Contacts of the helix formed by residues 1045 - 1054 (chain C) in PDB entry 5D4D
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C LEU* 3.0 18.5 + - + +
1043C TYR* 3.3 3.3 - - + -
1044C GLY* 1.3 77.4 - - - +
1046C ALA* 1.3 62.9 + - - +
1047C HIS 3.4 2.2 - - - -
1048C THR* 4.0 6.3 - - - +
1049C LEU* 3.3 20.4 + - - +
758D GLU* 3.4 31.9 - - + +
762D GLN* 4.3 2.7 - - - +
763D MET* 4.0 23.8 - - + -
1472D ILE* 5.1 1.1 - - - -
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Residues in contact with ALA1046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044C GLY 3.5 1.2 + - - -
1045C ALA* 1.3 74.0 - - - +
1047C HIS* 1.3 60.1 + - - +
1049C LEU* 3.5 3.7 + - - +
1050C GLN* 2.9 28.4 + - - +
758D GLU* 3.0 4.6 + - - -
1471D LEU* 3.7 25.0 - - + +
1472D ILE* 3.7 26.0 + - + -
1474D ALA 4.0 2.0 - - - +
1476D THR* 3.2 12.9 + - - +
1477D GLY* 3.7 19.1 - - - +
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Residues in contact with HIS1047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C ALA* 1.3 76.9 - - + +
1048C THR* 1.3 64.3 + - - +
1050C GLN* 3.2 7.2 + - - +
1051C GLU* 2.9 27.3 + - - +
752D SER* 4.7 2.7 - - - +
754D PHE* 3.3 60.8 - + + +
755D ALA* 4.3 5.4 - - - +
758D GLU* 2.8 28.0 + - - +
1471D LEU* 3.5 30.6 - - + +
1476D THR* 3.5 18.4 + - - -
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Residues in contact with THR1048 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C LEU* 3.8 17.7 - - + -
1045C ALA* 4.0 11.3 - - - +
1047C HIS* 1.3 73.2 - - - +
1049C LEU* 1.3 64.7 + - - +
1051C GLU* 3.2 6.9 + - - +
1052C MET* 3.0 30.0 + - + +
1056C LYS* 5.1 2.6 + - - +
701D LEU* 3.9 23.8 - - + -
750D PRO* 4.8 6.5 - - + +
755D ALA* 3.6 30.7 + - + +
758D GLU* 2.8 29.2 + - - +
759D ALA* 4.8 1.4 + - - +
763D MET* 5.0 2.6 - - - -
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Residues in contact with LEU1049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C PHE* 4.5 2.9 - - + -
1037C VAL* 3.7 33.7 - - + +
1040C LEU* 3.6 21.7 - - + +
1041C GLU* 3.6 33.0 - - + +
1045C ALA 3.3 11.6 + - - +
1046C ALA 3.5 9.0 - - - +
1048C THR* 1.3 80.2 - - - +
1050C GLN* 1.3 63.5 + - - +
1052C MET* 2.9 15.2 + - + +
1053C LEU* 2.9 34.7 + - + +
1466D VAL* 4.2 3.4 - - + -
1470D ARG 6.0 0.4 - - - +
1472D ILE* 4.0 26.9 - - + -
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Residues in contact with GLN1050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C ALA 2.9 17.8 + - - +
1047C HIS* 3.2 9.4 + - - +
1049C LEU* 1.3 75.8 - - - +
1051C GLU* 1.3 53.5 + - - +
1053C LEU* 3.3 9.8 + - - +
1054C THR* 2.2 40.9 + - - +
1078C GLU* 5.2 4.3 + - - +
1079C PRO* 3.4 34.5 + - + +
1469D GLY 3.1 24.5 + - - +
1470D ARG* 3.4 7.8 - - - +
1471D LEU* 3.3 41.2 - - + +
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Residues in contact with GLU1051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C HIS 2.9 10.9 + - - +
1048C THR* 3.2 9.7 - - - +
1050C GLN* 1.3 74.3 - - - +
1052C MET* 1.3 62.8 - - - +
1054C THR* 3.9 3.8 - - - -
1055C LEU* 3.2 30.8 + - + +
1056C LYS* 2.9 48.7 + - - +
1076C VAL* 4.5 1.9 - - - +
750D PRO* 4.0 0.2 - - - +
751D LEU* 2.9 29.1 + - + +
752D SER* 2.7 43.2 + - - -
755D ALA* 3.6 10.7 - - - +
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Residues in contact with MET1052 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C PHE* 3.9 41.1 - - + -
1040C LEU* 4.0 3.6 - - + -
1048C THR* 3.0 28.5 + - + +
1049C LEU* 2.9 7.7 + - + +
1051C GLU* 1.3 76.4 - - - +
1053C LEU* 1.3 67.5 + - + +
1054C THR 3.5 0.2 + - - -
1056C LYS* 3.8 28.0 - - - +
1057C SER* 3.6 12.0 + - - -
621D LYS* 3.8 3.1 - - + +
623D VAL* 3.3 48.7 - - + +
701D LEU* 4.2 5.8 - - + -
748D HIS* 3.9 26.7 - - + +
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Residues in contact with LEU1053 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C PHE* 5.9 0.4 - - + +
1037C VAL* 4.4 11.0 - - + -
1049C LEU* 2.9 41.6 + - + +
1050C GLN* 3.8 7.9 - - - +
1052C MET* 1.3 80.6 - - + +
1054C THR* 1.3 61.7 + - - +
1057C SER* 4.8 0.2 - - - -
1058C ASP* 3.4 7.0 - - - +
1082C PRO* 3.7 4.7 - - - +
618D LEU 4.5 3.1 - - - +
620D GLY* 5.3 1.6 - - - -
621D LYS* 3.1 46.2 + - + +
1466D VAL* 3.7 47.8 - - + +
1469D GLY* 4.3 17.0 - - - -
1470D ARG 4.8 4.5 - - - +
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Residues in contact with THR1054 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050C GLN* 2.2 30.4 + - + +
1051C GLU* 3.3 2.6 + - - -
1053C LEU* 1.3 83.7 - - - +
1055C LEU* 1.3 70.5 + - - +
1056C LYS 3.2 1.1 - - - -
1057C SER 3.0 12.0 + - - -
1059C ASP* 3.1 33.1 + - + +
1079C PRO* 3.2 27.6 - - + +
1080C SER 3.5 20.6 - - - +
1082C PRO* 4.2 9.0 - - + -
1469D GLY* 3.7 22.4 - - - +
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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