Contacts of the helix formed by residues 916 - 921 (chain A) in PDB entry 5C53
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 PHE 916 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A LEU* 3.6 38.4 - - + -
899A ALA* 4.0 8.1 - - + -
900A ALA* 3.6 31.2 - - + -
914A THR* 3.3 1.9 - - - -
915A ALA* 1.3 78.4 - - - +
917A GLY* 1.3 60.9 + - - +
918A TRP 3.2 6.1 + - - -
919A MET* 3.5 11.1 + - - +
920A THR* 3.3 18.9 + - + +
931A LEU* 4.2 14.1 - - + +
953A ARG* 4.1 16.2 - - - -
954A ILE* 4.3 12.6 - - + -
1055A SER* 4.0 9.0 + - - +
1056A GLU* 3.3 37.7 - - - +
1057A MET* 3.7 18.8 - - + -
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Residues in contact with GLY 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900A ALA* 3.6 27.2 - - - +
911A HIS 3.7 8.3 - - - +
912A GLY* 5.0 0.2 - - - -
914A THR* 3.2 22.8 + - - -
916A PHE* 1.3 78.9 - - - +
918A TRP* 1.3 57.5 + - - +
920A THR* 3.4 13.3 + - - -
921A LEU* 3.4 20.4 - - - +
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Residues in contact with TRP 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 5.8 9.3 - - - +
107A LEU* 4.7 11.9 - - + +
112A LEU* 3.6 39.0 - - + -
114A GLY 5.2 4.5 - - - -
115A GLN* 5.0 12.6 - - + -
116A PRO* 4.5 10.5 - - + -
912A GLY* 3.6 29.4 - - - +
914A THR 3.2 18.6 + - - +
915A ALA 4.4 4.0 - - - +
916A PHE 3.2 1.0 - - - -
917A GLY* 1.3 77.3 - - - +
919A MET* 1.3 67.1 - - + +
920A THR 3.4 0.8 + - - -
921A LEU* 4.0 10.2 - - + +
922A GLN* 3.3 62.4 + - + +
934A LYS* 5.9 3.8 - - - -
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Residues in contact with MET 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 6.3 1.1 - - - -
112A LEU* 4.1 24.2 - - + -
915A ALA 3.7 18.6 - - - +
916A PHE* 3.5 7.5 + - - +
918A TRP* 1.3 80.9 - - + +
920A THR* 1.3 65.5 + - - +
921A LEU 3.4 0.2 - - - -
922A GLN* 3.7 14.4 + - - +
923A GLY 4.1 4.5 + - - -
930A ASP 5.3 0.2 - - - -
931A LEU* 3.7 36.8 + - + +
934A LYS* 3.5 43.1 - - + +
935A THR* 6.3 0.2 - - + -
986A TYR* 5.9 3.4 - - - -
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Residues in contact with THR 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A LEU* 3.8 23.7 - - + +
897A TRP* 4.4 11.5 - - - -
900A ALA* 3.5 18.9 - - + +
916A PHE* 3.3 27.6 - - + +
917A GLY 3.4 13.3 + - - -
919A MET* 1.3 79.6 - - - +
921A LEU* 1.3 69.6 + - - +
922A GLN 3.2 3.3 + - - -
923A GLY 4.3 8.5 + - - +
930A ASP* 6.1 0.5 - - - +
931A LEU* 3.7 27.7 + - + +
1176A SER 5.2 1.0 - - - +
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Residues in contact with LEU 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG 5.9 2.7 - - - +
897A TRP* 4.1 22.7 - - + +
900A ALA* 5.5 1.1 - - + -
901A VAL* 6.1 0.4 - - + -
904A ASP* 5.2 2.0 - - - +
911A HIS* 4.1 15.9 - - + +
912A GLY* 5.0 8.7 - - - +
917A GLY 3.4 23.1 - - - +
918A TRP* 4.0 14.1 - - + +
919A MET 3.4 0.2 - - - -
920A THR* 1.3 80.4 + - - +
922A GLN* 1.3 63.9 + - - +
923A GLY 3.8 0.4 - - - -
1174A PRO* 3.6 39.0 - - + +
1176A SER* 4.2 23.7 + - - +
1177A VAL* 4.7 7.0 - - + -
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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