Contacts of the helix formed by residues 89 - 96 (chain 2) in PDB entry 5NET
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 GLY 89 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872 HIS* 3.1 14.1 + - - -
882 LYS* 1.3 79.8 - - - +
902 VAL* 1.3 66.7 + - - -
912 TYR 3.4 2.2 - - - -
922 GLY 4.1 0.2 - - - -
932 TYR* 3.4 20.3 + - - +
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Residues in contact with VAL 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552 VAL* 5.6 1.3 - - + -
572 GLN* 3.5 37.0 - - + +
582 ALA* 4.7 1.6 - - - +
602 ARG* 5.9 6.3 - - + +
872 HIS* 3.4 5.1 - - + -
892 GLY* 1.3 71.0 - - - -
912 TYR* 1.3 65.3 + - - +
932 TYR* 3.3 15.1 + - + +
942 LEU* 3.3 23.7 - - + +
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Residues in contact with TYR 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582 ALA* 4.0 30.0 - - + +
622 PHE* 5.3 1.1 - + - -
842 PRO* 3.7 23.2 - - + +
872 HIS* 3.3 34.5 - + + +
902 VAL* 1.3 80.2 - - - +
922 GLY* 1.3 60.4 + - - +
942 LEU* 3.1 25.2 + - + +
952 THR* 3.6 11.3 + - - -
1012 MET* 3.6 22.0 - - + -
1032 ASN* 2.4 34.7 + - - -
1052 TRP* 3.8 15.5 - + - -
1712 TYR* 3.5 19.5 - + - -
2052 PRO* 3.7 19.7 - - + -
2082 VAL* 4.0 4.9 - - + -
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Residues in contact with GLY 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872 HIS* 3.1 41.8 + - - +
892 GLY 4.1 0.7 - - - -
902 VAL 3.4 0.2 - - - -
912 TYR* 1.3 73.9 - - - +
932 TYR* 1.3 63.4 + - - +
952 THR* 3.6 21.2 + - - -
962 ASP* 3.8 8.0 + - - +
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Residues in contact with TYR 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892 GLY 3.4 13.4 + - - +
902 VAL* 3.3 13.9 + - + +
912 TYR 3.2 0.8 - - - -
922 GLY* 1.3 78.8 - - - +
942 LEU* 1.3 69.4 + - + +
962 ASP* 3.3 7.5 + - + +
972 SER* 3.2 39.8 + - - -
982 TYR* 6.3 1.3 - + - -
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Residues in contact with LEU 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552 VAL* 3.9 34.3 - - + -
582 ALA* 4.4 7.6 - - + -
902 VAL* 3.3 28.3 - - + +
912 TYR* 3.1 10.6 + - + +
932 TYR* 1.3 87.5 - - + +
952 THR* 1.3 59.2 + - - +
972 SER* 3.8 0.7 - - - -
982 TYR* 3.0 49.1 + - + +
1012 MET* 4.1 14.0 - - + +
2082 VAL* 4.1 11.4 - - + -
2102 VAL* 3.7 29.4 - - + -
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Residues in contact with THR 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842 PRO* 5.4 4.2 - - + +
912 TYR* 3.7 18.5 + - - -
922 GLY* 3.6 14.3 + - - -
932 TYR 3.2 0.8 - - - -
942 LEU* 1.3 78.6 - - - +
962 ASP* 1.3 59.0 + - + +
982 TYR 3.5 12.3 - - - +
1012 MET* 4.3 14.5 - - - -
1712 TYR* 4.6 20.4 - - + +
1722 LYS* 4.5 26.9 - - + +
2142 PHE* 4.4 5.4 - - - -
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Residues in contact with ASP 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922 GLY 3.8 6.8 + - - +
932 TYR* 3.3 9.6 + - + +
942 LEU 3.3 0.4 - - - -
952 THR* 1.3 78.1 - - - +
972 SER* 1.3 58.6 + - - +
982 TYR 3.8 0.2 - - - -
1722 LYS* 5.6 6.4 - - - +
2142 PHE* 4.1 16.0 - - - +
2152 PRO 5.8 0.2 - - - +
2172 LYS* 5.9 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