Contacts of the helix formed by residues 84 - 97 (chain C) in PDB entry 1R4N
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 ASN 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C ASP 3.4 13.4 + - - +
62C GLY 4.2 3.0 - - - -
63C ASN 2.8 21.6 + - - -
64C GLN* 4.7 1.6 - - - +
65C VAL* 4.1 1.6 - - - -
83C LYS* 1.3 76.4 - - - +
85C ARG* 1.3 66.3 + - - +
86C ALA* 3.0 17.7 - - - +
87C GLU* 2.7 26.7 + - + +
88C ALA* 2.8 12.5 + - - -
106C GLU* 2.9 54.8 - - - +
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Residues in contact with ARG 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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37C ASN* 4.2 8.7 + - - +
38C ALA* 2.9 28.7 + - + +
39C THR* 3.5 26.7 - - - +
61C ASP* 3.0 27.8 + - - +
63C ASN* 3.4 41.1 + - - +
64C GLN 5.0 0.8 + - - -
65C VAL* 3.4 25.0 - - + +
69C ASP* 3.5 33.5 + - - -
76C LEU* 4.3 12.0 - - + +
83C LYS 3.4 6.5 + - - -
84C ASN* 1.3 72.3 - - - +
86C ALA* 1.3 62.1 + - - +
89C ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 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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38C ALA* 4.7 0.2 - - - -
59C ILE* 3.8 24.8 - - + +
61C ASP* 3.2 46.5 - - + +
84C ASN* 2.7 13.7 + - - +
85C ARG* 1.3 78.3 - - - +
87C GLU* 1.3 64.2 + - - +
89C ALA* 3.8 1.6 - - - +
90C MET* 3.1 20.8 + - - +
104C PHE* 4.4 5.2 - - + -
105C VAL 4.1 3.1 - - - +
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LYS* 5.2 10.3 - - + +
84C ASN* 2.7 24.6 + - + +
86C ALA* 1.3 74.3 - - - +
88C ALA* 1.3 66.7 + - - +
90C MET* 3.0 18.6 + - - +
91C GLU* 3.2 26.3 + - + +
104C PHE* 3.4 51.4 - - + -
106C GLU* 4.4 8.8 - - - +
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Residues in contact with ALA 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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65C VAL* 4.1 8.5 - - + -
76C LEU* 3.6 19.5 - - + -
80C SER* 4.0 22.0 - - - +
83C LYS* 4.8 9.6 - - + +
84C ASN 2.8 19.3 + - - +
85C ARG 3.8 1.1 - - - +
87C GLU* 1.3 74.8 - - - +
89C ALA* 1.3 63.9 + - - +
91C GLU* 3.3 18.1 + - - +
92C PHE* 3.2 21.2 - - - -
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Residues in contact with ALA 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 ALA* 4.1 20.2 - - + +
43C THR* 4.3 8.1 - - - +
59C ILE* 4.3 1.3 - - + -
75C PHE 3.6 15.3 - - - +
76C LEU* 3.5 8.9 - - + +
85C ARG 2.9 21.8 + - - +
86C ALA 3.8 2.5 - - - +
88C ALA* 1.3 73.2 - - - +
90C MET* 1.3 66.6 + - - +
92C PHE* 2.9 14.2 + - - +
93C LEU* 3.1 28.7 + - + +
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Residues in contact with MET 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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57C PHE* 3.8 23.0 - - + -
59C ILE* 3.9 12.0 - - + +
86C ALA 3.1 10.0 + - - +
87C GLU* 3.0 12.9 + - - +
89C ALA* 1.3 79.1 - - - +
91C GLU* 1.3 64.6 + - + +
92C PHE 3.0 0.2 + - - -
93C LEU* 3.3 2.8 + - - +
94C GLN* 2.7 68.9 + - + +
102C GLY 3.8 19.1 - - - +
103C SER* 3.8 9.0 - - - +
104C PHE* 3.6 29.4 - - + -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LYS* 5.2 9.7 + - - +
87C GLU* 3.2 27.9 + - + +
88C ALA* 3.6 17.3 - - - +
