Contacts of the helix formed by residues 59 - 70 (chain B) in PDB entry 3RRA
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 ARG 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A ARG* 4.8 1.6 - - - +
377A GLY* 4.6 14.1 + - - -
55B GLN* 6.5 0.2 - - - -
56B ASP* 3.4 36.5 + - - +
57B PRO 3.3 1.8 - - - -
58B SER* 1.3 75.2 - - - +
60B ILE* 1.3 58.6 + - - +
61B ASN* 3.3 3.6 - - - -
62B ASP* 3.1 39.6 + - + +
63B LEU* 2.9 33.5 + - + +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO 3.3 17.9 - - - +
58B SER 3.1 3.0 + - - -
59B ARG* 1.3 75.4 - - - +
61B ASN* 1.3 53.6 + - - +
63B LEU* 3.7 6.9 - - - -
64B TRP* 2.7 34.5 + - + +
87B ASP* 3.5 24.2 - - - +
90B LEU* 3.6 38.6 - - + +
91B TRP* 3.7 34.1 - - + +
94B LYS* 3.5 28.5 - - + -
266B THR* 3.9 9.0 - - - +
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG 3.3 0.8 - - - -
60B ILE* 1.3 78.6 - - - +
62B ASP* 1.3 61.6 + - - +
64B TRP* 3.7 4.1 - - - +
65B GLN* 3.0 33.2 + - + +
91B TRP* 5.9 2.8 - - - -
266B THR* 3.8 20.6 - - - +
270B LYS* 4.9 5.7 + - - -
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 2.8 40.8 + - - -
377A GLY 4.4 0.6 - - - +
378A SER* 5.0 1.4 - - - -
379A VAL* 4.2 7.4 + - - +
59B ARG* 3.1 49.0 + - + +
61B ASN* 1.3 76.7 - - - +
63B LEU* 1.3 59.3 + - - +
65B GLN* 3.3 7.0 + - - +
66B THR* 2.6 36.1 + - - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 6.0 1.3 - - - +
3B ILE* 4.4 4.9 - - + -
51B TYR* 3.6 24.6 - - - +
52B LEU* 4.0 11.2 - - + -
55B GLN* 3.8 20.0 - - + -
56B ASP 3.5 22.9 - - - +
57B PRO* 4.0 11.7 - - + +
59B ARG* 2.9 22.4 + - + +
60B ILE 3.8 2.2 - - - +
62B ASP* 1.3 80.5 - - + +
64B TRP* 1.3 59.3 + - - +
66B THR* 3.2 7.0 + - - +
67B MET* 2.9 36.7 + - - +
90B LEU* 3.8 29.8 - - + -
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Residues in contact with TRP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 2.7 23.4 + - + +
61B ASN* 3.7 6.5 - - - +
63B LEU* 1.3 73.6 - - - +
65B GLN* 1.3 83.8 + - - +
67B MET* 3.5 12.1 + - + +
68B TYR* 3.0 69.0 + + + +
69B ARG* 4.9 1.3 - - - -
80B MET* 4.0 15.9 - - + -
83B ILE* 3.4 22.5 - - + +
87B ASP* 3.6 24.0 - - + +
90B LEU* 5.5 0.2 - - - +
240B ARG* 5.4 1.1 - - - -
263B GLY 2.9 20.0 + - - -
266B THR* 4.0 20.2 - - + -
267B GLU* 3.5 42.0 - - + -
270B LYS* 5.4 2.5 - - - -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A VAL* 3.6 17.5 - - + +
61B ASN* 3.0 24.1 + - + +
62B ASP* 3.7 5.8 - - - +
64B TRP* 1.3 97.8 - - + +
66B THR* 1.3 58.1 + - - +
68B TYR* 4.2 1.0 - - - -
69B ARG* 2.8 79.4 + - - +
270B LYS* 4.6 13.3 - - - +
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 4.0 20.6 - - + -
373A ARG* 3.4 22.6 + - - +
379A VAL* 3.4 12.0 - - + +
51B TYR* 3.8 36.0 - - + +
62B ASP* 2.6 23.2 + - - -
63B LEU* 3.2 10.0 + - + +
65B GLN* 1.3 74.3 - - - +
67B MET* 1.3 65.5 + - - +
70B ALA* 3.2 28.6 + - + +
71B GLY 4.3 2.9 + - - -
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.7 16.3 + - - -
48B LEU* 3.8 28.6 - - + +
51B TYR* 4.3 11.0 - - + -
52B LEU* 4.3 11.9 - - + -
63B LEU 2.9 23.3 + - - +
64B TRP* 3.8 16.8 - - + +
66B THR* 1.3 76.3 - - - +
68B TYR* 1.3 61.0 + - - +
79B LEU* 5.9 2.4 - - - +
83B ILE* 3.6 40.3 - - + +
86B ILE* 3.7 49.4 - - + -
87B ASP* 4.9 1.8 - - - +
90B LEU* 4.9 5.2 - - + -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 5.9 0.4 - - - -
64B TRP* 3.0 49.9 + + + +
65B GLN 3.9 2.7 - - - +
66B THR 3.3 0.4 - - - -
67B MET* 1.3 79.7 - - - +
69B ARG* 1.3 85.1 + - + +
72B PHE* 4.6 0.7 - - - +
73B TYR 4.4 3.6 - - - +
74B ARG* 3.5 46.0 - - + +
75B GLY* 3.7 23.8 + - - -
80B MET* 3.7 32.3 - - + -
83B ILE* 3.8 7.8 - - + +
239B SER* 4.5 7.9 - - - -
241B PHE* 3.3 31.6 - + - -
267B GLU* 5.5 1.6 - - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU* 4.6 5.7 + - - -
379A VAL* 4.0 17.5 - - + -
381A GLU* 3.1 51.4 + - - +
382A TRP* 3.0 27.2 + - - +
64B TRP* 4.9 1.4 - - - -
65B GLN* 2.8 51.6 + - - +
68B TYR* 1.3 95.6 - - + +
70B ALA* 1.3 63.1 + - - +
71B GLY 3.7 1.3 - - - -
72B PHE 3.5 9.3 - - - +
74B ARG* 3.4 25.6 - - + +
241B PHE* 5.6 3.8 - - - -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PRO 4.9 6.4 - - - +
371A VAL* 4.2 15.7 - - + -
372A TRP 5.3 2.1 + - - -
379A VAL* 3.7 29.8 - - + -
380A ALA 3.8 12.5 - - - +
382A TRP* 3.4 20.5 - - - +
51B TYR* 5.6 0.2 - - + -
65B GLN 3.9 0.2 + - - -
66B THR* 3.2 25.3 + - + +
67B MET 5.1 0.2 + - - -
68B TYR 3.9 0.4 - - - -
69B ARG* 1.3 78.5 - - - +
71B GLY* 1.3 59.3 + - - +
72B PHE 3.6 0.4 - - - -
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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