Contacts of the helix formed by residues 72 - 89 (chain G) in PDB entry 1RZR
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 72 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C ARG* 4.8 10.1 - - - +
69G ASP* 2.5 32.8 + - + +
70G ILE 3.2 0.8 - - - +
71G SER* 1.3 74.7 - - - +
73G ILE* 1.3 68.4 + - - +
74G PHE* 2.7 39.7 + - - +
75G TYR* 3.2 14.2 + - + -
76G ALA* 2.9 22.6 + - - +
221G TYR* 6.1 2.8 - - - +
249G GLU* 6.0 0.2 + - - -
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Residues in contact with ILE 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER 6.0 0.7 - - - -
73C ILE* 4.9 8.3 - - + -
278C ARG* 2.4 48.3 - - - +
71G SER 3.7 1.5 + - - -
72G ASN* 1.3 72.4 + - - +
74G PHE* 1.3 73.3 + - + +
76G ALA* 3.2 6.5 + - - +
77G GLU* 2.6 61.3 + - - +
249G GLU* 6.0 1.3 - - + -
277G THR* 2.7 42.4 - - + +
279G LEU* 5.0 10.5 - - + -
294G MSE 4.0 1.6 - - - -
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Residues in contact with PHE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ASN* 2.7 17.2 + - - +
73G ILE* 1.3 85.8 - - + +
75G TYR* 1.3 83.1 + + + +
77G GLU* 3.6 3.6 + - - +
78G LEU* 3.2 47.5 + - + +
146G ALA* 3.5 22.7 - - + -
275G ASP* 3.1 25.4 - - - +
292G GLN* 3.4 32.8 - - + -
294G MSE 3.3 29.5 - - + +
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Residues in contact with TYR 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ILE* 3.7 24.4 - - + +
68G PRO* 3.5 40.8 - - + +
69G ASP* 3.3 27.8 - - + +
70G ILE 4.8 0.4 - - - -
72G ASN* 3.2 17.9 + - + -
74G PHE* 1.3 98.2 - + - +
76G ALA* 1.3 60.4 + - - +
78G LEU* 3.5 9.7 - - + +
79G ALA* 2.7 33.1 + - - +
100G GLN* 3.8 12.3 + - - -
123G MSE 4.0 20.2 - - + -
124G SER 4.5 6.2 - - - -
125G GLY* 4.8 1.4 - - - -
146G ALA* 4.4 13.5 + - + -
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.3 27.3 - - - +
71C SER* 4.3 10.9 - - - +
73C ILE* 6.0 1.3 - - + +
76C ALA* 4.1 6.1 - - + -
70G ILE* 3.4 22.8 + - - +
71G SER 5.2 0.2 - - - +
72G ASN 2.9 15.0 + - - +
73G ILE* 3.2 6.7 + - - +
75G TYR* 1.3 80.9 - - - +
77G GLU* 1.3 66.1 + - - +
79G ALA* 3.2 11.2 + - - +
80G ARG* 3.2 12.0 + - - +
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Residues in contact with GLU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 4.0 23.0 - - - +
73G ILE* 2.6 48.8 + - - +
74G PHE 4.0 0.7 - - - +
76G ALA* 1.3 79.4 - - - +
78G LEU* 1.3 64.8 + - - +
80G ARG* 2.8 19.4 + - - +
81G GLY 3.2 9.2 + - - -
277G THR* 4.5 5.9 - - - -
278G ARG* 4.8 15.4 - - - +
294G MSE 3.7 38.1 - - + +
295G TYR* 4.2 14.4 - - + +
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Residues in contact with LEU 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G PHE* 3.2 47.0 + - + +
75G TYR* 3.2 16.7 + - + +
77G GLU* 1.3 77.9 - - - +
79G ALA* 1.3 61.6 + - - +
80G ARG 3.2 1.0 + - - -
81G GLY 3.4 0.9 + - - -
82G ILE* 3.3 26.0 + - - +
123G MSE 3.4 28.7 - - + -
145G ALA* 4.2 6.5 - - + -
146G ALA* 3.3 31.6 - - + +
294G MSE 3.8 29.4 - - - +
297G ILE* 4.1 8.1 - - + -
298G GLY* 3.8 6.4 - - - +
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Residues in contact with ALA 79 (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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70C ILE* 4.3 13.2 - - + +
95C LEU* 6.0 0.9 - - - +
67G ILE* 4.0 19.0 - - + +
70G ILE* 5.7 3.4 - - + -
75G TYR 2.7 22.7 + - - +
76G ALA* 3.7 5.4 - - - +
77G GLU 3.1 0.2 - - - -
78G LEU* 1.3 73.1 - - - +
80G ARG* 1.3 60.5 + - - +
82G ILE* 3.9 11.6 - - + +
83G GLU* 3.3 22.7 + - - +
93G ILE* 4.8 2.4 - - - +
95G LEU* 4.5 17.4 - - + +
123G MSE 5.5 0.7 - - + -
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Residues in contact with ARG 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 2.7 25.2 + - - +
70C ILE* 3.0 32.5 - - + -
71C SER* 4.0 10.8 - - - -
97C ASN* 3.0 23.6 + - - +
99C ASP* 3.0 33.0 + - - -
76G ALA 3.2 6.4 + - - +
77G GLU* 2.8 14.6 + - - +
79G ALA* 1.3 70.3 - - - +
81G GLY* 1.3 58.4 + - - +
82G ILE 3.1 1.6 - - - -
