Contacts of the helix formed by residues 38 - 52 (chain A) in PDB entry 1RMV
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 GLN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A THR* 1.3 74.0 - - - +
39A ALA* 1.3 81.9 + - - +
40A GLY 3.2 1.3 - - - -
41A ARG* 4.2 8.1 - - - +
42A ASP* 2.8 56.5 + - - +
90A ARG* 5.3 1.3 - - - +
92A ARG* 4.3 23.8 - - - +
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Residues in contact with ALA 39 (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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37A THR* 4.4 4.2 - - + -
38A GLN* 1.3 98.4 + - - +
40A GLY* 1.3 57.6 + - - +
43A THR* 2.8 34.5 + - - +
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Residues in contact with GLY 40 (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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33A GLN* 4.7 20.8 - - - +
37A THR* 4.1 13.6 + - - -
38A GLN 3.2 0.6 - - - -
39A ALA* 1.3 78.7 - - - +
41A ARG* 1.3 53.0 + - - +
43A THR* 3.1 7.5 - - - +
44A VAL* 2.8 43.1 + - - +
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Residues in contact with ARG 41 (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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34A SER 5.8 0.6 + - - -
35A TYR* 5.6 12.9 - - + -
37A THR* 3.2 24.5 + - - +
38A GLN* 4.1 5.9 - - - +
40A GLY* 1.3 72.2 - - - +
42A ASP* 1.3 84.2 + - - +
44A VAL* 3.2 15.4 - - - +
45A ARG 3.2 0.3 + - - -
86A SER 4.8 0.4 + - - -
87A PHE* 2.9 84.5 + - + +
88A ASP 4.7 0.6 + - - -
89A THR* 3.2 34.8 + - - +
90A ARG* 2.7 46.8 - - - +
92A ARG* 3.7 13.1 - - - +
117A ALA* 5.2 2.8 - - - +
121A ILE* 6.2 0.7 - - + -
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Residues in contact with ASP 42 (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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38A GLN* 2.8 45.8 + - - +
41A ARG* 1.3 86.3 + - - +
43A THR* 1.3 63.2 + - - +
45A ARG* 2.8 38.3 + - - +
46A GLN* 3.3 30.8 + - - +
87A PHE 5.3 0.5 - - - +
88A ASP 5.0 5.9 - - - +
92A ARG* 5.4 4.5 + - - -
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Residues in contact with THR 43 (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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38A GLN* 5.2 0.2 - - - +
39A ALA* 2.8 30.5 + - - +
40A GLY* 3.1 9.6 - - - +
42A ASP* 1.3 77.9 - - - +
44A VAL* 1.3 60.8 + - + +
46A GLN* 3.1 15.3 + - - +
47A GLN* 2.8 47.5 + - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 3.5 6.7 - - - +
29A SER 5.2 1.3 - - - +
30A ALA* 3.6 42.0 - - + +
33A GLN* 5.7 3.1 - - - +
40A GLY* 2.8 30.9 + - - +
41A ARG* 3.2 9.4 - - - +
43A THR* 1.3 77.1 - - + +
45A ARG* 1.3 58.3 + - - +
47A GLN* 2.7 46.7 + - - +
48A PHE 3.2 4.3 + - - -
83A LEU* 6.1 0.4 - - + -
84A MET* 3.5 19.6 - - + +
87A PHE* 3.7 11.2 - - + -
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Residues in contact with ARG 45 (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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41A ARG 3.2 1.4 + - - -
42A ASP* 2.8 37.1 + - - +
44A VAL* 1.3 78.8 - - - +
46A GLN* 1.3 75.4 + - + +
47A GLN 3.1 0.7 + - - -
48A PHE* 3.2 5.0 + - - +
49A ALA* 3.2 20.1 + - - +
52A LEU* 5.7 0.3 - - - +
84A MET* 3.1 46.0 + - + +
85A LYS* 3.5 30.7 - - - +
87A PHE* 3.0 41.3 + - + -
88A ASP* 3.6 16.0 + - - +
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Residues in contact with GLN 46 (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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42A ASP* 3.5 37.8 + - - +
43A THR* 3.1 16.3 + - - +
45A ARG* 1.3 92.9 - - + +
47A GLN* 1.3 61.2 + - - +
49A ALA* 3.6 15.1 - - + +
50A ASN* 3.4 21.1 + - - +
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Residues in contact with GLN 47 (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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26A GLN* 2.9 34.4 + - + +
29A SER* 4.5 12.8 + - - -
43A THR* 2.8 40.8 + - - +
44A VAL* 2.7 32.1 + - - +
46A GLN* 1.3 70.3 - - - +
48A PHE* 1.3 62.2 + - - -
50A ASN* 3.1 22.1 + - - +
51A LEU* 3.2 18.0 - - + +
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Residues in contact with PHE 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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23A MET* 3.3 48.7 - - + -
26A GLN* 2.7 22.4 + - + +
27A CYS* 5.1 12.3 - - - -
44A VAL 3.2 1.2 + - - -
45A ARG 3.2 8.3 + - - +
47A GLN* 1.3 75.6 - - - +
49A ALA* 1.3 60.3 - - - +
51A LEU* 3.2 17.8 + - + +
52A LEU* 2.9 32.4 + - + +
71A VAL* 3.8 17.5 - - + -
76A ILE* 4.2 5.6 - - + -
80A TYR* 3.4 30.3 - + + -
83A LEU* 6.0 2.2 - - + -
84A MET* 3.6 33.2 - - + -
128A LEU* 5.8 2.7 - - + -
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Residues in contact with ALA 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 ARG 3.2 12.1 + - - +
46A GLN* 3.6 15.7 - - + +
47A GLN 3.1 0.6 - - - -
48A PHE* 1.3 78.0 - - - +
50A ASN* 1.3 58.5 + - - +
51A LEU 3.0 0.2 - - - -
52A LEU* 2.9 40.6 + - + +
53A SER* 4.9 0.3 + - - -
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Residues in contact with ASN 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 GLN 3.4 16.9 + - - +
47A GLN* 3.1 14.8 + - - +
49A ALA* 1.3 77.2 - - - +
51A LEU* 1.3 66.6 + - + +
52A LEU 3.5 0.2 - - - -
53A SER* 3.4 14.6 + - - -
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Residues in contact with LEU 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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17A TRP 2.6 27.4 - - - +
18A ALA* 3.7 15.7 - - + +
22A PRO* 4.0 27.6 - - + +
23A MET* 4.3 4.5 - - - +
26A GLN* 3.9 27.6 - - + -
47A GLN* 3.2 21.3 - - + +
48A PHE* 3.5 21.5 - - + +
49A ALA 3.0 0.2 - - - -
50A ASN* 1.3 84.1 - - + +
52A LEU* 1.3 51.0 + - - +
53A SER* 2.8 13.1 + - - -
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Residues in contact with LEU 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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15A ALA* 3.0 30.0 + - + +
17A TRP 3.9 4.9 - - - -
48A PHE* 2.9 26.5 - - + +
49A ALA* 2.9 33.4 + - + +
51A LEU* 1.3 73.5 - - - +
53A SER* 1.3 64.7 + - - +
71A VAL* 3.4 38.4 - - + -
80A TYR* 3.5 30.3 - - + +
84A MET* 6.4 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