Contacts of the helix formed by residues 1045 - 1054 (chain M) in PDB entry 5D4E
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 ALA1045 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040M LEU* 3.1 15.0 + - + +
1043M TYR* 3.2 1.9 - - + -
1044M GLY* 1.3 77.0 - - - +
1046M ALA* 1.3 61.2 + - - +
1047M HIS 3.5 1.3 - - - -
1048M THR* 4.1 6.7 - - - +
1049M LEU* 3.5 19.9 + - - +
758N GLU* 3.3 33.7 - - + +
762N GLN* 4.0 5.6 - - - +
763N MET* 4.1 23.3 - - - -
1472N ILE* 4.5 2.4 - - - +
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Residues in contact with ALA1046 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044M GLY 3.5 1.6 + - - -
1045M ALA* 1.3 72.9 - - - +
1047M HIS* 1.3 62.2 + - - +
1049M LEU* 3.5 3.3 + - - +
1050M GLN* 2.9 28.9 + - - +
758N GLU* 3.1 4.6 + - - -
1471N LEU* 3.6 27.9 - - + +
1472N ILE* 3.8 25.3 + - + +
1474N ALA 4.0 1.3 - - - +
1476N THR* 3.2 14.3 + - - +
1477N GLY* 3.7 14.6 - - - +
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Residues in contact with HIS1047 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046M ALA* 1.3 76.7 - - + +
1048M THR* 1.3 59.7 + - - +
1050M GLN* 3.8 8.1 + - - +
1051M GLU* 2.9 31.0 + - - +
1078M GLU* 6.2 0.2 - - - -
752N SER* 4.7 3.0 + - - +
754N PHE* 3.3 60.3 - + + +
755N ALA* 4.4 4.5 - - - +
758N GLU* 2.9 29.1 + - - +
1471N LEU* 3.9 33.6 - - + +
1476N THR* 3.3 14.5 + - - -
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Residues in contact with THR1048 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040M LEU* 3.9 17.9 - - + -
1045M ALA* 4.1 10.3 - - - +
1046M ALA 3.4 0.2 - - - -
1047M HIS* 1.3 76.0 - - - +
1049M LEU* 1.3 58.9 + - - +
1051M GLU* 3.2 9.2 + - - +
1052M MET* 2.9 39.7 + - + +
701N LEU* 4.0 23.8 - - + -
750N PRO* 4.7 12.6 - - + -
755N ALA* 3.5 24.0 + - + +
758N GLU* 2.9 20.3 + - - +
759N ALA* 4.9 1.3 + - + +
763N MET* 5.0 3.1 - - - -
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Residues in contact with LEU1049 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032M PHE* 4.8 2.9 - - + -
1037M VAL* 3.7 34.1 - - + +
1040M LEU* 3.7 19.6 - - + +
1041M GLU* 3.7 18.2 - - + +
1045M ALA 3.5 15.4 + - - +
1046M ALA 3.5 3.5 + - - +
1047M HIS 3.3 0.2 - - - -
1048M THR* 1.3 79.7 - - - +
1050M GLN* 1.3 56.2 + - - +
1052M MET* 3.0 5.9 + - + +
1053M LEU* 2.9 49.2 + - + +
1466N VAL* 4.0 7.2 - - + -
1470N ARG 6.0 0.4 - - - +
1472N ILE* 3.7 42.0 - - + -
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Residues in contact with GLN1050 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046M ALA 2.9 18.3 + - - +
1047M HIS* 3.9 9.8 + - - +
1049M LEU* 1.3 76.4 - - - +
1051M GLU* 1.3 53.5 + - - +
1053M LEU* 3.3 9.8 + - - +
1054M THR* 2.4 40.4 + - - +
1078M GLU* 4.5 9.9 + - - +
1079M PRO* 3.4 33.2 - - + +
1469N GLY 3.4 18.4 + - - +
1470N ARG* 3.5 10.5 - - - +
1471N LEU* 3.3 43.6 - - + +
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Residues in contact with GLU1051 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047M HIS 2.9 16.2 + - - +
1048M THR* 3.2 6.8 - - - +
1050M GLN* 1.3 74.9 - - - +
1052M MET* 1.3 62.4 + - - +
1054M THR* 4.0 3.6 - - - -
1055M LEU* 3.3 26.5 + - + +
1056M LYS* 3.0 51.1 + - - +
1076M VAL* 4.2 4.2 - - - +
1079M PRO* 6.2 0.2 - - - -
750N PRO* 3.6 3.8 - - - +
751N LEU* 2.7 35.0 + - + +
752N SER* 2.7 40.2 + - - -
755N ALA* 3.7 6.3 - - - +
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Residues in contact with MET1052 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032M PHE* 3.9 30.5 - - + -
1040M LEU* 4.1 12.1 - - + -
1048M THR* 2.9 32.6 + - + +
1049M LEU* 3.0 8.5 + - + +
1051M GLU* 1.3 77.5 - - - +
1053M LEU* 1.3 64.1 + - + +
1054M THR 3.5 0.2 + - - -
1056M LYS* 3.7 32.5 - - - +
1057M SER* 3.9 12.5 + - - -
621N LYS* 4.3 1.6 - - - +
623N VAL* 3.3 44.6 - - + +
701N LEU* 4.3 6.3 - - + -
748N HIS* 3.8 28.5 - - + +
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Residues in contact with LEU1053 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032M PHE* 6.0 0.7 - - + -
1037M VAL* 4.5 10.1 - - + -
1049M LEU* 2.9 42.9 + - + +
1050M GLN* 3.9 7.4 - - - +
1052M MET* 1.3 80.7 - - + +
1054M THR* 1.3 61.5 + - - +
1057M SER 5.1 0.2 - - - -
1058M ASP* 2.8 22.1 - - - +
1082M PRO* 3.9 4.2 - - - +
618N LEU 4.2 2.5 - - - +
619N LEU 5.2 1.1 - - - +
620N GLY* 5.3 1.1 - - - +
621N LYS* 3.2 35.6 + - + +
1466N VAL* 3.5 46.4 - - + +
1469N GLY* 4.4 13.9 - - - -
1470N ARG 4.8 4.0 - - - +
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Residues in contact with THR1054 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050M GLN 2.4 27.4 + - - +
1052M MET 3.3 0.6 - - - -
1053M LEU* 1.3 83.6 - - - +
1055M LEU* 1.3 72.8 + - - +
1056M LYS 3.3 1.7 + - - -
1057M SER 3.3 5.9 + - - -
1058M ASP* 3.6 0.8 + - - -
1059M ASP* 3.0 37.6 + - - +
1079M PRO* 3.2 26.5 - - + +
1080M SER 3.5 19.5 - - - +
1082M PRO* 4.3 4.9 - - + -
1469N GLY* 3.6 30.3 - - - +
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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