Contacts of the strand formed by residues 81 - 87 (chain C) in PDB entry 4XZG
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 GLU 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C VAL 4.5 3.5 - - - +
77C VAL* 3.3 14.5 - - + +
78C ASN* 2.4 68.8 + - - +
79C ASN 3.1 0.6 - - - -
80C ASN* 1.3 79.9 - - - +
82C MET* 1.3 69.3 + - - +
83C VAL 3.8 0.2 + - - -
102C ASN* 5.0 1.9 - - - +
103C VAL* 3.3 35.7 + - + +
133C VAL* 3.4 3.0 - - - -
134C VAL* 3.0 28.1 + - - +
142G PHE* 3.8 23.6 - - + -
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Residues in contact with MET 82 (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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80C ASN 4.2 1.0 + - - -
81C GLU* 1.3 78.5 - - - +
83C VAL* 1.3 66.1 + - - +
102C ASN* 4.9 0.2 - - - -
103C VAL* 3.1 33.6 + - + +
131C GLU* 4.0 28.3 - - - +
132C GLY 3.2 14.8 - - - +
133C VAL* 4.3 12.1 - - + +
142G PHE* 5.3 0.2 - - - -
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Residues in contact with VAL 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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77C VAL* 3.8 33.0 - - + -
81C GLU 3.8 0.6 + - - -
82C MET* 1.3 80.9 - - - +
84C ALA* 1.3 61.4 + - - +
85C LEU* 4.2 4.7 + - + +
100C VAL* 3.7 20.0 - - + -
101C ASN 3.3 13.7 - - - +
102C ASN* 4.7 2.0 - - - +
103C VAL* 5.9 0.4 - - - -
108C VAL* 5.6 0.4 - - + -
132C GLY* 3.0 25.8 + - - +
134C VAL* 3.8 16.4 - - + -
144C MET* 5.9 0.2 - - - -
146C LEU* 3.4 32.5 - - + -
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Residues in contact with ALA 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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83C VAL* 1.3 74.8 - - - +
85C LEU* 1.3 65.5 + - - +
86C GLN* 6.0 0.7 - - + -
100C VAL* 3.5 4.5 - - - +
101C ASN* 2.6 50.2 + - + +
102C ASN 4.7 5.1 - - - +
103C VAL* 6.0 2.0 - - - -
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Residues in contact with LEU 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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83C VAL* 4.2 10.9 + - + +
84C ALA* 1.3 80.7 - - - +
86C GLN* 1.3 62.8 + - - +
98C ILE* 3.8 18.6 - - + -
99C LYS 3.6 1.6 - - - -
100C VAL* 4.3 17.5 - - + -
111C LEU* 4.2 6.7 - - + -
119C LEU* 4.2 19.3 - - + -
123C MET* 3.8 20.0 - - + +
130C ILE* 3.9 40.4 + - + +
132C GLY* 5.2 5.6 - - - +
146C LEU* 4.5 13.5 - - + -
148C MET* 4.6 7.4 - - + -
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Residues in contact with GLN 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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84C ALA* 3.9 1.3 + - + -
85C LEU* 1.3 75.9 - - - +
87C ARG* 1.3 72.6 + - - +
98C ILE* 4.0 3.3 - - - +
99C LYS* 2.8 73.0 + - + +
101C ASN* 2.8 33.1 + - - +
123C MET* 4.7 0.2 - - - -
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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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85C LEU 4.3 0.2 - - - -
86C GLN* 1.3 84.2 - - - +
88C ASP* 1.3 64.6 + - - +
89C PRO* 3.4 28.4 - - + +
95C LYS 3.0 28.7 + - - -
96C ASN* 3.1 8.3 + - - +
97C ALA 2.7 30.5 + - - +
98C ILE* 3.6 20.6 - - - +
99C LYS* 5.0 0.7 - - - +
120C ALA* 3.7 24.6 - - - +
123C MET* 3.9 25.7 - - + +
124C ASP* 2.8 42.5 + - - +
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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