Contacts of the helix formed by residues 81 - 86 (chain I) in PDB entry 1XFB
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 HIS 81 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I PHE 3.9 2.2 + - - -
80I PHE* 1.3 83.5 - - + +
82I GLU* 1.3 70.9 + - - +
84I LEU* 2.9 20.1 + - - +
85I TYR* 3.3 35.0 - + - -
107I ILE* 4.1 13.7 - - + +
108I LYS 5.0 5.2 + - - +
138I TYR* 2.6 38.2 + + + +
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Residues in contact with GLU 82 (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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37I VAL* 5.2 0.9 - - - +
53I GLU* 3.6 13.1 - - + +
56I ARG* 2.8 50.8 + - - +
60I ARG* 5.1 0.9 + - - -
80I PHE* 3.0 25.4 + - + -
81I HIS* 1.3 83.4 - - - +
83I THR* 1.3 64.3 + - - +
85I TYR* 2.9 25.2 + - - +
86I GLN* 3.5 38.9 + - + +
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Residues in contact with THR 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ALA 5.3 1.1 - - - +
60I ARG* 3.3 32.6 + - + +
64I PHE* 3.6 24.0 - - + -
79I PHE* 3.5 21.3 - - + -
80I PHE* 2.8 22.7 + - - +
82I GLU* 1.3 74.8 + - - +
84I LEU* 1.3 57.3 + - - -
85I TYR 2.8 12.2 + - - -
86I GLN* 2.9 34.7 + - - +
94I PHE* 3.9 8.8 - - + +
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Residues in contact with LEU 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 3.7 21.2 - - + -
80I PHE 3.1 7.7 + - - +
81I HIS* 2.9 14.1 + - - +
83I THR* 1.3 74.4 - - - +
85I TYR* 1.3 90.4 + - + +
86I GLN 3.6 1.2 - - - +
93I PRO* 6.1 0.3 - - - +
95I VAL* 3.2 40.5 - - + +
105I VAL* 3.9 21.1 - - + -
106I GLY 5.0 0.7 - - - +
107I ILE* 4.1 13.5 - - + -
138I TYR* 3.7 23.8 - - + +
141I ASP* 4.7 13.4 - - + +
143I ALA* 5.2 2.5 - - + -
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Residues in contact with TYR 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I HIS* 3.3 43.7 - + - -
82I GLU* 2.9 9.2 + - - +
83I THR 2.9 1.0 - - - -
84I LEU* 1.3 101.6 - - + +
86I GLN* 1.3 62.2 + - - +
87I LYS* 4.2 8.8 + - - +
93I PRO* 6.4 0.4 - - - -
137I GLN* 4.6 2.1 + - - +
138I TYR* 3.6 19.4 - - - -
141I ASP* 2.6 36.7 + - + -
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Residues in contact with GLN 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I GLU* 3.5 17.8 + - - +
57I ARG* 3.4 41.0 + - + +
60I ARG* 4.2 1.7 - - - +
82I GLU* 3.5 35.2 + - + +
83I THR* 2.9 31.2 + - - +
84I LEU 5.0 0.7 - - - +
85I TYR* 1.3 82.4 - - - +
87I LYS* 1.3 65.8 + - - +
93I PRO* 3.6 1.7 - - - +
94I PHE* 3.1 39.7 + - + +
95I VAL* 4.9 0.3 + - - +
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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