89C ALA 3.2 0.4 + - - -
90C MET* 1.3 88.6 - - + +
92C PHE* 1.3 67.0 + - + +
94C GLN* 3.4 17.8 - - - +
95C GLU* 3.6 16.0 + - - +
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Residues in contact with PHE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 3.5 39.2 - - + -
76C LEU* 4.5 1.3 - - - -
77C GLN* 4.2 41.1 - - + -
79C SER* 5.2 3.1 - - - -
80C SER* 4.9 9.0 - - - -
88C ALA* 3.2 25.4 - - - -
89C ALA 2.9 6.2 + - - +
91C GLU* 1.3 81.1 - - + +
93C LEU* 1.3 68.2 + - - +
94C GLN 3.0 0.9 - - - -
95C GLU* 2.9 31.1 + - - +
96C LEU* 3.7 3.8 + - - +
114D ARG* 3.6 41.6 + - - +
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Residues in contact with LEU 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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35C LEU* 5.7 0.4 - - + -
38C ALA* 6.3 0.2 - - + -
43C THR* 3.8 26.7 - - - +
46C LEU* 3.7 25.8 - - + -
47C LYS* 4.2 8.1 - - + +
50C VAL* 4.0 12.9 - - + +
57C PHE* 4.3 9.2 - - + -
59C ILE* 3.7 14.4 - - + -
75C PHE* 3.4 32.8 - - + -
89C ALA* 3.1 23.3 + - + +
90C MET* 3.9 2.5 - - - +
92C PHE* 1.3 74.8 - - - +
94C GLN* 1.3 55.9 + - - +
96C LEU* 2.6 48.8 + - + +
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Residues in contact with GLN 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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50C VAL* 5.4 0.8 - - - +
57C PHE* 4.4 9.3 - - + -
90C MET* 2.7 42.8 + - + +
91C GLU* 3.4 13.7 - - - +
93C LEU* 1.3 77.0 - - - +
95C GLU* 1.3 61.7 + - + +
96C LEU 3.5 0.2 + - - -
97C ASN 3.5 17.0 + - - +
98C SER* 4.5 4.4 + - - +
100C VAL* 3.2 26.0 + - - +
101C SER* 4.8 0.4 - - - +
102C GLY* 3.3 19.9 + - - +
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Residues in contact with GLU 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 GLU 3.7 14.7 - - - +
92C PHE* 2.9 25.0 + - - +
93C LEU 2.8 1.6 + - - -
94C GLN* 1.3 80.8 - - + +
96C LEU* 1.3 63.9 + - - +
97C ASN* 3.2 3.1 + - - -
98C SER* 4.7 1.4 + - - -
95D ARG* 3.6 32.7 + - - +
114D ARG* 5.2 10.8 + - - +
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Residues in contact with LEU 96 (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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12C LYS* 5.4 1.4 + - - -
47C LYS* 3.6 22.0 - - + +
50C VAL* 3.9 11.0 - - + -
51C LEU* 4.3 17.8 - - + +
75C PHE* 3.2 40.2 - - + -
92C PHE 4.3 0.9 - - - +
93C LEU* 2.6 33.1 + - + +
95C GLU* 1.3 73.4 - - - +
97C ASN* 1.3 60.4 + - - +
88D LEU 5.3 2.8 - - - +
92D PHE* 3.7 28.5 - - + +
95D ARG* 3.3 35.0 + - - +
110D PHE* 6.1 0.4 - - + -
114D ARG* 5.9 0.4 - - - +
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Residues in contact with ASN 97 (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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12C LYS* 3.0 31.5 + - - +
13C TYR* 3.3 13.2 + - - -
50C VAL* 3.5 23.7 + - + +
51C LEU* 3.4 19.5 + - - +
94C GLN 3.5 13.2 + - - +
95C GLU 3.2 1.2 - - - -
96C LEU* 1.3 82.2 + - - +
98C SER* 1.3 59.0 + - - +
99C ASP* 2.7 46.6 + - - +
100C VAL* 3.2 25.3 + - + +
88D LEU 5.2 1.4 + - - -
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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