Contacts of the helix formed by residues 995 - 1003 (chain A) in PDB entry 3POZ
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 SER 995 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SO4 3.6 13.6 + - - -
795A PHE* 3.6 18.5 - - - -
990A PRO* 3.9 8.3 - - - +
991A SER 2.9 18.3 + - - -
992A PRO 3.5 1.6 + - - -
994A ASP* 1.3 74.1 - - - +
996A ASN* 1.3 63.4 + - - +
997A PHE* 3.5 7.6 + - - +
998A TYR* 3.1 30.4 + - - +
999A ARG* 3.0 25.7 + - - +
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Residues in contact with ASN 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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2A SO4 2.9 29.8 + - - +
994A ASP 3.3 6.5 + - - +
995A SER* 1.3 72.3 - - - +
997A PHE* 1.3 52.0 + - - +
999A ARG* 3.5 11.6 + - - +
1000A ALA* 2.7 35.8 + - - +
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Residues in contact with PHE 997 (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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2A SO4 3.0 18.2 + - - +
718A LEU* 5.5 4.7 - - + -
794A PRO 3.3 20.0 - - - -
795A PHE* 3.6 13.0 - - + +
796A GLY* 3.4 33.4 - - - -
797A CYS 5.2 0.2 - - - -
800A ASP* 5.7 10.3 - - + -
805A HIS* 6.4 0.7 - - + -
995A SER* 3.2 4.5 - - - +
996A ASN* 1.3 73.6 - - - +
998A TYR* 1.3 65.3 + - - +
1000A ALA* 3.1 8.6 + - + +
1001A LEU* 3.0 52.5 + - + +
1023A 03P 5.4 4.0 - + - -
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Residues in contact with TYR 998 (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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794A PRO* 3.5 45.8 + - + +
795A PHE* 3.7 23.3 - + + -
992A PRO* 3.6 36.7 - - + +
995A SER* 3.1 26.7 + - - +
997A PHE* 1.3 74.7 - - - +
999A ARG* 1.3 61.5 + - + +
1001A LEU* 3.3 2.9 + - - +
1002A MET* 2.8 53.0 + - + +
1003A ASP* 5.1 3.6 - - - -
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Residues in contact with ARG 999 (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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992A PRO 4.3 5.8 - - - +
993A THR* 2.7 30.1 + - - +
994A ASP* 4.4 6.8 + - - +
995A SER 3.0 26.2 + - - +
996A ASN* 3.6 12.3 - - - +
998A TYR* 1.3 78.2 - - + +
1000A ALA* 1.3 60.2 + - - +
1003A ASP* 2.8 60.7 + - + +
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Residues in contact with ALA1000 (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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728A LYS* 4.4 7.3 - - - -
996A ASN 2.7 20.6 + - - +
997A PHE* 3.1 11.2 + - + +
999A ARG* 1.3 72.8 - - - +
1001A LEU* 1.3 68.8 + - + +
1003A ASP 4.9 2.8 + - - -
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Residues in contact with LEU1001 (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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718A LEU* 4.2 21.5 - - + -
728A LYS* 3.1 35.5 + - + +
792A LEU* 3.9 26.9 - - + +
793A MET 4.1 2.5 - - - +
794A PRO* 3.8 30.5 - - + +
997A PHE* 3.0 44.4 + - + +
998A TYR 3.7 6.1 - - - +
1000A ALA* 1.3 84.0 - - + +
1002A MET* 1.3 74.0 + - + +
1003A ASP 3.7 1.3 + - - -
1023A 03P 4.9 1.1 - - + -
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Residues in contact with MET1002 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741A PRO* 4.2 23.3 - - + -
792A LEU* 3.7 32.8 - - + +
794A PRO* 3.7 23.3 - - + -
998A TYR* 2.8 49.4 + - + +
1001A LEU* 1.3 80.0 - - + +
1003A ASP* 1.3 71.8 + - - +
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Residues in contact with ASP1003 (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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998A TYR* 5.1 4.2 - - - -
999A ARG* 2.8 54.2 + - + +
1000A ALA 5.1 2.5 - - - -
1001A LEU 5.0 2.2 - - - -
1002A MET* 1.3 86.1 - - - +
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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