Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 2RVE
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 PHE 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.7 53.1 - + + -
19A ASP 3.9 3.1 - - - -
20A VAL* 3.9 30.7 - - + -
43A ILE* 3.0 51.8 + - + +
44A PHE* 4.3 11.2 - + - +
46A LEU* 1.3 81.4 - - + +
48A SER* 1.3 57.6 + - - +
50A PRO* 3.3 11.8 - - - +
51A ILE* 3.7 17.7 - - - +
163A TYR* 5.3 1.1 - - - -
23B ILE* 4.9 1.1 - - + -
25B SER* 4.2 9.4 - - - -
27B GLU* 4.4 4.0 - - - -
31B TYR* 4.0 45.2 + + - -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 5.4 2.3 - - - +
44A PHE 2.9 18.3 + - - -
45A GLU 3.5 4.8 + - - -
46A LEU 3.1 1.2 - - - -
47A PHE* 1.3 74.4 - - - +
49A ARG* 1.3 66.8 + - - +
50A PRO* 3.0 3.1 - - - -
51A ILE* 2.8 23.4 + - - +
52A ILE* 3.1 19.0 + - - +
75A PHE* 5.2 0.4 - - - -
91A ILE* 3.5 27.3 - - - +
134A ILE* 4.8 1.9 - - - +
136A TYR* 3.1 25.8 + - - -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.4 33.3 + - - +
46A LEU* 3.9 28.9 + - - +
48A SER* 1.3 73.2 - - - +
50A PRO* 1.3 68.8 - - + +
52A ILE* 3.8 2.2 + - - +
53A ASN* 3.0 43.7 + - - +
65A GLU* 2.8 37.8 + - - -
75A PHE* 3.8 18.1 - - + -
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Residues in contact with PRO 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU 3.0 19.5 - - - +
47A PHE 3.3 11.0 - - - +
48A SER 3.0 7.4 - - - +
49A ARG* 1.3 91.7 - - + +
51A ILE* 1.4 53.9 + - + +
53A ASN* 3.0 7.2 + - + +
54A LYS* 2.7 40.7 + - - +
31B TYR* 4.0 19.7 - - + -
150B THR* 4.8 7.6 - - - +
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 7.2 - - + -
10A ALA* 3.8 25.8 - - + +
11A LEU* 3.2 38.8 - - + -
18A TYR* 3.9 21.5 - - + +
47A PHE 3.7 20.4 - - - +
48A SER* 2.8 12.2 + - - +
50A PRO* 1.4 71.6 - - + +
52A ILE* 1.4 64.7 + - + +
54A LYS* 3.0 22.4 + - - +
55A ILE* 2.9 23.7 + - + +
136A TYR* 4.7 0.7 - - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.2 22.9 - - + +
11A LEU* 5.9 1.3 - - + -
48A SER* 3.1 13.4 + - - +
49A ARG* 4.2 3.8 - - - +
51A ILE* 1.4 78.8 - - + +
53A ASN* 1.3 65.0 + - - +
55A ILE* 4.7 0.3 - - - +
56A ALA* 3.1 22.5 + - - +
63A VAL* 4.5 3.8 - - + -
75A PHE* 3.8 41.5 - - + -
77A LEU* 4.1 15.7 - - + -
89A ILE* 4.0 23.8 - - + -
91A ILE* 4.0 7.2 - - + -
134A ILE* 3.8 30.7 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG* 3.0 44.0 + - - +
50A PRO* 3.0 8.1 + - + +
52A ILE* 1.3 78.6 - - - +
54A LYS* 1.3 61.7 + - - +
56A ALA* 3.7 3.2 - - - +
57A GLU* 3.1 25.7 + - - +
63A VAL* 3.7 31.3 - - - +
65A GLU* 5.3 1.0 + - - -
75A PHE* 4.8 3.0 - - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.5 11.7 - - - +
50A PRO* 2.7 17.1 + - - +
51A ILE* 3.6 32.7 - - - +
53A ASN* 1.3 74.2 - - - +
55A ILE* 1.3 73.0 + - + +
57A GLU* 3.7 8.0 + - - +
58A LYS* 3.4 23.5 + - + +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.6 21.1 - - + +
6A ASP* 3.7 33.0 - - + +
7A LEU* 3.7 21.1 - - + +
10A ALA* 4.4 13.9 - - + -
51A ILE 2.9 14.5 + - - +
52A ILE 4.7 0.2 - - - +
54A LYS* 1.3 87.5 - - + +
56A ALA* 1.3 64.0 + - - +
58A LYS* 3.3 37.1 - - + +
59A HIS* 3.3 20.3 - - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.4 8.5 - - + -
52A ILE 3.1 20.1 + - - +
53A ASN 3.7 1.3 - - - +
55A ILE* 1.3 74.2 - - - +
57A GLU* 1.3 55.9 + - - +
58A LYS 3.0 1.3 - - - -
59A HIS* 2.7 32.9 + - - +
60A GLY 3.4 3.8 + - - -
61A TYR* 3.5 14.3 + - + +
63A VAL* 3.7 15.9 - - + -
77A LEU* 3.5 27.4 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN 3.1 14.0 + - - +
54A LYS* 4.1 6.6 - - - +
56A ALA* 1.3 78.9 - - - +
58A LYS* 1.3 57.8 + - + +
59A HIS 3.0 4.6 + - - -
60A GLY* 3.3 10.7 + - - -
61A TYR 4.1 13.1 + - - +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASP* 2.6 43.2 + - - +
54A LYS* 3.4 10.7 + - + +
55A ILE* 3.3 31.0 - - + +
56A ALA 2.9 2.0 + - - -
57A GLU* 1.3 80.1 - - + +
59A HIS* 1.3 72.5 + - - +
60A GLY 3.7 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