Contacts of the helix formed by residues 5134 - 5152 (chain v) 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 THR5134 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5121v LEU* 6.3 0.2 - - - -
5132v ASN 4.7 1.6 - - - -
5133v LEU* 1.3 74.5 - - - +
5135v GLU* 1.3 70.1 + - - +
5136v LYS* 3.4 24.4 + - + +
5137v ASP* 2.6 21.8 + - - +
5138v LEU* 2.9 32.3 + - - +
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Residues in contact with GLU5135 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5099v VAL* 4.8 7.2 - - - +
5103v LYS* 3.5 33.7 + - - -
5134v THR* 1.3 80.4 + - - +
5136v LYS* 1.3 66.3 + - - +
5138v LEU* 4.1 14.1 - - - +
5139v VAL* 2.9 45.3 + - + +
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Residues in contact with LYS5136 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5051v GLN* 5.3 12.3 - - - +
5054v GLU* 4.9 16.0 + - - +
5134v THR* 3.3 13.9 - - + +
5135v GLU* 1.3 77.3 - - - +
5137v ASP* 1.3 61.7 + - - +
5139v VAL* 2.7 24.4 - - + +
5140v ALA* 3.7 9.5 + - - +
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Residues in contact with ASP5137 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5054v GLU* 4.4 7.4 - - - +
5057v ARG* 5.5 0.5 + - - -
5058v LEU* 3.9 27.5 - - + +
5133v LEU* 3.1 23.4 - - + -
5134v THR* 2.6 40.7 + - - +
5135v GLU 2.9 1.2 - - - -
5136v LYS* 1.3 77.0 - - - +
5138v LEU* 1.3 61.8 + - - +
5139v VAL 3.2 1.6 - - - -
5140v ALA* 3.0 7.3 + - - +
5141v ILE* 3.0 31.7 + - - +
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Residues in contact with LEU5138 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5099v VAL* 4.0 14.7 - - + +
5102v MET* 3.6 39.9 - - + +
5103v LYS* 4.6 12.6 - - + -
5121v LEU* 3.4 30.3 - - + -
5133v LEU* 3.3 34.3 - - + -
5134v THR 2.9 17.9 + - - +
5135v GLU* 4.1 18.8 - - - +
5137v ASP* 1.3 69.1 - - - +
5139v VAL* 1.3 65.2 + - - +
5140v ALA 3.2 0.2 + - - -
5141v ILE* 4.2 0.4 - - + -
5142v ALA* 3.2 25.8 + - - +
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Residues in contact with VAL5139 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5047v LEU* 5.4 1.2 - - - +
5051v GLN* 5.4 6.5 - - - +
5095v ILE* 2.8 47.5 - - + +
5099v VAL* 4.6 4.9 - - + -
5135v GLU* 2.9 41.3 + - + +
5136v LYS* 2.7 35.2 - - + +
5138v LEU* 1.3 78.2 - - - +
5140v ALA* 1.3 60.6 + - + +
5142v ALA* 4.2 0.2 - - - +
5143v GLY* 3.7 2.6 + - - -
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Residues in contact with ALA5140 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5047v LEU* 5.7 3.1 - - - -
5051v GLN* 3.7 33.8 - - + +
5052v TYR* 6.1 0.3 - - - -
5054v GLU* 4.8 6.1 - - + -
5055v GLY* 3.7 12.9 - - - +
5058v LEU* 6.5 0.2 - - + -
5136v LYS 3.7 11.2 - - - +
5137v ASP* 3.0 9.8 + - - +
5139v VAL* 1.3 78.0 - - + +
5141v ILE* 1.3 67.8 + - + +
5142v ALA 3.1 1.1 - - - -
5143v GLY* 2.7 14.3 + - - +
5144v HIS 2.8 10.6 + - - -
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Residues in contact with ILE5141 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5055v GLY* 3.5 11.1 - - - +
5058v LEU* 3.4 45.3 - - + -
5059v PHE* 4.1 14.1 - - + -
5062v ALA* 4.9 7.2 - - + -
5102v MET* 3.2 31.6 - - + -
5133v LEU* 4.0 15.5 - - + -
5137v ASP 3.0 17.3 + - - +
5138v LEU* 4.2 0.4 - - + -
5140v ALA* 1.3 69.1 - - - +
5142v ALA* 1.3 52.1 + - - +
5144v HIS* 2.8 24.4 + - - +
5145v ILE* 2.8 33.3 - - + +
6041v HEM 4.0 12.1 - - + -
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Residues in contact with ALA5142 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5095v ILE* 4.2 17.0 - - + +
5098v LEU* 3.0 54.5 - - + +
5102v MET* 4.1 5.6 - - - +
5138v LEU 3.2 18.0 + - - +
5139v VAL 4.2 4.3 - - - +
5141v ILE* 1.3 81.1 - - - +
5143v GLY* 1.3 60.4 + - - +
5145v ILE* 4.0 2.7 - - - -
5146v LEU* 3.2 15.8 + - - +
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Residues in contact with GLY5143 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036v VAL* 5.0 2.5 - - - -
5047v LEU* 4.6 10.3 - - - -
5095v ILE* 4.3 12.1 - - - +
5139v VAL 3.7 6.9 + - - -
5140v ALA* 2.7 19.2 + - - -
5142v ALA* 1.3 70.9 - - - +
5144v HIS* 1.3 52.7 + - - -
5146v LEU* 2.9 7.9 + - - +
5147v VAL* 2.7 47.0 + - - +
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Residues in contact with HIS5144 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5052v TYR* 3.4 24.9 - + + +
