Contacts of the helix formed by residues 84 - 97 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61G ASP 3.5 12.9 + - - +
62G GLY 4.3 3.0 - - - -
63G ASN 2.8 21.3 + - - -
64G GLN* 4.6 2.0 - - + +
65G VAL* 4.1 0.9 - - - -
83G LYS* 1.3 77.6 - - - +
85G ARG* 1.3 66.4 + - - +
86G ALA* 3.0 17.4 - - - +
87G GLU* 2.7 27.9 + - + +
88G ALA* 2.8 12.4 + - - -
106G GLU* 2.9 54.2 - - - +
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Residues in contact with ARG 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ASN* 4.2 7.9 - - - +
38G ALA* 2.8 27.7 + - + +
39G THR* 3.5 27.8 - - - +
61G ASP* 3.0 28.9 + - - +
63G ASN* 3.4 41.8 + - - +
64G GLN 5.0 1.0 + - - -
65G VAL* 3.4 24.5 - - + +
69G ASP* 3.5 32.3 + - - -
76G LEU* 4.3 12.0 - - + +
83G LYS 3.4 6.9 + - - -
84G ASN* 1.3 71.5 - - - +
86G ALA* 1.3 63.6 + - - +
89G ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ALA* 4.7 0.2 - - - -
59G ILE* 3.8 24.2 - - + +
61G ASP* 3.2 47.5 - - + +
84G ASN* 2.7 13.9 + - - +
85G ARG* 1.3 79.2 - - - +
87G GLU* 1.3 66.6 + - - +
89G ALA* 3.8 1.7 - - - +
90G MET* 3.1 18.2 + - - +
104G PHE* 4.4 5.2 - - + -
105G VAL 4.1 2.7 - - - +
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Residues in contact with GLU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G LYS* 5.2 9.8 - - + +
84G ASN* 2.7 24.7 + - + +
86G ALA* 1.3 75.0 - - - +
88G ALA* 1.3 65.3 + - - +
90G MET* 3.0 18.8 + - - +
91G GLU* 3.2 28.4 + - + +
104G PHE* 3.4 49.1 - - + -
106G GLU* 4.5 8.4 - - - +
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Residues in contact with ALA 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G VAL* 4.2 8.3 - - + -
76G LEU* 3.6 19.3 - - + -
80G SER* 4.0 21.5 - - - +
83G LYS* 4.8 9.6 - - + +
84G ASN 2.8 18.9 + - - +
85G ARG 3.8 1.1 - - - +
87G GLU* 1.3 75.2 + - - +
89G ALA* 1.3 64.1 + - - +
91G GLU* 3.3 18.2 + - - +
92G PHE* 3.2 19.8 - - - -
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Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ALA* 4.1 20.4 - - + +
43G THR* 4.3 9.4 - - - +
59G ILE* 4.3 1.6 - - + -
75G PHE* 3.7 12.5 - - - +
76G LEU* 3.5 8.7 - - + +
85G ARG 2.9 22.0 + - - +
86G ALA 3.8 2.5 - - - +
88G ALA* 1.3 72.7 - - - +
90G MET* 1.3 66.8 + - - +
92G PHE* 2.9 14.6 + - - +
93G LEU* 3.1 27.1 + - + +
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Residues in contact with MET 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G PHE* 3.8 22.6 - - + -
59G ILE* 3.9 12.0 - - + +
86G ALA 3.1 9.8 + - - +
87G GLU* 3.0 12.7 + - - +
89G ALA* 1.3 78.2 - - - +
91G GLU* 1.3 65.9 + - + +
92G PHE 3.0 0.3 + - - -
93G LEU* 3.3 3.1 + - - +
94G GLN* 2.7 69.0 + - + +
102G GLY 3.8 5.4 - - - +
103G SER* 3.8 21.5 - - - +
104G PHE* 3.7 28.5 - - + -
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Residues in contact with GLU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G LYS* 5.2 9.7 + - - +
