Contacts of the helix formed by residues 927 - 936 (chain B) in PDB entry 1P48
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 927 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B VAL* 3.3 15.2 - - - +
674B THR* 3.2 23.2 - - - -
676B ALA 4.6 1.1 - - - -
925B PHE* 3.3 26.7 + - - -
926B ALA* 1.3 75.6 - - - +
928B GLU* 1.3 60.8 + - - -
929B ASN 3.0 4.7 + - - -
930B PHE* 3.2 14.2 + - - +
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Residues in contact with GLU 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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674B THR* 3.2 31.6 - - - +
675B GLY* 3.5 14.7 - - - +
676B ALA 5.3 0.7 - - - +
677B LYS* 5.5 6.6 + - - -
926B ALA 3.3 0.8 + - - -
927B GLY* 1.3 73.1 - - - -
929B ASN* 1.3 64.7 + - - +
930B PHE* 3.2 17.9 + - - -
931B HIS* 5.0 1.2 + - - +
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Residues in contact with ASN 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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925B PHE 5.5 0.6 + - - -
926B ALA* 2.9 17.6 + - - +
928B GLU* 1.3 84.9 + - - +
930B PHE* 1.3 64.2 + - - +
931B HIS* 3.2 3.4 - - - -
932B HIS* 3.1 15.5 + - + +
933B GLY* 3.2 11.4 + - - -
936B LEU* 3.7 32.2 - - + +
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Residues in contact with PHE 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B VAL* 3.8 9.2 - - + -
650B PHE* 3.9 17.5 - + - -
674B THR* 3.7 19.5 - - + -
792B VAL* 3.8 38.1 - - + -
816B GLN* 4.0 21.8 - - + -
892B THR 3.1 20.8 - - - +
893B GLY 3.6 21.1 - - - +
894B GLN* 3.4 26.5 + - + +
926B ALA* 3.9 4.4 + - - -
927B GLY 3.2 18.8 + - - +
928B GLU* 3.2 12.9 - - - -
929B ASN* 1.3 77.3 - - - +
931B HIS* 1.3 85.9 + - + +
932B HIS 3.2 0.5 + - - -
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Residues in contact with HIS 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B GLN* 2.7 32.8 + - + +
840B ASP* 3.2 47.5 + - - +
863B PHE* 5.6 0.3 - - - -
866B GLY 4.3 3.0 + - - -
868B GLY* 3.3 30.2 - - - -
869B VAL 4.6 0.2 + - - -
892B THR 4.7 1.0 - - - +
894B GLN* 3.8 4.4 + - - +
928B GLU 5.8 0.9 - - - +
929B ASN 3.2 1.1 - - - -
930B PHE* 1.3 98.9 - - + +
932B HIS* 1.3 95.1 + + + +
933B GLY 4.1 0.3 + - - -
934B ASP* 4.5 0.9 - - - +
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Residues in contact with HIS 932 (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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863B PHE 5.8 0.2 - - - -
866B GLY* 2.9 41.3 + - - -
867B TRP 3.9 10.2 + - - -
929B ASN* 3.1 10.8 + - + +
931B HIS* 1.3 106.1 + + + +
933B GLY* 1.3 64.0 + - - +
934B ASP* 3.1 19.7 + - - +
935B LYS* 3.1 32.2 + - + +
936B LEU* 3.8 8.1 + - - +
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Residues in contact with GLY 933 (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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645B VAL* 3.6 10.3 - - - +
891B ARG* 3.0 10.2 + - - +
892B THR 3.3 22.4 + - - -
893B GLY* 4.2 7.0 - - - -
926B ALA* 4.9 0.2 - - - -
929B ASN 3.2 10.8 + - - -
932B HIS* 1.3 75.4 - - - +
934B ASP* 1.3 62.1 + - - +
936B LEU* 3.1 33.3 + - - +
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Residues in contact with ASP 934 (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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640B LYS* 5.7 0.7 - - - +
863B PHE* 3.4 57.3 - - + +
890B LEU 4.7 2.0 - - - +
891B ARG* 2.9 38.9 + - + +
892B THR 4.1 1.2 + - - -
931B HIS 4.5 0.5 - - - +
932B HIS* 3.5 26.7 + - - -
933B GLY* 1.3 77.9 + - - +
935B LYS* 1.3 74.1 + - - +
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Residues in contact with LYS 935 (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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863B PHE 5.8 3.6 - - - -
932B HIS* 3.1 27.7 + - + +
934B ASP* 1.3 96.4 - - - +
936B LEU* 1.3 66.4 + - + +
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Residues in contact with LEU 936 (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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640B LYS* 4.4 10.6 + - - +
643B PRO* 5.7 4.3 - - - -
645B VAL* 3.9 26.9 - - + -
891B ARG* 2.7 33.1 + - - -
924B VAL* 4.3 15.7 - - + -
925B PHE 4.7 1.6 - - - +
926B ALA* 3.9 29.2 - - - +
929B ASN* 3.7 34.3 - - + +
932B HIS 4.2 6.5 - - - +
933B GLY* 3.1 17.9 + - - +
934B ASP 3.4 0.2 - - - -
935B LYS* 1.3 82.7 - - + +
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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