5055v GLY* 3.7 15.3 - - - -
5056v LYS* 3.4 35.3 + - + +
5059v PHE* 3.1 52.7 - + + +
5140v ALA 2.8 6.2 + - - +
5141v ILE 2.8 12.7 + - - +
5143v GLY* 1.3 74.1 - - - +
5145v ILE* 1.3 54.4 + - - -
5147v VAL* 3.5 8.2 - - - +
5148v GLU* 2.9 66.8 + - + +
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Residues in contact with ILE5145 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059v PHE* 3.5 37.7 - - + -
5080v LEU* 3.7 36.6 - - + +
5085v LEU* 3.9 11.6 - - + +
5098v LEU* 3.6 26.0 - - + -
5141v ILE* 2.8 41.3 - - + +
5142v ALA* 4.0 1.8 - - - -
5143v GLY 3.1 0.6 - - - -
5144v HIS* 1.3 76.6 - - - +
5146v LEU* 1.3 56.6 + - - +
5149v PRO* 2.9 25.3 - - - +
5156v TRP* 3.5 11.7 + - - -
6041v HEM 4.0 11.9 - - + -
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Residues in contact with LEU5146 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036v VAL* 4.7 15.7 - - + -
5037v PRO* 4.7 8.1 - - + +
5082v THR* 4.2 16.6 + - + +
5085v LEU* 3.9 19.3 - - + -
5093v ASP* 3.9 25.4 - - + +
5094v ASN* 4.2 7.9 - - - +
5095v ILE* 4.2 13.2 - - + +
5098v LEU* 3.6 24.0 - - + -
5142v ALA 3.2 20.2 - - - +
5143v GLY* 2.9 5.4 + - - +
5145v ILE* 1.3 76.4 - - + +
5147v VAL* 1.3 63.7 + - - +
5149v PRO* 3.8 10.3 - - - +
5150v LYS* 3.5 24.9 - - - +
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Residues in contact with VAL5147 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5033v VAL* 4.6 10.3 - - + +
5034v LEU* 5.0 9.9 - - + -
5036v VAL* 4.0 7.6 - - + -
5047v LEU* 3.4 28.0 - - + -
5052v TYR* 4.2 35.0 - - + +
5143v GLY 2.7 37.0 + - - +
5144v HIS* 3.5 8.7 - - - +
5146v LEU* 1.3 73.5 - - - +
5148v GLU* 1.3 68.0 + - - +
5150v LYS* 3.0 25.5 - - - +
5151v ILE* 3.3 10.1 + - + +
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Residues in contact with GLU5148 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5052v TYR* 3.5 15.6 + - - -
5056v LYS* 4.9 4.3 + - - -
5144v HIS* 2.9 51.5 + - - +
5147v VAL* 1.3 70.6 - - + +
5149v PRO* 1.3 65.9 - - + +
5150v LYS 2.9 1.1 - - - -
5151v ILE* 2.2 47.6 + - - +
5152v LEU* 2.9 24.7 + - + +
5156v TRP* 3.6 36.2 - - + -
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Residues in contact with PRO5149 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5061e ARG* 5.0 0.3 + - - -
5081v ARG* 5.0 7.9 - - - +
5082v THR* 3.6 27.4 - - - +
5145v ILE 2.9 28.7 - - - +
5146v LEU 3.8 6.7 - - - +
5147v VAL 3.9 0.2 - - - -
5148v GLU* 1.3 84.3 - - + +
5150v LYS* 1.3 62.4 + - + +
5151v ILE 3.1 0.7 + - - -
5152v LEU 3.3 26.4 - - - +
5153v GLY* 3.7 14.8 + - - +
5156v TRP* 3.3 28.0 - - + -
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Residues in contact with LYS5150 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5310a LYS* 3.4 21.9 + - - -
5061e ARG* 4.3 2.8 + - - -
5032v GLU 4.9 2.6 + - - -
5033v VAL* 3.2 38.2 + - + +
5035v THR 3.1 31.5 + - - -
5036v VAL* 3.8 12.5 - - + +
5037v PRO* 4.4 7.0 - - - +
5146v LEU* 3.5 22.7 - - - +
5147v VAL* 3.0 11.8 + - - +
5148v GLU 2.6 5.3 + - - -
5149v PRO* 1.3 75.1 - - + +
5151v ILE* 1.3 57.0 + - - +
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Residues in contact with ILE5151 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5310a LYS* 2.8 52.1 - - + +
5311a GLY* 3.7 23.3 - - - +
5312a ASN* 4.3 6.1 - - - +
5061e ARG* 3.0 28.1 + - - -
5029v LEU* 4.7 8.3 - - + -
5033v VAL* 4.8 8.3 - - + -
5034v LEU* 6.4 0.4 - - + -
5052v TYR* 4.2 13.9 - - + +
5147v VAL* 3.7 14.8 - - + +
5148v GLU* 2.2 38.9 + - - +
5150v LYS* 1.3 67.0 - - + +
5152v LEU* 1.3 81.3 + - + +
5153v GLY 3.2 1.7 + - - -
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Residues in contact with LEU5152 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5304a HIS* 5.7 5.4 - - + +
5307a ILE* 5.5 2.5 - - + -
5311a GLY 3.8 13.5 - - - +
5312a ASN* 5.4 0.7 - - - -
5313a VAL* 5.2 9.0 - - + +
5414c ILE* 5.8 7.6 - - + -
5069v GLY* 5.7 2.5 - - - -
5148v GLU* 2.9 23.3 + - + +
5149v PRO* 3.3 13.1 - - - +
5151v ILE* 1.3 90.8 - - + +
5153v GLY* 1.3 53.2 + - - +
5154v ASP* 2.5 23.8 + - - -
5155v LYS* 3.5 31.1 + - + +
5156v TRP* 3.8 35.0 - - + +
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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