Contacts of the helix formed by residues 944 - 948 (chain B) in PDB entry 3B7B
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 944 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912B LEU* 3.7 52.3 - - + +
913B HIS* 3.7 16.2 - - + +
916B ALA* 3.7 5.9 - - - +
933B ASP 3.9 3.8 - - - +
934B VAL* 3.3 26.9 - - + +
936B LEU 3.3 13.2 - - - +
943B THR* 1.3 89.5 - - - +
945B LEU* 1.3 59.6 + - - +
947B CYS* 2.8 22.7 + - + +
948B ALA 3.2 7.8 + - - -
958B LEU* 3.9 8.1 - - + -
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Residues in contact with LEU 945 (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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934B VAL* 4.9 8.5 - - + +
943B THR* 3.2 8.2 + - - +
944B PRO* 1.3 81.4 - - - +
946B GLN* 1.3 63.0 + - + +
947B CYS 3.0 4.7 + - - -
948B ALA* 3.1 17.8 + - - +
955B TRP* 3.6 36.9 - - + +
958B LEU* 3.4 37.1 - - + +
959B GLN* 3.9 26.7 - - + +
962B LYS* 5.3 8.1 - - + -
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Residues in contact with GLN 946 (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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937B LYS* 5.1 4.2 - - - +
941B GLY 3.7 15.9 + - - +
942B GLU* 3.8 20.4 - - + +
943B THR* 3.2 45.1 + - - +
944B PRO 3.2 0.4 - - - -
945B LEU* 1.3 79.7 - - + +
947B CYS* 1.3 60.3 + - - +
948B ALA 4.5 3.1 - - - +
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Residues in contact with CYS 947 (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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913B HIS* 4.1 12.1 - - - +
917B ARG* 3.1 66.0 - - + +
938B ASN* 4.3 0.2 - - - -
942B GLU* 3.6 23.8 - - - -
943B THR 3.2 22.0 - - - -
944B PRO* 2.8 10.6 + - + +
946B GLN* 1.3 76.2 - - - +
948B ALA* 1.3 65.7 + - - +
949B SER 3.9 0.5 + - - -
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Residues in contact with ALA 948 (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 ALA* 3.8 14.3 - - + +
944B PRO 3.2 3.0 + - - -
945B LEU 3.1 16.6 + - - +
946B GLN 4.5 2.9 - - - +
947B CYS* 1.3 84.4 - - - +
949B SER* 1.3 62.5 + - - +
950B LEU 3.7 1.7 + - - -
954B VAL* 4.1 2.2 - - + -
955B TRP* 3.9 26.2 - - + +
958B LEU* 3.8 25.1 - - + -
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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