Contacts of the helix formed by residues 82 - 95 (chain C) in PDB entry 3RJM
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 THR 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C GLN* 1.3 73.7 - - - +
83C ALA* 1.3 66.3 + - - +
84C GLN* 3.5 6.5 + - - +
85C GLU* 2.9 46.0 + - + +
86C MET* 2.8 23.6 + - - +
120C GLY* 3.9 1.3 - - - -
121C VAL* 4.0 13.7 - - + +
122C ASP* 3.6 30.3 - - + +
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Residues in contact with ALA 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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82C THR* 1.3 73.3 - - - +
84C GLN* 1.3 63.0 + - - +
86C MET* 3.4 17.9 + - + +
87C GLN* 3.1 23.2 + - - +
120C GLY* 3.7 2.4 - - - -
122C ASP* 3.2 7.6 + - - +
124C LYS* 3.5 41.3 - - + +
125C LEU 4.3 12.6 - - - +
126C LEU* 4.4 5.7 - - + +
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Residues in contact with GLN 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 THR* 3.2 6.5 + - - +
83C ALA* 1.3 77.6 - - - +
85C GLU* 1.3 60.2 + - - +
87C GLN* 3.3 6.7 + - + +
88C GLU* 2.7 66.1 + - + +
122C ASP* 5.1 1.2 + - - -
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Residues in contact with GLU 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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80C ASP 4.2 2.8 - - - +
81C GLN* 3.4 32.0 + - + +
82C THR* 2.9 50.1 + - + +
84C GLN* 1.3 75.5 - - + +
86C MET* 1.3 57.4 + - - +
88C GLU* 4.7 6.7 - - - +
89C LYS* 3.0 52.2 + - - +
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Residues in contact with MET 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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40C LEU* 3.9 26.0 - - + +
42C ASN* 3.3 27.4 - - - -
81C GLN* 3.6 17.9 - - + -
82C THR 2.8 17.3 + - - +
83C ALA* 3.5 22.2 - - - +
84C GLN 3.2 0.2 - - - -
85C GLU* 1.3 70.5 - - - +
87C GLN* 1.3 60.0 + - - +
89C LYS* 3.9 1.3 - - - -
90C LEU* 2.9 40.0 + - + +
118C ILE* 4.1 17.7 - - + +
119C TYR 4.0 5.4 - - - +
120C GLY* 3.7 15.9 - - - +
126C LEU* 3.7 29.2 - - + -
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Residues in contact with GLN 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 ALA 3.1 13.8 + - - +
84C GLN* 3.7 9.9 - - + +
86C MET* 1.3 76.1 - - - +
88C GLU* 1.3 73.5 + - - +
90C LEU* 3.9 4.2 - - - +
91C GLN* 3.1 34.9 + - - +
126C LEU* 3.8 28.6 - - + +
130C GLU* 3.8 22.3 + - + +
134C LEU* 4.2 23.8 - - + +
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Residues in contact with GLU 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 GLN* 2.7 55.4 + - + +
85C GLU* 4.0 7.2 - - - +
87C GLN* 1.3 86.6 - - - +
89C LYS* 1.3 62.0 + - + +
91C GLN* 3.4 11.0 + - - +
92C ASN* 2.9 34.2 + - - +
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Residues in contact with LYS 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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38C LEU* 5.0 2.0 - - - +
78C LEU* 3.8 37.3 - - + +
81C GLN* 2.8 34.2 + - - +
85C GLU* 3.0 33.8 + - - +
86C MET* 4.4 1.1 - - - +
88C GLU* 1.3 76.9 - - + +
90C LEU* 1.3 60.9 + - - +
92C ASN* 3.8 14.0 - - + +
93C PHE* 3.0 27.4 + - - +
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Residues in contact with LEU 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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38C LEU* 3.4 27.6 - - + -
40C LEU* 4.4 5.4 - - + -
78C LEU* 5.5 0.2 - - - +
86C MET* 2.9 30.0 + - + +
87C GLN* 3.9 1.1 - - - +
89C LYS* 1.3 76.3 - - - +
91C GLN* 1.3 56.0 + - - +
93C PHE* 3.2 5.0 + - - +
94C ALA* 2.8 30.7 + - - +
107C VAL* 4.1 10.8 - - + -
109C LEU* 4.0 25.1 - - + -
126C LEU* 3.8 11.9 - - + -
131C VAL* 3.7 33.4 - - + -
134C LEU* 3.5 17.0 - - + -
135C PHE* 4.0 12.1 - - + -
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Residues in contact with GLN 91 (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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87C GLN* 3.1 30.9 + - - +
88C GLU* 3.4 13.6 + - - +
90C LEU* 1.3 72.9 - - - +
92C ASN* 1.3 70.0 + - - +
94C ALA* 3.3 4.1 + - + +
95C GLN* 3.0 40.8 + - + +
134C LEU* 3.7 30.6 - - + +
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Residues in contact with ASN 92 (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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88C GLU* 2.9 23.8 + - - +
89C LYS* 3.9 14.6 - - - +
90C LEU 3.4 0.2 - - - -
91C GLN* 1.3 78.7 - - - +
93C PHE* 1.3 63.1 + - - +
95C GLN* 3.2 8.4 + - - +
96C LEU* 3.1 27.4 + - + +
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Residues in contact with PHE 93 (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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36C LEU* 3.7 37.7 - - + -
37C ALA 4.0 2.2 - - - -
38C LEU* 3.8 43.1 - - + -
76C HIS* 4.2 21.1 - + - -
89C LYS 3.0 19.7 + - - +
90C LEU* 3.4 6.3 - - - +
91C GLN 3.2 0.2 - - - -
92C ASN* 1.3 74.5 - - - +
94C ALA* 1.3 64.3 + - - +
96C LEU* 3.1 25.8 + - + +
99C HIS* 2.8 24.8 + + - -
105C CYS* 3.8 23.1 - - - -
107C VAL* 3.9 13.2 - - + -
135C PHE* 3.7 15.3 - + - -
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Residues in contact with ALA 94 (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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90C LEU 2.8 17.3 + - - +
91C GLN* 3.8 4.5 - - - +
93C PHE* 1.3 75.6 - - - +
95C GLN* 1.3 65.4 + - - +
96C LEU 3.3 0.4 - - - +
99C HIS* 3.5 10.9 - - - -
134C LEU* 3.5 30.7 - - + +
135C PHE* 3.6 28.5 - - + -
140C CYS* 3.3 22.3 - - - -
142C SER* 5.5 1.6 - - - -
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Residues in contact with GLN 95 (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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91C GLN* 3.0 30.2 + - + +
92C ASN* 3.6 7.4 - - - +
93C PHE 3.1 0.4 - - - -
94C ALA* 1.3 82.0 + - - +
96C LEU* 1.3 65.6 + - - +
97C PRO* 3.3 5.9 - - - +
134C LEU 4.5 6.7 + - - -
139C ASN* 2.9 30.6 + - - +
140C CYS* 4.6 1.0 - - - +
141C PRO* 5.6 2.3 - - - +
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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