Contacts of the helix formed by residues 5009 - 5032 (chain j) 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 PRO5009 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5015e THR* 5.0 1.1 - - + +
5007j ARG 3.3 9.6 - - - +
5008j ILE* 1.4 94.1 - - + +
5010j LEU* 1.3 65.2 + - - +
5011j TRP* 3.5 26.9 - - + +
5012j ILE* 3.8 23.4 - - + -
5013j VAL* 3.0 21.0 + - - +
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Residues in contact with LEU5010 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5014e ILE* 6.0 1.3 - - - -
5015e THR* 4.6 8.4 + - - +
5008j ILE 3.8 0.8 + - - -
5009j PRO* 1.3 68.2 - - - +
5011j TRP* 1.3 54.3 + - - +
5012j ILE 2.6 16.1 + - - -
5013j VAL* 2.7 19.3 + - - +
5014j ALA* 2.8 17.6 + - - +
5041k ALA 5.7 1.6 - - - +
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Residues in contact with TRP5011 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5009j PRO* 3.5 23.7 - - + +
5010j LEU* 1.3 76.6 - - - +
5012j ILE* 1.3 83.8 - - + +
5014j ALA* 4.3 6.7 - - - -
5015j THR* 3.0 20.6 + - - +
5038k VAL* 3.5 28.7 - - + -
5041k ALA* 3.4 39.6 + - + +
5042k ALA* 3.3 31.2 + - + +
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Residues in contact with ILE5012 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5008j ILE* 4.6 12.3 - - + -
5009j PRO* 3.4 24.0 + - + +
5010j LEU 2.6 6.9 + - - -
5011j TRP* 1.3 121.8 - - + +
5013j VAL* 1.3 60.0 + - - +
5014j ALA 3.2 0.9 - - - -
5015j THR* 3.7 5.4 - - - +
5016j VAL* 2.9 41.0 + - + +
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Residues in contact with VAL5013 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014e ILE* 3.2 36.3 - - + +
5020e TRP* 3.5 34.5 - - + -
5008j ILE* 3.5 22.4 - - + +
5009j PRO 3.0 16.3 + - - +
5010j LEU* 2.7 11.7 + - - +
5012j ILE* 1.3 71.5 - - - +
5014j ALA* 1.3 72.1 + - - +
5016j VAL* 3.8 2.9 - - - +
5017j ALA* 3.2 21.5 + - + +
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Residues in contact with ALA5014 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5010j LEU* 2.8 16.0 + - + +
5011j TRP* 4.5 1.8 - - - -
5013j VAL* 1.3 76.0 - - - +
5015j THR* 1.3 59.5 + - - +
5017j ALA* 2.7 10.0 + - - +
5018j GLY* 2.6 32.8 + - - -
5130x BCR 3.3 36.6 - - + -
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Residues in contact with THR5015 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5011j TRP* 3.0 20.4 + - - +
5012j ILE* 3.7 8.0 + - - +
5014j ALA* 1.3 77.7 - - - +
5016j VAL* 1.3 60.6 + - - +
5019j MET* 2.8 45.9 + - - +
5038k VAL* 3.3 47.1 - - + +
5130x BCR 3.6 32.0 - - + +
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Residues in contact with VAL5016 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5012j ILE* 2.9 33.8 + - + +
5013j VAL* 3.8 4.3 - - - +
5014j ALA 2.8 4.4 + - - -
5015j THR* 1.3 80.6 + - - +
5017j ALA* 1.3 60.5 + - - +
5019j MET* 3.6 16.5 - - + +
5020j GLY* 2.8 25.5 + - - -
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Residues in contact with ALA5017 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5020e TRP* 6.3 2.2 - - + -
5013j VAL* 3.2 13.3 + - + +
5014j ALA* 2.7 12.3 + - - +
5016j VAL* 1.3 75.2 - - - +
5018j GLY* 1.3 54.9 + - - +
5020j GLY* 2.8 4.6 + - - +
5021j VAL* 2.8 41.0 + - + +
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Residues in contact with GLY5018 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5014j ALA 2.6 20.8 + - - -
5015j THR 3.7 1.3 - - - -
5017j ALA* 1.3 72.1 - - - +
5019j MET* 1.3 61.9 + - - +
5020j GLY 2.9 1.2 + - - -
5021j VAL* 3.0 13.6 + - - +
5022j ILE* 3.0 17.5 + - - +
5130x BCR 3.7 29.4 - - - -
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Residues in contact with MET5019 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5015j THR* 2.8 44.7 + - - +
5016j VAL* 3.6 16.4 - - + +
5018j GLY* 1.3 71.6 - - - -
5020j GLY* 1.3 63.1 + - - +
5022j ILE* 3.3 13.0 + - - +
5023j VAL* 3.1 28.5 + - + +
5130x BCR 3.2 45.9 - - + +
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Residues in contact with GLY5020 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5016j VAL 2.8 12.8 + - - -
5017j ALA* 2.8 11.9 + - - -
5019j MET* 1.3 77.0 - - - +
5021j VAL* 1.3 56.8 + - - -
5023j VAL* 2.9 29.2 + - - +
5024j ILE* 3.3 6.9 + - - +
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Residues in contact with VAL5021 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 3.5 35.2 - - + -
5017j ALA* 2.8 20.7 + - + +
5018j GLY* 3.8 6.3 - - - +
5020j GLY* 1.3 68.4 - - - +
5022j ILE* 1.3 61.4 + - + +
5023j VAL 3.0 1.8 - - - -
5024j ILE* 3.6 13.2 - - + -
