Contacts of the helix formed by residues 58 - 72 (chain B) in PDB entry 5GRH
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 GLU 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ALA 3.1 5.6 + - - +
57B ASP* 1.3 68.8 + - - +
59B GLU* 1.3 53.7 + - + +
60B ASP 2.7 5.7 + - - -
61B ILE* 2.4 43.9 + - - +
62B ARG* 3.0 46.6 + - + +
92B ARG* 3.3 27.1 + - - +
95B ILE* 4.2 7.6 - - - +
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Residues in contact with GLU 59 (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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57B ASP* 3.2 6.4 - - + +
58B GLU* 1.3 78.7 - - + +
60B ASP* 1.3 59.8 + - - +
61B ILE 3.2 0.2 - - - -
62B ARG* 3.7 16.2 - - + -
63B ASN* 3.1 38.8 + - - +
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Residues in contact with ASP 60 (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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51B HIS 4.0 10.9 - - - +
52B VAL* 3.9 24.5 - - + +
53B SER* 2.6 50.1 + - - +
55B ASN* 4.9 7.9 + - + +
57B ASP* 3.5 16.0 + - + +
58B GLU 2.7 4.2 + - - -
59B GLU* 1.3 76.6 - - - +
61B ILE* 1.3 58.5 + - + +
63B ASN* 4.3 5.2 + - - +
64B ALA* 4.1 8.7 + - - +
92B ARG* 6.0 1.8 - - + +
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Residues in contact with ILE 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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52B VAL* 4.0 28.9 - - + -
58B GLU* 2.4 56.9 + - + +
60B ASP* 1.3 68.4 - - + +
62B ARG* 1.3 66.8 + - - +
63B ASN 3.3 2.0 - - - -
64B ALA* 3.5 5.6 + - + +
65B ILE* 3.3 21.1 + - + +
79B ILE* 4.7 3.6 - - + -
92B ARG* 3.9 47.8 - - + +
95B ILE* 4.4 22.2 - - + -
96B LEU* 4.1 20.0 - - + -
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Residues in contact with ARG 62 (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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58B GLU* 3.0 47.0 + - + +
59B GLU* 3.5 15.9 + - + -
61B ILE* 1.3 77.2 - - - +
63B ASN* 1.3 65.4 + - - +
65B ILE* 3.2 16.5 + - - +
66B MET* 3.2 28.0 + - + +
95B ILE* 4.0 19.2 - - - +
99B SER* 3.7 23.4 + - - -
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Residues in contact with ASN 63 (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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50B VAL* 4.6 9.0 - - + -
51B HIS 6.1 0.2 - - - +
59B GLU* 3.1 31.8 + - - +
60B ASP* 4.3 5.8 + - - +
61B ILE 3.3 0.2 - - - -
62B ARG* 1.3 78.4 - - - +
64B ALA* 1.3 56.5 + - - +
66B MET* 3.3 26.6 + - - +
67B ALA* 3.0 28.0 + - - +
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Residues in contact with ALA 64 (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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19B THR* 5.9 0.4 - - + -
21B ILE* 4.5 13.5 - - + -
50B VAL* 4.0 22.1 - - + +
52B VAL* 4.4 20.0 - - + -
60B ASP 4.1 1.2 + - - +
61B ILE* 3.5 10.8 + - + +
62B ARG 3.3 0.4 - - - -
63B ASN* 1.3 75.1 - - - +
65B ILE* 1.3 60.2 + - - +
67B ALA* 3.2 3.1 + - - +
68B ILE* 2.8 38.2 + - + +
96B LEU* 4.4 13.0 - - + -
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Residues in contact with ILE 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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61B ILE* 3.3 16.4 - - + +
62B ARG* 3.3 23.8 - - - +
63B ASN 3.2 0.4 - - - -
64B ALA* 1.3 77.4 - - - +
66B MET* 1.3 59.2 + - + +
68B ILE* 3.2 4.3 + - - +
69B ARG* 2.9 74.0 + - + +
95B ILE* 4.6 3.4 - - + +
96B LEU* 3.6 26.7 - - + -
99B SER* 3.4 30.7 - - - +
100B LEU* 4.2 11.6 - - + +
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Residues in contact with MET 66 (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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62B ARG* 3.2 11.2 + - + +
63B ASN* 3.5 32.5 - - - +
64B ALA 3.3 0.2 - - - -
65B ILE* 1.3 82.2 - - + +
67B ALA* 1.3 61.2 + - - +
69B ARG* 3.6 10.8 + - - +
70B ARG* 3.1 30.7 + - - +
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Residues in contact with ALA 67 (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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19B THR* 3.4 15.5 + - + +
48B GLU* 4.6 1.1 - - - +
50B VAL* 3.7 26.9 - - + -
63B ASN 3.0 13.3 + - - +
64B ALA 3.5 8.1 - - - +
65B ILE 3.2 0.2 - - - -
66B MET* 1.3 77.6 - - - +
68B ILE* 1.3 60.9 + - - +
70B ARG* 3.3 30.5 + - - +
71B ASN* 3.1 21.1 + - - -
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Residues in contact with ILE 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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19B THR* 3.9 14.1 - - + +
21B ILE* 4.3 15.0 - - + -
64B ALA 2.8 25.2 + - - +
65B ILE 3.8 2.5 - - - +
67B ALA* 1.3 69.5 - - - +
69B ARG* 1.3 58.7 + - - +
71B ASN 4.4 0.4 - - - +
72B ARG* 2.6 34.0 + - - +
73B VAL 4.7 8.3 - - - +
74B ALA* 4.0 26.9 - - + -
96B LEU* 4.2 15.5 - - + -
100B LEU* 3.7 35.7 - - + -
264B TYR* 4.0 11.3 - - + -
266B VAL* 4.3 17.3 - - + -
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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
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65B ILE* 2.9 45.4 + - - +
66B MET* 3.7 12.3 - - - +
68B ILE* 1.3 76.6 - - - +
70B ARG* 1.3 62.3 + - - +
72B ARG* 3.8 13.3 - - - +
99B SER* 3.1 30.1 + - - -
100B LEU* 3.9 13.0 - - + +
264B TYR* 3.5 36.8 + - - +
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Residues in contact with ARG 70 (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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48B GLU* 2.5 36.3 + - - -
50B VAL* 5.5 0.4 - - - +
66B MET* 3.1 22.7 + - - +
67B ALA* 3.4 28.2 - - - +
68B ILE 3.1 0.4 - - - -
69B ARG* 1.3 79.8 - - - +
71B ASN* 1.3 67.5 + - - +
72B ARG* 4.3 4.0 - - - +
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Residues in contact with ASN 71 (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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17B THR* 3.3 41.1 - - - +
18B VAL 4.3 1.4 - - - -
19B THR* 3.1 28.9 + - - +
48B GLU* 3.4 29.2 + - - +
67B ALA 3.1 13.0 + - - +
68B ILE 4.5 0.2 - - - +
70B ARG* 1.3 87.6 - - - +
72B ARG* 1.3 67.0 + - - +
73B VAL* 3.2 18.3 + - - +
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Residues in contact with ARG 72 (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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68B ILE* 2.6 24.4 + - - -
69B ARG 3.8 16.2 - - - +
70B ARG 4.3 4.0 - - - +
71B ASN* 1.3 74.1 + - - +
73B VAL* 1.3 69.5 + - + +
263B VAL* 3.2 46.2 + - - +
264B TYR* 3.6 18.4 - - + -
265B ALA* 3.3 21.3 + - - +
299B HIS* 5.0 2.7 + - - -
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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