* 4.3 6.3 - - + +
5018t PHE* 1.3 106.6 - + - +
5020t ALA* 1.3 56.2 + - - +
5021t ILE 3.4 0.2 - - - -
5023t PHE* 2.7 52.2 + + - +
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Residues in contact with ALA5020 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5259d ILE* 2.8 22.3 - - - +
6062d MGE 3.4 34.1 - - + +
5018l TYR* 3.6 22.7 - - + -
5016t LEU* 3.6 8.6 + - + +
5017t PHE 3.2 4.3 + - - +
5019t PHE* 1.3 77.4 - - - +
5021t ILE* 1.3 61.5 + - - +
5022t PHE 3.6 0.4 - - - -
5023t PHE 4.6 0.9 - - - +
5024t ARG* 3.9 16.7 - - - +
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Residues in contact with ILE5021 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5027a ARG* 4.0 0.5 - - - -
5028a LEU* 4.5 11.2 - - + -
5258d GLY* 3.9 17.9 - - - +
5259d ILE* 3.3 28.3 - - + -
6062d MGE 4.1 25.1 - - + -
1046t BCR 4.0 24.9 - - + -
5017t PHE* 2.7 34.8 - - + +
5018t PHE* 3.2 5.0 + - - +
5020t ALA* 1.3 79.5 - - - +
5022t PHE* 1.3 87.9 + - + +
5024t ARG* 3.4 24.6 + - - +
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Residues in contact with PHE5022 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B BCR 3.4 38.4 - - + -
5027a ARG* 4.1 33.2 + - + +
5028a LEU* 5.1 7.0 - - + -
1046t BCR 3.5 46.2 - - + -
5018t PHE* 3.1 48.0 + + + +
5021t ILE* 1.3 109.1 - - + +
5023t PHE* 1.3 69.4 + - + +
5024t ARG* 3.2 12.5 + - - +
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Residues in contact with PHE5023 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B CYS* 5.6 5.6 - - - -
1045B BCR 4.6 22.0 - - + -
1048B BCR 6.6 0.2 - - + -
5014l ARG* 3.5 39.4 + - - +
5018l TYR* 4.3 12.2 + - - +
5018t PHE* 4.2 20.4 - + - -
5019t PHE* 2.7 43.4 + + - +
5020t ALA* 4.9 0.5 - - - -
5022t PHE* 1.3 89.6 - - + +
5024t ARG* 1.3 62.4 + - - +
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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