Contacts of the helix formed by residues 64 - 78 (chain B) in PDB entry 4RHW
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 ASP 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.9 13.3 - - - +
34B PHE* 4.4 5.1 - - - -
63B LYS* 1.3 81.0 - - - +
65B ASN* 1.3 65.5 + - - +
66B ASP* 3.4 20.9 + - - +
67B SER* 3.0 38.6 + - - -
68B TYR 3.3 4.7 + - - -
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Residues in contact with ASN 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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1B MET* 3.2 10.5 - - - +
2B ASP* 2.9 52.4 + - - +
64B ASP* 1.3 76.4 - - - +
66B ASP* 1.3 64.7 + - - +
68B TYR* 3.1 15.4 + - - +
69B VAL* 3.1 17.2 + - - +
92B PRO* 3.6 26.7 - - + +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.2 35.5 - - + -
64B ASP* 3.3 14.5 - - - +
65B ASN* 1.3 77.7 - - - +
67B SER* 1.3 56.9 + - - +
69B VAL* 3.1 10.7 + - - +
70B SER* 2.8 28.9 + - - -
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.4 0.2 - - - -
29B MET* 3.8 7.1 - - - +
34B PHE* 3.8 24.0 + - - +
60B ILE* 4.9 5.6 - - - +
63B LYS* 3.3 39.6 - - - +
64B ASP* 3.0 24.9 + - - -
66B ASP* 1.3 76.6 - - - +
68B TYR* 1.3 55.9 + - - +
70B SER* 3.3 2.9 + - - -
71B PHE* 3.0 28.4 + - - +
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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
----------------------------------------------------------
1B MET* 3.6 34.7 - - + +
5B ALA* 3.3 23.1 - - + -
8B CYS* 3.4 16.2 - - + -
9B LEU* 3.4 24.5 - - + -
60B ILE* 5.0 3.4 - - + -
64B ASP 3.3 3.3 + - - +
65B ASN* 3.1 12.4 + - - +
67B SER* 1.3 77.8 - - - +
69B VAL* 1.3 57.3 + - - +
71B PHE* 3.2 9.0 + - + +
72B TYR* 2.9 24.7 + - + +
87B LEU* 3.0 38.9 + - + +
90B GLY* 3.5 7.9 - - - -
91B ILE* 3.3 37.2 - - + -
92B PRO* 3.7 11.7 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASN 3.1 13.6 + - - +
66B ASP* 3.1 13.1 + - - +
68B TYR* 1.3 72.7 - - - +
70B SER* 1.3 61.5 + - - +
72B TYR* 3.3 2.9 + - + +
73B ASN* 2.9 47.9 + - - +
91B ILE* 4.2 34.3 - - + -
92B PRO* 4.6 8.3 - - + -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 5.3 0.3 - - - +
29B MET* 3.5 18.1 - - - +
32B ASP* 2.8 36.6 + - - +
34B PHE* 3.5 29.1 - - - -
66B ASP 2.8 6.0 + - - -
67B SER 3.4 9.6 - - - -
69B VAL* 1.3 76.7 - - - +
71B PHE* 1.3 58.4 + - - +
73B ASN* 3.3 5.4 + - - +
74B ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.3 19.5 - - + -
16B LEU* 4.4 21.5 - - + -
20B ILE* 4.5 15.3 - - + -
25B ILE* 3.8 27.8 - - + -
29B MET* 4.2 6.9 - - - -
56B LEU* 4.5 2.5 - - + -
57B ILE* 4.8 8.7 - - + -
60B ILE* 3.5 35.0 - - + -
67B SER 3.0 12.9 + - - +
68B TYR* 3.3 11.4 - + - +
70B SER* 1.3 73.3 - - - +
72B TYR* 1.3 65.6 + - - +
74B ALA* 3.2 5.0 + - - +
75B LEU* 3.0 38.4 + - + +
87B LEU* 3.9 28.3 - - + -
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Residues in contact with TYR 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 TYR* 2.9 19.0 + - + +
69B VAL* 3.7 4.5 - - + +
71B PHE* 1.3 76.8 - - - +
73B ASN* 1.3 76.3 + - - +
75B LEU* 3.2 12.8 + - - +
76B LEU* 3.0 54.6 + - + +
84B ALA* 3.2 42.9 - - + +
87B LEU* 4.6 7.9 - - + -
88B HIS* 3.8 32.0 - + + +
91B ILE* 3.7 28.5 - - + -
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Residues in contact with ASN 73 (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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28B HIS* 5.4 0.4 - - - -
32B ASP* 5.1 5.3 + - - +
69B VAL* 2.9 39.5 + - - +
70B SER* 3.6 6.1 - - - +
72B TYR* 1.3 88.9 - - - +
74B ALA* 1.3 61.3 + - - +
76B LEU* 4.4 8.0 - - - +
77B HIS* 2.9 57.1 + - + +
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Residues in contact with ALA 74 (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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25B ILE* 3.6 29.8 - - + +
28B HIS* 3.7 34.5 + - + +
29B MET* 5.0 0.9 - - + -
70B SER 2.9 14.8 + - - +
71B PHE* 3.4 9.9 - - - +
73B ASN* 1.3 76.0 - - - +
75B LEU* 1.3 62.9 + - - +
77B HIS* 3.9 0.5 - - - +
78B GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 22.7 - - + -
20B ILE* 4.0 24.5 - - + -
25B ILE* 3.7 21.3 - - + +
71B PHE* 3.0 29.5 + - + +
72B TYR* 3.4 8.3 - - - +
74B ALA* 1.3 77.4 - - - +
76B LEU* 1.3 59.8 + - - +
78B GLU 3.3 0.3 + - - -
79B GLY 3.3 3.8 + - - -
80B TYR* 2.9 46.3 + - + +
83B LEU* 4.2 14.8 - - + +
84B ALA* 4.3 9.2 - - + +
87B LEU* 3.9 21.1 - - + -
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Residues in contact with LEU 76 (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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72B TYR* 3.0 47.6 + - + +
73B ASN* 3.7 9.9 - - - +
75B LEU* 1.3 75.7 - - - +
77B HIS* 1.3 71.4 + - + +
79B GLY* 3.1 18.9 + - - -
80B TYR 4.3 2.1 + - - +
81B LYS* 4.9 15.1 + - + +
84B ALA* 3.6 22.9 - - + +
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Residues in contact with HIS 77 (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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28B HIS* 4.0 23.9 + - + -
73B ASN* 2.9 44.4 + - + +
74B ALA 4.1 0.2 - - - +
76B LEU* 1.3 89.5 - - + +
78B GLU* 1.3 61.7 + - - +
79B GLY 3.3 1.0 + - - -
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Residues in contact with GLU 78 (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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24B TYR* 3.3 39.8 - - + +
25B ILE* 4.6 3.4 - - + -
28B HIS* 2.7 36.5 + - + +
74B ALA 3.0 18.4 + - - +
76B LEU 3.2 0.4 - - - -
77B HIS* 1.3 77.3 - - - +
79B GLY* 1.3 61.3 + - - +
80B TYR* 3.4 28.1 + - + -
14E LEU* 4.9 1.9 - - - +
18E GLU* 5.2 2.6 - - - +
52E ARG* 4.7 6.6 + - - -
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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