5025j VAL* 2.9 41.7 + - + +
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Residues in contact with ILE5022 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5479c UNK 5.8 0.3 - - - +
5357d BCR 6.2 3.1 - - + -
5358d SQD 4.2 25.8 - - + -
5018j GLY* 3.0 17.4 + - - +
5019j MET* 3.4 15.9 - - - +
5020j GLY 3.1 0.4 - - - -
5021j VAL* 1.3 80.5 - - + +
5023j VAL* 1.3 58.4 + - + +
5025j VAL* 4.0 5.8 - - + +
5026j GLY* 3.1 21.3 + - - -
5130x BCR 5.3 0.7 - - + -
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Residues in contact with VAL5023 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5019j MET* 3.1 18.6 - - + +
5020j GLY* 2.9 11.8 + - - +
5022j ILE* 1.3 79.5 - - + +
5024j ILE* 1.3 57.5 + - - +
5026j GLY* 2.8 3.2 + - - -
5027j LEU* 2.7 35.8 + - + +
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Residues in contact with ILE5024 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 6.0 0.2 - - + -
5031e PHE* 4.2 12.6 - - + -
5034f LEU* 3.2 56.8 - - + +
5038f ALA* 4.7 6.1 - - + -
5020j GLY 3.3 3.6 + - - +
5021j VAL* 3.2 29.4 - - + +
5023j VAL* 1.3 79.8 - - - +
5025j VAL* 1.3 76.8 + - + +
5026j GLY 3.1 0.2 - - - -
5027j LEU* 3.2 9.7 + - + +
5028j PHE* 3.1 45.9 + - + -
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Residues in contact with VAL5025 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 3.4 47.3 - - + -
5359d MGE 5.6 8.3 - - + -
5021j VAL* 2.9 23.9 + - + +
5022j ILE* 4.0 5.2 - - + +
5024j ILE* 1.3 85.0 - - + +
5026j GLY* 1.3 59.0 + - - +
5028j PHE* 3.7 17.2 - - + +
5029j PHE* 3.3 33.7 + - + -
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Residues in contact with GLY5026 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5479c UNK 3.5 27.0 - - - +
5022j ILE 3.1 14.1 + - - -
5023j VAL* 2.8 8.8 + - - -
5025j VAL* 1.3 76.4 - - - +
5027j LEU* 1.3 64.4 + - - +
5028j PHE 3.0 1.6 - - - -
5029j PHE* 3.0 4.0 + - - +
5030j TYR* 2.9 21.5 + - - +
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Residues in contact with LEU5027 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5031e PHE* 6.0 0.2 - - + -
5035e TRP* 5.2 2.5 - - + -
5038f ALA* 3.5 44.2 - - + +
5041f GLN* 3.9 13.0 - - + +
5042f PHE* 3.7 28.0 - - + -
5023j VAL* 2.7 17.2 + - + +
5024j ILE* 3.5 13.5 - - + +
5026j GLY* 1.3 71.4 - - - +
5028j PHE* 1.3 61.3 + - + +
5030j TYR* 3.4 14.5 + - + +
5031j GLY 3.1 16.6 + - - -
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Residues in contact with PHE5028 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 4.0 14.1 - - + -
5359d MGE 3.9 43.9 + - + +
5034f LEU* 3.8 23.6 - - + -
5037f ILE* 3.1 35.9 - - + -
5038f ALA* 3.7 16.4 - - + -
5041f GLN* 3.0 21.5 + - + -
5024j ILE* 3.1 41.8 + - + +
5025j VAL* 3.7 19.7 - - + +
5027j LEU* 1.3 78.0 - - + +
5029j PHE* 1.3 55.7 + - + +
5031j GLY* 2.7 26.3 + - - -
5032j ALA* 3.4 4.0 + - - +
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Residues in contact with PHE5029 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5479c UNK 3.8 18.3 - - + +
5508c DGD 3.8 37.9 - - + -
5509c DGD 3.4 76.7 - - + -
5359d MGE 4.7 22.0 - - + -
5025j VAL* 3.3 26.3 + - + +
5026j GLY 3.0 8.8 + - - +
5028j PHE* 1.3 79.3 - - - +
5030j TYR* 1.3 61.9 + - - +
5032j ALA* 3.5 8.0 - - - +
5033j TYR* 3.3 23.5 - - - -
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Residues in contact with TYR5030 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5479c UNK 3.7 41.0 - - + +
5041f GLN* 4.3 17.3 - - + -
5042f PHE* 4.8 13.4 - + - -
5026j GLY 2.9 11.6 + - - +
5027j LEU* 3.6 24.0 - - + +
5029j PHE* 1.3 73.9 - - - +
5031j GLY* 1.3 63.8 + - - +
5032j ALA 2.7 8.6 + - - -
5033j TYR* 2.7 27.6 + - + +
5034j ALA* 3.6 26.2 - - + +
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Residues in contact with GLY5031 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5359d MGE 2.5 21.3 + - - -
5041f GLN* 3.3 22.4 - - - -
5027j LEU 3.1 4.8 + - - -
5028j PHE 2.7 11.9 + - - -
5030j TYR* 1.3 87.3 - - - +
5032j ALA* 1.3 60.1 + - - -
5033j TYR 3.0 8.9 - - - +
5035j GLY* 3.0 13.3 + - - -
5038j SER 4.8 0.2 + - - -
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Residues in contact with ALA5032 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5509c DGD 3.0 65.3 + - - +
5359d MGE 3.7 13.2 + - - +
5028j PHE 3.4 4.6 + - - +
5029j PHE* 3.5 16.6 - - - +
5030j TYR 2.7 5.1 + - - -
5031j GLY* 1.3 74.0 - - - +
5033j TYR* 1.3 62.7 + - + +
5037j GLY 3.7 1.9 - - - +
5038j SER* 3.4 15.6 - - - -
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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