Contacts of the helix formed by residues 1081 - 1085 (chain I) in PDB entry 6PST
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 PRO1081 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ARG* 3.7 40.4 - - + +
34H GLY* 6.2 2.0 - - - -
820I GLU* 3.9 9.4 - - + +
1078I LYS* 4.2 7.9 - - - +
1079I ILE 3.5 6.0 - - - +
1080I ASN* 1.3 98.8 - - - +
1082I ILE* 1.3 61.4 + - - +
1083I GLU* 3.1 23.8 - - - +
1084I ASP* 2.9 35.3 + - + +
1085I MET* 3.4 6.6 - - - +
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Residues in contact with ILE1082 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ARG* 4.0 2.4 + - - -
48G LEU* 3.4 48.5 - - + +
819I SER* 4.0 18.6 - - - +
820I GLU* 4.2 10.4 - - + +
821I ARG* 3.7 42.4 - - + +
824I GLN* 5.0 9.6 - - - +
1080I ASN 3.6 1.2 + - - -
1081I PRO* 1.3 72.3 - - + +
1083I GLU* 1.3 66.9 + - - +
1084I ASP 3.5 0.3 + - - -
1085I MET* 3.6 9.0 + - - +
1093I PRO* 3.7 26.0 - - + +
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Residues in contact with GLU1083 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ARG* 4.2 13.3 + - - +
45G ARG* 3.9 45.8 + - + +
48G LEU* 3.9 28.9 - - + +
49G SER* 4.1 22.5 - - - -
33H ARG* 4.6 13.4 + - - +
34H GLY* 4.6 3.6 - - - -
1081I PRO* 3.7 19.5 - - - +
1082I ILE* 1.3 85.1 + - - +
1084I ASP* 1.3 62.6 + - - +
1085I MET 3.4 0.9 - - - -
1215I GLY* 3.4 23.1 - - - +
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Residues in contact with ASP1084 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 2.2 37.2 + - - -
34H GLY* 5.3 5.2 - - - -
37H HIS* 4.5 7.8 - - - -
807I TRP* 3.1 23.8 - - + -
1078I LYS* 4.5 5.0 + - - -
1080I ASN* 3.2 26.7 + - - +
1081I PRO* 2.9 22.4 + - + +
1083I GLU* 1.3 79.4 - - - +
1085I MET* 1.3 60.8 + - - +
1215I GLY* 4.0 9.9 - - - -
1216I ARG* 3.5 18.9 + - + +
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Residues in contact with MET1085 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 4.3 5.0 + - - -
817I LEU* 3.5 15.0 - - + +
819I SER* 3.3 37.0 - - - +
1080I ASN* 3.3 25.4 - - + -
1081I PRO 3.4 16.2 - - - +
1082I ILE 3.6 9.5 + - - +
1083I GLU 3.4 1.2 - - - -
1084I ASP* 1.3 79.6 - - - +
1086I PRO* 1.3 76.3 - - + +
1087I TYR* 3.5 6.2 + - - -
1093I PRO* 4.3 4.2 - - + +
1094I VAL 3.3 21.3 - - - +
1096I ILE 4.7 0.9 - - - +
1097I VAL* 3.4 32.3 - - + -
1215I GLY* 3.4 17.2 - - - -
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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
------------------------------------------------------------
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