Contacts of the helix formed by residues 835 - 842 (chain B) in PDB entry 4G0U
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 835 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831B ARG* 3.3 13.6 + - - +
832B LEU 4.0 7.6 - - - +
833B LEU 3.5 8.3 - - - +
834B PHE* 1.3 88.8 - - - +
836B ALA* 1.3 65.8 + - - +
837B VAL* 4.2 9.9 - - + -
838B ASP* 3.1 26.3 + - + +
839B ASP* 4.0 2.3 + - - +
858B ILE 4.6 4.7 - - - +
860B ILE* 3.7 18.4 - - + -
1049B ARG* 3.5 29.6 - - - +
1183B ASP* 4.0 9.0 - - - +
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Residues in contact with ALA 836 (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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831B ARG* 3.5 34.5 + - + +
834B PHE 3.4 2.4 + - - -
835B PRO* 1.3 70.8 - - - +
837B VAL* 1.3 64.1 + - - +
839B ASP* 2.9 24.4 + - - +
840B ASN* 4.4 1.7 + - - -
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Residues in contact with VAL 837 (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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835B PRO* 4.2 10.3 - - + -
836B ALA* 1.3 78.1 - - - +
838B ASP* 1.3 64.0 + - - +
840B ASN* 2.9 37.6 + - - +
841B LEU* 4.8 1.7 - - - +
1049B ARG* 3.9 41.1 - - + +
1052B TRP* 4.5 6.0 - - + -
1053B LEU* 4.1 28.5 - - + -
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Residues in contact with ASP 838 (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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835B PRO* 3.1 19.6 + - + +
836B ALA 3.0 1.0 + - - -
837B VAL* 1.3 74.4 - - - +
839B ASP* 1.3 58.0 + - - +
840B ASN 3.0 2.9 - - - -
841B LEU* 2.8 47.5 + - + +
842B LEU* 3.5 10.1 - - + +
858B ILE* 4.2 14.6 - - + +
1042B ARG* 2.9 29.8 + - - -
1049B ARG* 2.9 44.3 + - - +
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Residues in contact with ASP 839 (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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750B PHE* 5.6 0.3 - - - +
831B ARG* 3.1 36.2 + - - -
835B PRO 4.1 1.9 - - - +
836B ALA 2.9 16.6 + - - +
838B ASP* 1.3 76.2 - - - +
840B ASN* 1.3 58.8 + - - +
841B LEU 3.0 5.7 + - - -
842B LEU* 3.2 27.6 + - - +
844B PHE* 3.3 36.2 - - + -
857B TYR* 3.7 12.4 + - - -
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Residues in contact with ASN 840 (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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836B ALA 4.6 1.6 + - - -
837B VAL* 2.9 30.9 + - - +
838B ASP 3.0 0.6 - - - -
839B ASP* 1.3 77.0 - - - +
841B LEU* 1.3 62.6 + - + +
842B LEU 3.5 2.1 - - - +
1052B TRP* 3.4 59.8 + - + +
1110B GLN* 4.8 6.2 + - - -
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Residues in contact with LEU 841 (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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837B VAL 4.8 1.1 - - - +
838B ASP* 2.8 43.2 + - + +
840B ASN* 1.3 82.5 - - + +
842B LEU* 1.3 65.7 + - + +
843B LYS 4.0 0.3 + - - -
858B ILE* 5.8 0.4 - - + -
1045B TYR* 3.6 48.2 + - + +
1048B LEU* 4.1 14.4 - - + +
1049B ARG* 3.6 23.6 - - + +
1052B TRP* 4.0 31.0 - - + -
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Residues in contact with LEU 842 (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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838B ASP* 3.5 10.5 - - + +
839B ASP* 3.2 29.4 + - - +
840B ASN 4.9 1.2 - - - +
841B LEU* 1.3 87.8 + - + +
843B LYS* 1.3 61.0 + - - +
844B PHE* 3.5 19.5 + - + -
854B PRO* 4.0 13.9 - - + -
856B TRP* 3.6 28.7 - - + +
857B TYR* 3.7 33.0 - - + -
858B ILE* 3.8 29.4 - - + +
1045B TYR* 5.1 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