Contacts of the helix formed by residues 989 - 993 (chain B) in PDB entry 2ZM3
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 989 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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987B TYR 4.8 0.4 - - - +
988B VAL* 1.3 94.0 - - + +
990B ASP* 1.3 63.7 + - - +
991B GLU* 3.3 7.9 + - + +
992B TRP* 3.4 30.0 + - + +
993B GLU* 4.3 2.3 + - - +
1052B SER* 5.2 0.4 - - - +
1055B LYS* 3.2 29.2 - - - +
1264C SER* 5.5 6.7 - - - +
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Residues in contact with ASP 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272A PRO* 6.0 1.6 - - - +
985B ASP* 4.6 9.2 - - - +
988B VAL 3.9 7.6 - - - +
989B PRO* 1.3 72.1 - - - +
991B GLU* 1.3 65.3 + - - +
992B TRP 3.1 0.2 - - - -
993B GLU* 3.0 35.8 + - - +
1070B SER* 5.4 3.0 + - - -
1071B GLN* 5.8 2.7 + - - -
1264C SER* 5.3 9.4 + - - +
1267C LYS* 5.2 16.6 - - - +
1268C GLU* 5.0 7.8 - - - +
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Residues in contact with GLU 991 (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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989B PRO* 3.1 5.4 - - + -
990B ASP* 1.3 79.0 - - - +
992B TRP* 1.3 88.9 + - + +
993B GLU 3.2 5.0 + - - +
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Residues in contact with TRP 992 (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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988B VAL* 4.9 1.8 - - + -
989B PRO* 3.8 26.9 - - + +
990B ASP 3.1 1.4 - - - -
991B GLU* 1.3 93.1 + - + +
993B GLU* 1.3 62.8 + - - +
994B VAL* 3.9 1.4 - - - +
1055B LYS* 3.1 75.3 - - + +
1056B GLU* 5.2 6.3 - - - -
1065B LEU* 4.2 22.7 - - + -
1066B LEU 4.9 3.5 - - - +
1067B GLY* 3.4 14.3 - - - -
1068B VAL* 3.0 32.2 + - + +
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Residues in contact with GLU 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272A PRO* 6.2 0.2 - - - +
989B PRO 4.3 2.5 + - - +
990B ASP* 3.0 30.0 + - - +
991B GLU 3.2 4.2 - - - +
992B TRP* 1.3 80.2 - - - +
994B VAL* 1.3 74.4 + - - +
995B ALA* 4.8 1.1 - - - +
1068B VAL* 3.1 9.0 - - - +
1069B VAL* 4.0 3.5 - - - +
1070B SER* 3.0 42.3 + - - +
1071B GLN* 3.2 27.7 + - - +
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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