Contacts of the helix formed by residues 909 - 920 (chain B) in PDB entry 2HRC
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 PRO 909 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708B ARG* 6.0 1.6 - - - +
907B VAL 3.5 9.8 - - - +
908B ASN* 1.3 87.8 - - - +
910B VAL* 1.3 62.3 + - + +
911B CYS 3.4 0.3 + - - -
912B ARG* 3.6 12.9 + - + +
913B GLU* 3.4 22.8 + - - +
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Residues in contact with VAL 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B ASP* 3.6 7.9 - - - +
704B ASN* 3.8 22.0 - - + +
707B TYR* 3.8 17.9 - - + -
708B ARG* 3.2 39.0 - - - +
908B ASN* 3.0 34.3 + - - +
909B PRO* 1.3 78.8 - - - +
911B CYS* 1.3 63.0 + - - +
913B GLU* 3.2 9.3 + - - +
914B THR* 2.9 43.3 + - - +
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Residues in contact with CYS 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B CYS* 5.5 3.8 - - - -
704B ASN* 4.4 11.9 - - - -
902B SER* 4.5 5.5 + - - +
906B CYS* 3.6 9.4 - - - -
908B ASN* 3.2 26.4 + - - +
910B VAL* 1.3 85.3 - - - +
912B ARG* 1.3 57.1 + - - +
914B THR* 3.4 2.7 + - - -
915B LYS* 2.9 29.7 + - - +
1502B FES 2.4 48.9 - - - -
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Residues in contact with ARG 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 4.6 13.8 + - - +
902B SER* 4.6 6.8 + - - +
908B ASN 4.4 0.8 + - - +
909B PRO* 3.6 11.2 + - + +
910B VAL 3.3 0.2 - - - -
911B CYS* 1.3 78.0 - - - +
913B GLU* 1.3 59.5 + - + +
915B LYS* 3.5 19.9 + - - +
916B SER* 3.0 37.1 + - - +
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Residues in contact with GLU 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B TYR* 3.0 48.3 + - + -
708B ARG* 5.1 3.3 + - - -
909B PRO* 3.4 15.7 - - - +
910B VAL* 3.2 21.3 + - - +
912B ARG* 1.3 75.0 - - + +
914B THR* 1.3 60.0 + - - +
916B SER* 3.4 6.1 + - - -
917B PHE* 2.9 27.4 + - - +
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Residues in contact with THR 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B LEU* 3.5 44.2 - - + +
704B ASN* 2.7 31.9 + - - +
707B TYR* 3.8 13.7 - - + +
899B LEU* 6.1 1.3 - - + -
910B VAL* 2.9 20.2 + - - +
911B CYS 3.6 4.0 - - - -
913B GLU* 1.3 74.1 - - - +
915B LYS* 1.3 67.3 + - - +
917B PHE* 3.1 15.6 + - - +
918B PHE* 3.3 15.4 - - + -
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Residues in contact with LYS 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 5.2 2.6 - - - +
899B LEU* 3.2 37.4 - - + +
900B THR* 3.4 28.0 + - - +
902B SER* 3.7 21.5 + - - +
911B CYS 2.9 17.8 + - - +
912B ARG* 3.7 24.0 - - - +
913B GLU 3.3 0.2 - - - -
914B THR* 1.3 77.4 - - - +
916B SER* 1.3 65.0 + - - +
918B PHE* 3.2 5.2 + - - +
919B THR* 2.9 47.5 + - + +
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Residues in contact with SER 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912B ARG* 3.0 23.8 + - - +
913B GLU* 3.7 6.7 - - - -
915B LYS* 1.3 82.5 - - - +
917B PHE* 1.3 66.0 + - - +
919B THR* 3.5 9.5 + - - -
920B SER* 2.8 36.4 + - - -
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Residues in contact with PHE 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B ILE* 3.9 20.0 - - + -
707B TYR* 4.2 25.8 - + + -
710B TYR* 3.9 28.9 - + + -
711B ASN* 6.0 0.2 - - - -
717B PRO* 3.8 23.3 - - + -
721B TRP* 3.9 11.9 - + - -
913B GLU 2.9 14.5 + - - +
914B THR* 3.1 11.6 + - - +
916B SER* 1.3 77.1 - - - +
918B PHE* 1.3 87.7 + + - +
920B SER* 4.3 1.7 - - - -
921B GLN* 2.9 47.9 + - - +
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Residues in contact with PHE 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B ALA* 4.2 3.1 - - + -
703B LEU* 4.0 29.6 - - + -
706B ILE* 4.1 14.6 - - + -
721B TRP* 4.4 9.9 - + + -
722B SER* 3.9 22.7 - - - -
723B THR* 3.7 34.8 - - + -
894B LEU* 3.5 21.1 - - - +
895B CYS* 4.6 5.8 - - + -
899B LEU* 4.7 9.0 - - + -
914B THR* 3.3 37.8 + - + -
915B LYS 3.2 6.0 + - - +
916B SER 3.2 0.4 - - - -
917B PHE* 1.3 103.3 - + - +
919B THR* 1.3 65.1 + - - +
920B SER 3.1 2.1 + - - -
921B GLN* 3.3 16.5 + - - +
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Residues in contact with THR 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894B LEU* 3.6 18.2 - - - +
895B CYS* 3.9 21.1 - - - -
900B THR* 4.1 12.8 - - + -
915B LYS* 2.9 37.1 + - + +
916B SER* 3.5 11.3 + - - -
918B PHE* 1.3 77.0 - - - +
920B SER* 1.3 63.5 + - - +
921B GLN 3.4 0.6 - - - +
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Residues in contact with SER 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916B SER* 2.8 28.6 + - - -
917B PHE* 4.3 2.7 - - - -
919B THR* 1.3 81.0 + - - +
921B GLN* 1.3 66.4 + - - +
922B GLN* 3.5 1.7 + - - -
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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