Contacts of the helix formed by residues 57 - 69 (chain B) in PDB entry 2ARV
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 SER 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 5.0 4.2 - - - +
107A ASN* 3.8 26.3 + - - +
58B PHE* 1.3 53.6 + - - +
59B HIS* 4.1 4.9 + - - +
60B SER* 3.0 29.9 + - - -
61B THR* 2.5 47.6 + - - -
115B CYS 5.6 0.7 - - - -
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Residues in contact with PHE 58 (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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20A PHE* 3.9 20.2 - + - -
25A TRP* 3.3 37.9 - + - -
28A TRP* 4.2 17.7 - + - -
29A ILE* 4.4 1.3 - - + -
35A TYR* 4.1 6.5 - - - -
91A MET* 4.4 13.9 - - + -
105A ILE* 4.4 13.7 - - + -
106A GLN 4.6 4.0 + - - +
107A ASN* 4.3 4.7 + - - +
108A MET* 2.9 48.5 - - + -
57B SER* 1.3 72.1 + - - +
59B HIS* 1.3 64.1 + - - +
61B THR* 3.0 9.0 - - + -
62B VAL* 3.0 33.8 + - + +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 4.8 1.1 - - - -
37A ALA* 3.9 14.1 - - + +
38A ASN 2.9 25.0 + - - -
39A TYR* 4.4 4.9 - - + -
83A PRO* 4.8 8.1 - - + +
86A LEU* 4.0 11.0 - - + +
107A ASN 3.3 19.6 + - - +
108A MET 3.4 22.2 - - - +
110A VAL* 3.2 29.7 - - + +
57B SER* 3.1 2.8 - - - +
58B PHE* 1.3 80.8 - - - +
60B SER* 1.3 66.0 + - - +
62B VAL* 3.2 19.4 + - + +
63B ILE* 3.3 37.6 + - + +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.0 26.8 + - - -
59B HIS* 1.3 83.2 + - - +
61B THR* 1.3 58.3 + - - +
63B ILE* 3.2 6.6 + - - +
64B ASN* 2.8 31.1 + - - +
115B CYS 4.0 14.9 + - - -
116B SER* 3.7 26.7 + - - +
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Residues in contact with THR 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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25A TRP* 3.8 24.5 - - + -
57B SER 2.5 31.6 + - - -
58B PHE* 3.0 18.0 - - + -
60B SER* 1.3 72.9 - - - +
62B VAL* 1.3 60.4 + - - +
64B ASN* 3.2 9.7 + - + +
65B HIS* 3.1 19.9 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.7 27.4 - - + -
18A VAL* 3.9 15.9 - - + -
23A ILE* 4.6 14.6 - - + -
25A TRP* 4.1 13.7 - - + -
35A TYR* 4.7 5.2 - - - +
58B PHE* 3.0 40.8 + - + +
59B HIS* 3.2 12.3 + - + +
61B THR* 1.3 72.2 - - - +
63B ILE* 1.3 70.3 + - + +
65B HIS* 3.2 13.9 + - - +
66B TYR* 3.1 25.0 - - + -
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Residues in contact with ILE 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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16A PHE* 3.9 27.8 - - + -
39A TYR* 4.3 7.4 - - + -
59B HIS* 3.3 39.0 - - + +
60B SER* 3.2 9.6 + - - +
62B VAL* 1.3 78.2 - - + +
64B ASN* 1.3 61.8 + - - +
66B TYR* 3.2 7.2 + - - +
67B ARG* 3.1 43.0 + - - +
74B PHE* 4.0 31.2 - - + +
77B LEU* 4.5 8.3 - - + -
116B SER* 5.0 6.7 - - - +
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Residues in contact with ASN 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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46B SER 4.4 13.2 + - - +
60B SER 2.8 13.4 + - - +
61B THR* 3.2 13.4 + - + +
63B ILE* 1.3 74.9 - - - +
65B HIS* 1.3 67.3 + - - +
67B ARG* 3.5 23.8 + - - +
68B MET* 3.1 36.8 + - - +
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Residues in contact with HIS 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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23A ILE* 3.8 49.3 + - + +
25A TRP* 5.1 12.2 + - + -
61B THR 3.1 11.9 + - - +
62B VAL* 3.3 13.0 - - - +
63B ILE 3.2 0.4 - - - -
64B ASN* 1.3 78.8 - - - +
66B TYR* 1.3 70.2 + + + +
68B MET* 3.2 12.2 + - - +
69B ARG* 3.3 45.8 + - + +
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Residues in contact with TYR 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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16A PHE* 3.5 34.0 - + - -
17A PHE 5.1 0.7 + - - -
18A VAL* 5.1 2.1 - - + -
19A SER 4.1 9.9 + - - -
22A ASP* 3.2 28.9 + - - +
23A ILE* 2.8 34.0 - - + +
62B VAL* 3.1 27.1 + - + -
63B ILE 3.2 2.5 + - - +
65B HIS* 1.3 81.2 - + - +
67B ARG* 1.3 61.4 + - - +
69B ARG* 2.8 48.0 + - - +
71B HIS* 3.7 29.2 + + + +
73B PRO* 6.3 0.4 - - + -
74B PHE* 3.5 24.0 - + + -
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Residues in contact with ARG 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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63B ILE* 3.1 22.9 + - - +
64B ASN* 3.5 34.0 + - - +
66B TYR* 1.3 75.5 - - - +
68B MET* 1.3 66.5 + - - +
69B ARG 2.4 19.3 - - - +
74B PHE* 3.5 26.2 + - + +
75B ALA* 4.2 15.1 - - - +
77B LEU* 2.8 50.8 + - - +
79B SER* 4.0 27.1 - - - +
116B SER* 4.4 7.5 + - - -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 4.4 25.4 - - - +
64B ASN* 3.1 35.6 + - - +
65B HIS* 3.6 6.3 - - - +
66B TYR 3.2 0.2 - - - -
67B ARG* 1.3 86.8 - - - +
69B ARG* 1.3 63.9 + - + +
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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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22A ASP* 2.9 42.6 + - - -
65B HIS* 3.3 39.3 + - + +
66B TYR* 2.8 26.6 + - - +
67B ARG 2.4 28.1 - - - +
68B MET* 1.3 76.3 - - + +
70B GLY* 1.3 58.7 + - - +
71B HIS* 3.0 39.9 + - + +
75B ALA* 5.0 0.5 - - - +
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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