Contacts of the helix formed by residues 988 - 996 (chain A) in PDB entry 1ATZ
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 LYS 988 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955A ILE* 3.3 26.0 - - + +
956A SER* 2.9 27.5 + - - +
957A LYS 4.3 0.8 + - - -
958A ALA 2.7 26.6 + - - -
959A ASN* 4.9 0.6 - - - +
960A ILE* 4.0 24.1 - - + +
986A PRO 3.9 3.4 + - - +
987A GLU* 1.3 74.0 + - - +
989A ALA* 1.3 56.9 + - - +
991A LEU* 3.1 8.1 + - + +
992A LEU* 2.8 44.6 + - + +
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Residues in contact with ALA 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A GLU* 3.3 5.9 + - + +
988A LYS* 1.3 76.2 - - - +
990A HIS* 1.3 56.9 + - - +
992A LEU* 3.9 10.3 - - - +
993A SER* 3.0 28.4 + - - -
1099B THR 3.9 4.9 - - - +
1100B LEU* 3.9 33.4 - - + +
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Residues in contact with HIS 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984A VAL* 4.4 9.4 - - + +
985A VAL* 3.3 39.3 + - + -
987A GLU* 2.9 14.2 + - + +
989A ALA* 1.3 77.1 - - - +
991A LEU* 1.3 62.7 + - - +
993A SER* 2.7 23.7 + - - -
994A LEU* 3.2 17.9 + - + +
953B ALA* 4.3 21.0 - - + -
956B SER* 4.3 13.8 + - - -
957B LYS* 3.8 34.8 - - + +
1098B VAL 4.6 0.4 + - - -
1099B THR* 3.4 36.5 + - + +
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Residues in contact with LEU 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A ILE* 3.9 17.7 - - + +
960A ILE* 3.5 41.3 - - + -
967A VAL* 4.6 9.2 - - + +
980A VAL* 4.0 16.7 - - + +
984A VAL* 3.4 33.9 - - + +
985A VAL 4.2 5.2 - - - +
986A PRO* 4.3 6.3 - - + -
987A GLU 2.9 22.4 + - - +
988A LYS* 3.6 6.5 - - - +
990A HIS* 1.3 74.9 - - - +
992A LEU* 1.3 64.6 + - - +
994A LEU* 3.0 19.2 + - + +
995A VAL* 3.2 16.2 + - - +
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Residues in contact with LEU 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952A LYS* 3.5 54.9 - - + +
955A ILE* 4.0 14.4 - - + -
956A SER* 3.7 17.9 - - - +
988A LYS* 2.8 31.8 + - + +
989A ALA* 3.9 8.5 - - - +
991A LEU* 1.3 72.2 - - - +
993A SER* 1.3 57.0 + - - +
995A VAL* 3.1 7.3 + - - +
996A ASP* 2.9 34.0 + - - +
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Residues in contact with SER 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989A ALA 3.0 16.3 + - - -
990A HIS* 2.7 21.6 + - - -
992A LEU* 1.3 77.2 - - - +
994A LEU* 1.3 60.0 + - - +
996A ASP* 3.5 9.9 + - - +
997A VAL* 3.4 28.8 + - - +
957B LYS* 3.0 28.1 + - - +
1099B THR 5.2 1.6 + - - -
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Residues in contact with LEU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979A ASP 4.2 11.2 - - - +
980A VAL* 3.8 28.6 - - + +
981A PRO* 4.7 5.8 - - + -
984A VAL* 4.1 28.3 - - + -
990A HIS* 3.5 25.8 - - + +
991A LEU* 3.0 10.8 + - - +
993A SER* 1.3 74.3 - - - +
995A VAL* 1.3 65.9 + - - +
997A VAL* 3.3 20.7 - - + +
998A MET* 3.5 11.4 - - - +
956B SER* 4.5 13.0 - - - +
957B LYS* 3.9 28.0 - - + +
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Residues in contact with VAL 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948A LYS* 3.3 30.9 - - + +
951A ALA* 4.2 6.5 - - + -
952A LYS* 3.6 28.0 - - + -
955A ILE* 3.8 24.9 - - + -
969A VAL* 4.3 6.7 - - + -
980A VAL* 3.8 12.3 - - + -
991A LEU 3.2 13.1 + - - +
992A LEU* 3.1 7.7 + - - +
994A LEU* 1.3 76.3 - - - +
996A ASP* 1.3 64.4 + - - +
998A MET* 2.9 36.7 + - - +
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Residues in contact with ASP 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948A LYS* 3.0 25.6 + - - +
952A LYS* 2.9 36.4 + - - +
992A LEU* 2.9 21.5 + - - +
993A SER* 3.8 10.7 - - - +
994A LEU 3.4 0.2 - - - -
995A VAL* 1.3 77.1 - - - +
997A VAL* 1.3 59.5 + - + +
999A GLN* 4.4 3.5 + - - -
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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