Contacts of the helix formed by residues 38 - 47 (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 LYS 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 2.8 12.7 + - - +
37A THR* 1.3 79.4 + - - +
39A VAL* 1.3 64.4 + - - +
40A LEU 3.1 2.7 + - - -
41A SER* 3.3 14.4 + - - -
42A THR* 3.6 10.0 + - - -
38B LYS* 3.5 39.1 - - + +
1C C 4.1 8.3 + - - -
2C G 3.9 32.7 + - - +
8D G 4.0 21.0 - - - +
1E C 5.2 4.8 + - - -
8F G 5.8 1.8 - - - +
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Residues in contact with VAL 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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23A ILE* 6.4 2.0 - - + -
33A LEU* 3.8 26.9 - - + -
34A GLY 5.9 0.7 - - - +
36A ASP* 3.4 18.8 + - + +
38A LYS* 1.3 76.6 - - - +
40A LEU* 1.4 56.7 + - + +
42A THR* 3.1 24.4 + - - -
43A ILE* 3.2 12.1 + - + +
23B ILE* 6.0 1.6 - - + -
38B LYS* 4.0 8.5 - - + +
39B VAL* 3.9 25.6 - - + -
42B THR* 3.2 43.1 - - + +
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Residues in contact with LEU 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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20A VAL* 4.9 0.7 - - + -
33A LEU* 4.1 10.5 - - + -
34A GLY 4.4 10.5 - - - +
35A SER* 5.2 2.9 - - - -
36A ASP 3.6 15.7 + - - +
37A THR* 4.5 2.2 - - + +
38A LYS 3.1 0.4 - - - -
39A VAL* 1.4 72.2 - - - +
41A SER* 1.3 66.4 + - - +
42A THR 3.0 1.8 - - - -
43A ILE* 2.9 38.0 + - + +
44A PHE* 3.2 22.2 + - + -
138A TYR* 3.3 48.7 - - + +
162A PRO* 4.5 17.7 - - + +
163A TYR* 4.5 19.5 - - + -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR 4.2 8.4 + - - -
38A LYS* 3.3 12.6 + - - -
40A LEU* 1.3 80.1 - - - +
42A THR* 1.3 59.6 + - - +
44A PHE* 3.9 3.7 + - - +
45A GLU* 3.9 16.1 + - - +
91A ILE* 5.6 2.6 + - - +
93A THR* 3.3 38.7 + - - +
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Residues in contact with THR 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 LYS 3.6 7.3 + - - -
39A VAL 3.1 13.6 + - - +
40A LEU 3.0 0.6 - - - -
41A SER* 1.3 76.8 - - - +
43A ILE* 1.3 66.1 + - + +
45A GLU* 3.2 18.9 + - - +
46A LEU* 3.3 25.3 + - + +
23B ILE* 5.7 0.4 - - + -
36B ASP* 3.5 29.2 + - + +
38B LYS* 4.8 3.3 - - - +
39B VAL* 3.8 26.4 - - + +
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Residues in contact with ILE 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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20A VAL* 3.9 20.6 - - + -
33A LEU* 3.4 33.4 - - + -
39A VAL* 3.3 17.5 - - + +
40A LEU* 2.9 25.2 + - + +
42A THR* 1.3 75.3 - - + +
44A PHE* 1.4 57.7 + - + +
45A GLU 2.8 5.8 + - - -
46A LEU* 2.7 28.4 + - + +
47A PHE* 3.0 44.0 + - + -
163A TYR* 5.8 1.6 - - - +
23B ILE* 4.5 18.6 - - + -
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Residues in contact with PHE 44 (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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18A TYR* 4.5 10.5 - + + -
40A LEU* 3.2 22.4 + - + +
41A SER 4.3 2.5 - - - +
42A THR 3.5 0.2 - - - -
43A ILE* 1.4 80.1 - - + +
45A GLU* 1.3 57.5 + - - +
47A PHE* 4.2 9.4 - + - +
48A SER* 2.9 24.9 + - - -
91A ILE* 3.8 8.8 - - + +
93A THR* 2.9 30.5 - - + +
136A TYR* 3.9 32.8 - + + -
138A TYR* 3.5 35.9 - + + -
163A TYR* 3.6 38.6 - + - -
166A VAL* 4.2 19.5 - - + -
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Residues in contact with GLU 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 SER 3.9 9.7 + - - +
42A THR* 3.2 15.8 + - - +
43A ILE 2.8 1.2 - - - -
44A PHE* 1.3 80.8 - - - +
46A LEU* 1.3 65.0 + - + +
47A PHE 3.3 0.4 - - - -
48A SER* 3.7 4.3 - - - +
49A ARG* 3.4 40.6 + - - +
65A GLU* 5.3 1.8 - - - +
74A ASP* 3.7 23.3 - - - +
75A PHE* 4.6 9.7 - - + -
91A ILE* 4.6 13.3 - - + +
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Residues in contact with LEU 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 THR* 3.3 21.9 + - + +
43A ILE* 2.7 11.1 + - + +
45A GLU* 1.3 78.1 - - + +
47A PHE* 1.3 61.5 + - + +
49A ARG* 3.6 25.7 + - - +
50A PRO* 3.0 27.2 - - - +
23B ILE* 3.3 35.4 - - + -
31B TYR* 4.0 24.9 - - + -
32B PRO* 3.7 24.7 - - + +
33B LEU* 5.3 1.8 - - + -
34B GLY* 5.1 10.1 - - - +
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Residues in contact with PHE 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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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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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