Contacts of the helix formed by residues 923 - 930 (chain B) in PDB entry 3B8R
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 ASN 923 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B 887 6.1 1.8 - - - -
921B PHE 4.3 0.3 - - - +
922B GLY* 1.3 72.7 - - - -
924B LEU* 1.3 63.6 + - - +
925B SER* 2.9 18.5 + - - -
926B THR* 2.7 49.5 + - - -
927B TYR* 3.1 17.8 + - - +
1031B ALA 3.9 0.4 - - - +
1032B ARG* 3.6 34.2 - - + +
1034B ILE 3.2 7.0 - - - -
1035B LEU* 4.1 7.1 - - + +
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Residues in contact with LEU 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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922B GLY 3.6 1.3 + - - -
923B ASN* 1.3 72.8 - - - +
925B SER* 1.3 57.9 + - - +
927B TYR* 3.8 13.9 - - + -
928B LEU* 2.8 49.3 + - + +
1008B TYR* 4.1 36.8 - - + -
1012B VAL* 5.6 0.9 - - + -
1031B ALA* 3.6 9.3 + - + +
1034B ILE* 2.8 37.1 + - + +
1036B LEU* 4.5 8.1 - - + -
1042B VAL* 4.4 13.0 - - + -
1094B LEU* 5.2 2.9 - - + -
1098B ILE* 3.9 33.2 - - + -
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Residues in contact with SER 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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923B ASN* 2.9 10.2 + - - -
924B LEU* 1.3 78.7 - - - +
926B THR* 1.3 63.6 + - - +
928B LEU* 4.7 1.6 - - - -
929B ARG* 2.7 54.0 + - - +
1031B ALA* 3.6 28.0 + - - +
1032B ARG* 4.5 3.4 - - - -
1097B GLU* 4.5 6.1 + - - -
1102B GLY* 3.7 19.4 + - - -
1103B ALA 5.2 0.9 + - - -
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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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921B PHE 5.9 0.9 - - - -
923B ASN* 2.7 40.1 + - - -
925B SER* 1.3 73.7 + - - +
927B TYR* 1.3 62.8 - - - +
929B ARG* 3.4 18.6 + - - +
930B SER* 3.2 22.8 + - - -
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Residues in contact with TYR 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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921B PHE* 4.3 34.8 + + + +
923B ASN 3.1 15.2 + - - +
924B LEU* 3.6 9.9 - - + +
926B THR* 1.3 77.9 - - - +
928B LEU* 1.3 75.1 + - + +
930B SER* 2.6 27.9 + - - -
931B LYS* 3.2 49.1 + - + +
998B ASP* 6.1 0.3 - - - +
1000B LEU* 4.4 11.1 - - + +
1008B TYR* 4.0 13.3 + - - -
1036B LEU* 3.2 34.4 - - + +
1040B ASN* 5.0 3.8 + - - -
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Residues in contact with LEU 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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924B LEU* 2.8 48.3 + - + +
925B SER* 3.8 1.8 - - - +
927B TYR* 1.3 78.2 - - + +
929B ARG* 1.3 64.3 + - - +
931B LYS* 2.9 14.6 + - - +
932B ARG* 3.6 8.5 + - - +
1000B LEU* 3.5 26.0 - - + -
1005B LEU* 4.1 9.0 - - + -
1008B TYR* 4.2 15.5 - - + -
1031B ALA* 6.1 1.6 - - + -
1097B GLU 4.2 1.1 - - - +
1098B ILE* 3.6 37.7 - - + +
1101B LEU* 3.7 30.1 - - + +
1102B GLY* 3.7 6.7 - - - +
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Residues in contact with ARG 929 (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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1079A ASP* 4.2 27.9 + - - -
1081A VAL* 4.3 15.4 - - - +
925B SER* 2.7 44.5 + - - +
926B THR* 3.5 18.2 + - - +
928B LEU* 1.3 77.7 - - - +
930B SER* 1.3 58.9 + - - +
931B LYS 3.2 4.2 + - - -
932B ARG* 3.4 38.8 + - - +
1101B LEU 3.5 6.8 + - - -
1102B GLY 3.0 25.0 + - - +
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Residues in contact with SER 930 (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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926B THR* 3.2 12.9 + - - -
927B TYR* 2.6 28.0 + - - -
929B ARG* 1.3 74.9 - - - +
931B LYS* 1.3 68.5 + - - +
932B ARG 3.6 0.7 - - - -
933B ASN 5.4 0.8 + - - -
934B GLU* 4.4 6.2 - - - +
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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