Contacts of the helix formed by residues 84 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP 3.4 13.3 + - - +
62A GLY 4.2 3.0 - - - -
63A ASN 2.8 22.1 + - - +
64A GLN* 4.7 2.0 - - + +
65A VAL* 4.1 1.1 - - - -
83A LYS* 1.3 76.3 - - - +
85A ARG* 1.3 67.6 + - - +
86A ALA* 3.0 17.9 - - - +
87A GLU* 2.7 27.2 + - + +
88A ALA* 2.8 12.2 + - - -
106A GLU* 2.9 54.2 - - - +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 4.2 8.5 + - - +
38A ALA* 3.0 27.6 + - + +
39A THR* 3.5 27.4 - - - +
61A ASP* 3.0 29.3 + - - +
63A ASN* 3.4 41.5 + - - +
64A GLN 5.0 0.8 + - - -
65A VAL* 3.4 24.0 - - + +
69A ASP* 3.5 32.7 + - - -
76A LEU* 4.3 10.9 - - + +
83A LYS 3.4 6.1 + - - -
84A ASN* 1.3 71.0 - - - +
86A ALA* 1.3 63.7 + - - +
88A ALA* 3.8 0.4 - - - +
89A ALA* 2.9 29.3 + - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 4.7 0.2 - - - -
59A ILE* 3.8 23.8 - - + +
61A ASP* 3.2 47.2 - - + +
84A ASN* 2.8 12.8 + - - +
85A ARG* 1.3 79.0 - - - +
87A GLU* 1.3 64.7 + - - +
89A ALA* 3.7 1.9 - - - +
90A MET* 3.0 20.4 + - - +
104A PHE* 4.4 5.2 - - + -
105A VAL 4.1 3.1 - - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 5.2 10.0 - - + +
84A ASN* 2.7 25.1 + - + +
86A ALA* 1.3 74.7 - - - +
88A ALA* 1.3 66.3 + - - +
90A MET* 3.0 14.3 + - - +
91A GLU* 3.2 32.0 + - + +
104A PHE* 3.4 49.7 - - + -
106A GLU* 4.5 9.1 - - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 4.1 8.3 - - + -
76A LEU* 3.6 19.5 - - + -
80A SER* 4.0 21.8 - - - +
83A LYS* 4.8 8.9 - - + +
84A ASN 2.8 19.3 + - - +
85A ARG 3.8 1.3 - - - +
87A GLU* 1.3 75.1 - - - +
89A ALA* 1.3 63.6 + - - +
91A GLU* 3.4 17.8 + - - +
92A PHE* 3.2 21.5 - - - -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 4.1 21.3 - - + +
43A THR* 4.3 14.4 - - - +
59A ILE* 4.2 6.3 - - + -
75A PHE* 3.7 13.0 - - - +
76A LEU* 3.5 8.4 - - + +
85A ARG 2.9 21.7 + - - +
86A ALA 3.7 2.7 - - - +
88A ALA* 1.3 72.1 - - - +
90A MET* 1.3 66.3 + - - +
92A PHE* 2.9 14.6 + - - +
93A LEU* 3.1 18.0 + - + +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.8 22.4 - - + -
59A ILE* 3.8 12.5 - - + +
86A ALA 3.0 11.4 + - - +
87A GLU* 3.2 12.3 - - - +
89A ALA* 1.3 78.0 - - - +
91A GLU* 1.3 65.0 + - + +
92A PHE 3.0 0.3 + - - -
93A LEU* 3.2 2.9 + - - +
94A GLN* 2.7 68.8 + - + +
102A GLY 3.8 18.4 - - - +
103A SER* 3.8 9.6 - - - +
104A PHE* 3.7 29.2 - - + -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 5.2 9.4 + - - +
87A GLU* 3.2 27.2 + - + +
88A ALA* 3.7 18.2 - - - +
89A ALA 3.3 0.4 - - - -
90A MET* 1.3 89.9 - - + +
92A PHE* 1.3 65.4 + - + +
94A GLN* 3.4 16.9 - - - +
95A GLU* 3.7 16.5 + - - +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.5 39.7 - - + -
76A LEU* 4.5 1.3 - - - -
77A GLN* 4.2 39.9 - - + -
79A SER* 5.2 2.7 - - - -
80A SER* 4.9 9.6 - - - -
88A ALA* 3.2 25.8 - - - -
89A ALA 2.9 6.3 + - - +
91A GLU* 1.3 81.7 - - + +
93A LEU* 1.3 67.6 + - - +
94A GLN 3.1 1.1 - - - -
95A GLU* 3.0 31.2 + - - +
96A LEU* 3.7 3.8 + - - +
95B ARG* 5.6 0.2 + - - -
114B ARG* 3.7 40.1 + - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.7 0.2 - - + -
43A THR* 3.8 27.1 - - - +
46A LEU* 3.7 25.1 - - + -
47A LYS* 4.2 7.6 - - + +
50A VAL* 3.9 13.0 - - + +
57A PHE* 4.3 9.4 - - + -
59A ILE* 3.7 15.0 - - + -
75A PHE* 3.5 32.3 - - + -
89A ALA* 3.1 23.3 + - + +
90A MET* 3.9 2.7 - - - +
92A PHE* 1.3 75.3 - - - +
94A GLN* 1.3 56.6 + - - +
96A LEU* 2.6 48.1 + - + +
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 5.5 1.1 - - - +
57A PHE* 4.4 9.5 - - + -
90A MET* 2.7 43.7 + - + +
91A GLU* 3.4 13.5 - - - +
93A LEU* 1.3 76.4 - - - +
95A GLU* 1.3 60.6 + - + +
96A LEU 3.5 0.2 + - - -
97A ASN 3.6 15.7 + - - +
98A SER* 4.6 5.3 + - - +
100A VAL* 3.2 26.6 + - - +
101A SER* 4.8 0.2 - - - +
102A GLY* 3.3 20.4 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU 3.7 15.9 - - - +
92A PHE* 3.0 25.5 + - - +
93A LEU 2.8 0.6 + - - -
94A GLN* 1.3 81.0 - - + +
96A LEU* 1.3 65.1 + - - +
97A ASN* 3.2 2.6 + - - -
98A SER* 4.7 1.6 + - - -
95B ARG* 3.8 33.3 + - - +
114B ARG* 5.2 9.4 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 5.4 1.2 + - - -
47A LYS* 3.6 22.0 - - + +
50A VAL* 3.8 11.4 - - + -
51A LEU* 4.3 19.2 - - + +
75A PHE* 3.2 40.4 - - + -
92A PHE 4.2 1.1 - - - +
93A LEU* 2.6 33.2 + - + +
95A GLU* 1.3 73.5 - - - +
97A ASN* 1.3 60.2 + - - +
88B LEU 5.3 3.3 - - - +
92B PHE* 3.8 26.5 - - + +
95B ARG* 3.3 34.0 + - - +
110B PHE* 6.3 0.4 - - + -
114B ARG* 6.0 0.4 - - - +
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 2.9 34.2 + - - +
13A TYR* 3.3 10.9 + - - -
50A VAL* 3.5 24.1 + - + +
51A LEU* 3.4 19.5 + - - +
94A GLN 3.6 13.2 + - - +
95A GLU 3.2 0.8 + - - -
96A LEU* 1.3 83.0 + - - +
98A SER* 1.3 58.7 + - - +
99A ASP* 2.7 46.6 + - - +
100A VAL* 3.1 25.4 + - + +
88B LEU 5.3 1.2 + - - -
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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