Contacts of the helix formed by residues 907 - 918 (chain K) in PDB entry 5ANC
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 ALA 907 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733K GLN* 3.3 21.3 - - - +
746K ASN* 3.3 25.8 - - - +
905K GLN* 3.3 5.1 + - - +
906K GLY* 1.3 75.5 - - - +
908K SER* 1.3 63.2 + - - +
909K ASP 3.4 2.0 - - - +
910K LEU* 3.8 4.2 - - - +
911K ALA* 3.2 25.6 + - - +
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Residues in contact with SER 908 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733K GLN* 5.1 2.6 - - - +
907K ALA* 1.3 73.9 - - - +
909K ASP* 1.3 63.2 + - - +
911K ALA* 3.2 2.6 + - - -
912K LYS* 2.9 27.7 + - - +
1119K ASN* 3.1 42.7 + - - +
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Residues in contact with ASP 909 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730K GLU* 4.0 2.9 - - - +
732K ILE* 5.5 4.6 - - - +
733K GLN* 3.7 26.0 + - - +
743K THR 3.5 12.8 - - - +
744K THR 4.0 17.2 - - - +
746K ASN* 4.6 5.8 - - + +
908K SER* 1.3 77.8 - - - +
910K LEU* 1.3 63.7 + - - +
912K LYS* 3.2 11.7 + - - +
913K GLU* 3.0 22.5 + - - +
1120K LYS* 2.9 51.8 + - + +
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Residues in contact with LEU 910 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745K PRO 3.2 23.8 - - - +
746K ASN* 3.9 15.7 - - + +
748K LEU* 4.3 14.1 - - + -
904K GLU* 3.5 37.0 - - + +
905K GLN 3.1 34.5 - - - +
906K GLY* 4.0 8.1 - - - +
907K ALA 3.7 9.7 + - - +
908K SER 3.2 0.2 - - - -
909K ASP* 1.3 79.9 - - - +
911K ALA* 1.3 57.9 + - - +
913K GLU* 3.2 5.7 + - + +
914K GLY* 2.9 25.9 + - - -
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Residues in contact with ALA 911 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907K ALA 3.2 12.3 + - - +
908K SER* 3.2 10.4 + - - +
910K LEU* 1.3 80.9 - - - +
912K LYS* 1.3 56.8 + - - +
914K GLY* 3.2 3.1 + - - -
915K GLN* 2.9 30.0 + - - +
1119K ASN* 4.0 10.3 - - - +
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Residues in contact with LYS 912 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744K THR* 5.7 5.3 - - - +
908K SER 2.9 12.7 + - - +
909K ASP* 3.3 10.8 - - - +
911K ALA* 1.3 75.9 - - - +
913K GLU* 1.3 68.3 + - - +
915K GLN* 3.2 9.3 + - - +
916K GLU* 2.9 46.9 + - + +
1110K ALA* 4.0 8.5 - - - +
1115K THR 4.4 3.1 - - - +
1116K LEU 2.7 29.1 + - - +
1118K LYS* 3.7 33.8 - - + +
1119K ASN* 3.8 20.4 + - + +
1120K LYS* 3.9 28.2 - - - +
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Residues in contact with GLU 913 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744K THR* 4.0 8.1 - - - +
745K PRO* 3.3 38.4 - - + +
748K LEU* 4.4 13.0 - - + -
909K ASP 3.0 12.7 + - - +
910K LEU* 3.2 10.3 + - + +
912K LYS* 1.3 85.7 + - - +
914K GLY* 1.3 55.7 + - - +
916K GLU* 2.9 30.8 + - - +
917K GLU* 2.9 35.9 + - - +
919K GLU* 4.5 8.1 - - - +
956K PRO* 5.9 1.3 - - + -
960K GLN* 3.1 31.2 + - - +
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Residues in contact with GLY 914 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910K LEU* 2.9 13.9 + - - +
911K ALA* 3.2 4.7 + - - -
913K GLU* 1.3 75.7 - - - +
915K GLN* 1.3 54.9 + - - +
918K ASN* 2.7 36.7 + - - +
919K GLU* 3.8 19.9 + - - -
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Residues in contact with GLN 915 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911K ALA 2.9 14.5 + - - +
912K LYS* 3.4 11.1 - - - +
914K GLY* 1.3 76.8 - - - +
916K GLU* 1.3 62.6 + - - +
918K ASN* 3.4 20.3 + - - +
1118K LYS* 3.6 37.3 + - - +
1119K ASN* 6.2 0.2 - - - +
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Residues in contact with GLU 916 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J LEU* 5.4 5.4 - - - +
912K LYS* 2.9 25.2 + - + +
913K GLU* 2.9 29.8 - - - +
915K GLN* 1.3 80.0 - - - +
917K GLU* 1.3 71.1 - - - +
918K ASN* 4.0 6.6 + - - -
957K PHE* 4.6 1.3 - - - -
960K GLN* 4.3 1.9 + - - -
1110K ALA* 3.0 44.4 - - - +
1111K GLU* 3.3 33.0 - - - +
1115K THR* 4.0 12.2 - - - +
1118K LYS* 4.5 11.8 - - - +
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Residues in contact with GLU 917 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J LEU* 5.1 9.4 - - - +
236J VAL* 4.8 5.2 - - - +
913K GLU* 2.9 27.7 + - - +
916K GLU* 1.3 99.2 - - - +
918K ASN* 1.3 71.6 + - - +
919K GLU* 3.3 28.4 + - - +
930K LEU* 4.1 14.9 - - - +
931K GLN* 3.5 40.4 + - - +
956K PRO* 5.8 1.8 - - + -
957K PHE* 3.5 29.1 + - - +
960K GLN* 5.3 2.2 - - - +
1111K GLU* 4.0 6.1 - - - +
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Residues in contact with ASN 918 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914K GLY 2.7 21.1 + - - +
915K GLN* 3.4 20.1 + - - +
916K GLU 4.0 5.5 + - - -
917K GLU* 1.3 75.0 + - - +
919K GLU* 1.3 57.9 + - - +
920K THR 4.2 0.7 + - - -
928K GLN* 4.0 17.2 + - - -
930K LEU* 4.4 13.3 - - + +
954K TYR* 4.5 0.2 + - - -
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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