83G GLU* 4.2 2.5 - - - +
84G ASP* 2.6 63.3 + - - +
295G TYR* 4.6 13.7 - - + -
17L ARG* 2.7 40.3 - - - +
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Residues in contact with GLY 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLU 3.2 8.1 + - - -
78G LEU 4.0 1.1 - - - -
80G ARG* 1.3 78.7 - - - +
82G ILE* 1.3 64.3 + - - +
84G ASP* 3.6 1.7 - - - +
85G ILE* 3.2 14.0 + - - +
295G TYR* 3.4 42.4 - - - -
299G ALA* 3.2 21.3 - - - -
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G VAL* 4.5 7.6 - - + -
78G LEU 3.3 11.2 + - - +
79G ALA* 3.9 7.6 - - - +
80G ARG 3.1 0.4 - - - -
81G GLY* 1.3 74.3 - - - +
83G GLU* 1.3 60.5 + - - +
85G ILE* 2.8 5.5 + - - -
86G ALA 2.7 30.8 + - - -
93G ILE* 4.4 10.1 - - + -
121G ILE* 3.4 38.1 - - + -
123G MSE 3.6 20.6 - - + -
145G ALA* 5.2 0.9 - - + -
298G GLY* 3.4 30.3 - - - +
301G ALA* 5.1 0.2 - - + -
302G MSE 3.1 33.0 - - + +
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Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 5.7 0.4 - - + -
95C LEU* 3.4 22.5 - - + +
96C SER* 3.5 8.7 + - - -
97C ASN* 3.2 44.1 + - - +
79G ALA 3.3 14.5 + - - +
80G ARG* 4.0 6.5 - - - +
82G ILE* 1.3 77.8 - - - +
84G ASP* 1.3 73.2 + - - +
86G ALA* 2.8 4.3 + - - -
87G THR* 2.8 50.0 + - - -
93G ILE* 3.2 27.7 - - + +
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Residues in contact with ASP 84 (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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80G ARG* 2.6 59.5 + - - +
81G GLY 3.6 6.7 - - - +
83G GLU* 1.3 81.1 - - - +
85G ILE* 1.3 62.9 + - + +
87G THR* 3.5 4.5 + - - -
88G MSE 3.1 19.8 + - - +
295G TYR* 2.3 31.7 + - + +
17L ARG* 4.3 5.9 - - - +
20L THR* 4.0 13.0 - - - +
24L GLN* 5.2 0.5 - - - +
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Residues in contact with ILE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLY 3.2 13.1 + - - +
82G ILE 2.8 12.5 + - - +
84G ASP* 1.3 74.6 - - + +
86G ALA* 1.3 66.7 + - - +
87G THR 3.1 1.8 - - - -
88G MSE 3.1 7.9 + - - +
89G TYR* 3.0 32.8 + - + -
299G ALA* 3.9 18.6 - - + +
302G MSE 3.5 7.0 - - + -
303G ARG* 3.5 32.3 - - + +
306G THR* 5.0 0.4 - - + -
20L THR* 3.4 23.3 - - + +
47L ILE* 3.1 44.2 - - + -
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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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82G ILE 2.7 15.7 + - - +
83G GLU* 3.6 4.9 - - - +
85G ILE* 1.3 72.2 - - - +
87G THR* 1.3 57.5 + - - +
89G TYR* 3.2 7.3 + - - -
91G TYR* 2.6 48.2 + - + +
93G ILE* 3.3 34.3 - - + -
302G MSE 3.5 20.6 - - - +
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Residues in contact with THR 87 (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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96C SER* 5.0 2.4 + - - -
97C ASN 5.6 0.3 + - - -
108C LEU* 5.8 0.3 - - - +
947C SO4 3.7 28.4 + - - +
83G GLU* 2.8 37.1 + - - -
84G ASP* 3.7 8.5 - - - -
86G ALA* 1.3 66.9 - - - +
88G MSE 1.3 58.8 + - - +
89G TYR 2.8 4.0 - - - -
90G LYS* 2.6 28.9 + - - -
91G TYR 3.7 7.7 + - - +
24L GLN* 5.9 0.4 - - - +
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Residues in contact with MSE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASP 3.1 8.9 + - - +
85G ILE* 3.1 8.2 + - + +
87G THR* 1.3 82.8 - - - +
89G TYR* 1.3 85.1 + - + +
90G LYS 3.6 1.4 + - - -
20L THR* 3.5 31.0 - - + +
23L VAL* 5.1 7.4 - - - +
24L GLN* 2.7 61.2 - - + +
27L SER* 6.0 0.2 - - - -
47L ILE* 3.7 20.2 - - + -
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Residues in contact with TYR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 3.0 36.0 + - + +
86G ALA 3.2 3.3 + - - +
87G THR 2.6 5.1 + - - -
88G MSE 1.3 98.4 - - + +
90G LYS* 1.3 81.3 + - - +
91G TYR* 3.0 13.1 - - + -
303G ARG* 2.7 54.3 + - - -
306G THR* 3.8 24.7 - - + -
310G ASN* 4.3 11.4 - - - -
45L LYS 4.9 8.3 + - - -
47L ILE* 5.7 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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