Contacts of the helix formed by residues 82 - 90 (chain C) in PDB entry 6XAV
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C TYR* 3.6 15.8 + - - -
81C VAL* 1.3 74.3 - - - +
83C PRO* 1.3 71.5 - - - +
84C SER* 3.2 14.7 + - - -
85C GLN* 3.2 34.2 + - - +
86C ILE* 3.3 12.0 + - - +
1022I LYS* 3.5 30.4 - - - +
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLY* 4.4 9.6 - - - +
62C PHE* 4.2 20.4 - - + +
80C TYR* 3.6 15.7 - - - +
81C VAL 3.7 2.0 - - - +
82C SER* 1.3 86.7 - - - +
84C SER* 1.3 60.0 + - - +
86C ILE* 3.2 14.2 + - + +
87C ARG* 3.0 33.0 + - + +
1022I LYS* 3.9 11.4 - - - +
1030I GLU* 4.1 18.4 - - - +
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C SER* 3.2 12.1 + - - -
83C PRO* 1.3 80.3 - - - +
85C GLN* 1.3 62.2 + - - +
87C ARG* 3.3 11.5 + - - +
88C ARG* 3.0 27.5 + - - +
1018I TYR* 4.5 27.3 + - - +
1019I ASP* 5.6 0.3 - - - -
1022I LYS* 3.4 27.2 - - - +
1026I GLU* 5.3 7.9 - - - -
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Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C VAL* 4.4 3.4 - - + +
82C SER* 3.2 30.4 + - - +
84C SER* 1.3 77.6 + - - +
86C ILE* 1.3 61.5 + - - +
88C ARG* 4.2 6.1 - - - -
89C PHE* 3.0 49.5 + - + +
91C LEU* 4.0 9.6 - - + +
113C LEU* 2.3 62.2 + - + +
114C LEU 4.3 5.3 + - - -
1019I ASP* 5.0 11.1 + - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 5.4 0.2 - - + -
57C ILE* 4.2 24.5 - - + -
61C GLY 3.5 25.1 - - - +
62C PHE* 4.5 2.9 - - - -
63C GLY 4.6 1.3 - - - +
81C VAL* 3.8 25.4 - - + +
82C SER 3.4 15.3 - - - +
83C PRO* 3.2 11.8 + - + +
85C GLN* 1.3 77.7 - - - +
87C ARG* 1.3 58.1 + - + +
90C ASN* 3.0 29.5 + - - -
91C LEU* 3.5 33.4 - - + +
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PRO* 3.0 22.8 + - + +
84C SER* 3.8 8.1 - - - +
86C ILE* 1.3 78.4 - - + +
88C ARG* 1.3 61.8 + - - +
90C ASN* 3.6 13.0 - - - +
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C SER 3.0 17.6 + - - +
85C GLN* 3.8 6.1 - - - +
86C ILE 3.3 0.4 - - - -
87C ARG* 1.3 80.8 - - - +
89C PHE* 1.3 88.3 + - + +
90C ASN* 3.8 4.9 + - - +
128C ARG* 5.2 14.9 + - - +
28D ARG* 5.9 1.4 + - - -
1011I LEU* 4.6 15.4 + - - +
1014I LEU* 4.0 30.6 - - - +
1015I ALA* 5.3 15.2 - - + +
1018I TYR* 5.5 16.8 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLN* 3.0 34.7 + - + +
88C ARG* 1.3 98.1 - - + +
90C ASN* 1.3 72.0 + - - +
91C LEU* 3.3 25.2 - - + +
113C LEU* 6.3 1.3 - - + -
116C VAL* 3.7 33.4 - - + -
124C PRO* 6.0 6.5 - - + -
128C ARG* 5.3 21.5 - - + +
28D ARG* 6.2 0.2 - - - -
1015I ALA* 5.1 12.8 - - + -
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE 3.0 12.1 + - - +
87C ARG* 3.6 14.5 - - - +
88C ARG 4.7 3.5 + - - -
89C PHE* 1.3 80.7 - - - +
91C LEU* 1.3 65.7 + - - +
92C ARG* 3.7 10.2 + - - +
95C ASP* 4.2 2.6 - - - +
28D ARG* 3.2 48.0 + - - +
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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