Contacts of the helix formed by residues 920 - 928 (chain B) in PDB entry 5JP2
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 GLY 920 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918B PRO* 2.9 4.0 + - - +
919B ALA* 1.3 79.2 - - - +
921B ILE* 1.3 59.2 + - - +
922B THR* 3.2 1.2 + - - -
923B ARG* 3.7 17.9 + - - +
924B ILE* 3.7 15.2 + - - +
636F PHE* 4.6 15.4 - - - -
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Residues in contact with ILE 921 (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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883B TRP* 4.0 30.3 - - + -
884B PRO 4.7 9.0 - - - +
885B VAL* 5.1 0.4 - - + -
917B PHE* 3.9 31.2 - - + -
918B PRO* 2.8 28.9 + - + +
920B GLY* 1.3 76.1 - - - +
922B THR* 1.3 67.9 + - + +
923B ARG 3.4 0.2 - - - -
924B ILE* 3.3 12.1 + - + +
925B PHE* 2.9 59.3 + - + -
979B LEU* 4.5 4.0 - - + -
992B TYR* 6.4 0.2 - - + -
1132B TYR* 4.5 6.3 - - + -
636F PHE* 4.7 3.3 - - + -
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Residues in contact with THR 922 (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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919B ALA 3.2 19.4 + - - +
921B ILE* 1.3 80.3 - - + +
923B ARG* 1.3 68.6 + - - +
925B PHE* 2.7 12.9 + - - +
926B THR* 2.5 43.1 + - - -
979B LEU* 4.2 31.0 - - + +
980B GLN* 5.3 4.9 - - - -
983B ALA* 4.8 5.8 - - + -
992B TYR* 4.1 22.2 - - + -
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Residues in contact with ARG 923 (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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919B ALA 5.5 0.2 - - - +
920B GLY* 3.7 15.4 + - - +
921B ILE 3.4 0.4 - - - -
922B THR* 1.3 88.0 + - - +
924B ILE* 1.3 64.8 + - + +
926B THR* 4.0 7.3 - - - -
927B ALA* 3.1 25.6 + - - +
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Residues in contact with ILE 924 (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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878B SER* 4.2 26.9 - - - +
879B ALA* 4.3 15.7 - - + +
883B TRP* 3.5 42.0 - - + +
920B GLY 3.7 15.3 - - - +
921B ILE* 3.3 14.6 + - + +
922B THR 3.0 0.6 - - - -
923B ARG* 1.3 81.1 - - + +
925B PHE* 1.3 68.7 + - + +
927B ALA* 4.1 2.3 - - - +
928B ASN* 3.2 25.9 + - + +
931B ALA* 5.1 0.2 - - - +
636F PHE* 5.0 4.7 - - + -
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Residues in contact with PHE 925 (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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883B TRP* 4.9 5.4 - + - -
917B PHE* 4.5 4.5 - + - -
921B ILE* 2.9 46.8 + - + -
922B THR* 2.7 13.7 + - - +
924B ILE* 1.3 73.8 - - + +
926B THR* 1.3 65.5 + - - +
928B ASN 3.1 21.4 - - - +
929B PRO* 4.1 1.9 - - - +
931B ALA* 4.0 17.5 - - + -
934B LEU* 5.7 0.2 - - + -
972B MET* 3.7 19.3 - - + -
975B LEU* 3.9 16.4 - - + -
976B THR* 3.7 32.6 + - + +
979B LEU* 3.6 30.7 - - + -
1132B TYR* 3.7 25.4 - + - -
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Residues in contact with THR 926 (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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922B THR* 2.5 25.8 + - - -
923B ARG* 4.0 7.3 - - - -
925B PHE* 1.3 74.5 - - - +
927B ALA* 1.3 62.7 + - + +
928B ASN 3.4 0.2 + - - -
929B PRO* 4.5 8.0 - - - +
976B THR* 3.9 1.7 - - - +
980B GLN* 3.0 41.7 + - - +
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Residues in contact with ALA 927 (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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923B ARG 3.1 16.4 + - - +
924B ILE* 4.2 3.1 - - - +
926B THR* 1.3 82.1 - - + +
928B ASN* 1.3 60.4 - - + +
929B PRO* 3.4 8.7 - - - +
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Residues in contact with ASN 928 (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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883B TRP* 6.0 2.2 - - - -
924B ILE* 3.2 16.7 + - + +
925B PHE 3.1 12.1 - - - +
926B THR 3.3 0.4 - - - -
927B ALA* 1.3 78.7 - - + +
929B PRO* 1.3 63.3 - - - +
930B ASN* 2.8 30.8 + - - +
931B ALA* 3.3 34.2 + - + +
932B PRO* 5.1 3.6 - - - +
976B THR* 5.5 0.7 + - - -
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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