87G GLU* 3.2 28.9 + - + +
88G ALA* 3.7 18.0 - - - +
89G ALA 3.3 0.4 - - - -
90G MET* 1.3 90.1 - - + +
92G PHE* 1.3 66.2 + - + +
94G GLN* 3.4 16.8 - - - +
95G GLU* 3.7 16.9 + - - +
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Residues in contact with PHE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G PHE* 3.5 38.7 - - + -
76G LEU* 4.5 1.1 - - - -
77G GLN* 4.2 39.9 - - + -
79G SER* 5.2 2.5 - - - -
80G SER* 4.9 9.0 - - - -
88G ALA* 3.2 25.4 - - - -
89G ALA 2.9 6.7 + - - +
91G GLU* 1.3 82.6 - - + +
93G LEU* 1.3 67.2 + - - +
94G GLN 3.1 0.7 - - - -
95G GLU* 3.0 31.4 + - - +
96G LEU* 3.7 3.6 + - - +
114H ARG* 3.6 40.9 + - - +
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Residues in contact with LEU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU* 5.7 0.2 - - + -
43G THR* 3.9 26.0 - - - +
46G LEU* 3.7 26.0 - - + -
47G LYS* 4.2 7.9 - - + +
50G VAL* 4.0 12.5 - - + +
57G PHE* 4.3 10.1 - - + -
59G ILE* 3.7 14.6 - - + -
75G PHE* 3.4 31.9 - - + -
89G ALA* 3.1 23.9 + - + +
90G MET* 3.9 2.5 - - - +
92G PHE* 1.3 74.4 - - - +
94G GLN* 1.3 56.5 + - - +
96G LEU* 2.6 48.6 + - + +
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Residues in contact with GLN 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G VAL* 5.4 1.1 - - - +
57G PHE* 4.4 9.1 - - + -
90G MET* 2.7 44.3 + - + +
91G GLU* 3.4 12.8 - - - +
93G LEU* 1.3 76.8 - - - +
95G GLU* 1.3 61.5 + - + +
96G LEU 3.4 0.5 + - - -
97G ASN 3.7 16.2 + - - +
98G SER* 4.6 4.5 + - - +
100G VAL* 3.2 25.8 + - - +
101G SER* 4.8 0.2 - - - +
102G GLY* 3.4 19.9 + - - +
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLU 3.7 14.8 - - - +
92G PHE* 3.0 23.4 + - - +
93G LEU 2.8 1.6 + - - -
94G GLN* 1.3 80.2 - - + +
96G LEU* 1.3 63.3 + - - +
97G ASN* 3.2 2.4 + - - -
98G SER 4.7 1.4 + - - -
95H ARG* 3.7 32.2 + - - +
114H ARG* 5.1 12.4 + - - +
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Residues in contact with LEU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LYS* 5.4 1.2 + - - -
47G LYS* 3.6 21.8 - - + +
50G VAL* 3.9 11.0 - - + -
51G LEU* 4.2 17.5 - - + +
75G PHE* 3.2 40.4 - - + -
92G PHE 4.3 1.3 - - - +
93G LEU* 2.6 32.7 + - + +
95G GLU* 1.3 73.9 - - - +
97G ASN* 1.3 61.3 + - - +
88H LEU 5.3 2.8 - - - +
92H PHE* 3.7 28.9 - - + -
95H ARG* 3.3 34.0 + - - +
110H PHE* 6.1 0.7 - - + -
114H ARG* 5.9 0.4 - - - +
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Residues in contact with ASN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LYS* 2.9 33.8 + - - +
13G TYR* 3.3 9.8 + - - -
50G VAL* 3.5 23.5 + - + +
51G LEU* 3.5 19.5 + - - +
53G GLY* 4.7 0.2 - - - -
94G GLN* 3.7 12.0 + - - +
95G GLU 3.2 1.6 + - - -
96G LEU* 1.3 82.4 + - - +
98G SER* 1.3 58.3 + - - +
99G ASP* 2.7 47.3 + - - +
100G VAL* 3.1 25.9 + - + +
88H LEU 5.1 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