Contacts of the helix formed by residues 37 - 51 (chain A) in PDB entry 4RG7
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.1 21.3 + - - +
36A HIS* 1.3 83.0 - - - +
38A GLU* 1.3 61.1 + - - +
39A GLU* 3.8 8.4 + - - +
40A ALA* 3.2 26.0 + - - +
41A LEU* 3.0 26.0 + - - +
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Residues in contact with GLU 38 (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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36A HIS 3.8 0.4 + - - -
37A SER* 1.3 73.2 - - - +
39A GLU* 1.3 57.4 + - - +
41A LEU* 3.7 7.7 - - - +
42A PHE* 3.1 26.2 + - - +
66A CYS* 3.5 26.9 - - - -
68A THR* 4.1 16.2 - - + -
70A GLN* 4.2 3.2 - - - +
71A CYS* 3.9 5.9 - - - -
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Residues in contact with GLU 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 SER* 3.2 7.3 - - - +
38A GLU* 1.3 78.7 - - - +
40A ALA* 1.3 60.5 + - - +
42A PHE* 3.5 10.3 + - + +
43A LEU* 3.0 27.4 + - - +
70A GLN* 4.6 10.3 - - - +
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Residues in contact with ALA 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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28A ALA* 5.0 1.7 - - - +
31A LEU* 4.0 31.3 - - + +
32A TYR* 4.0 10.5 - - - +
35A VAL* 4.0 13.5 - - + +
37A SER* 3.2 23.8 + - - +
39A GLU* 1.3 74.0 - - - +
41A LEU* 1.3 65.4 + - - +
43A LEU* 3.3 7.5 + - - +
44A LEU* 3.0 24.4 + - - +
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Residues in contact with LEU 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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32A TYR* 3.4 28.4 - - + +
36A HIS 5.2 0.2 - - - +
37A SER 3.0 19.1 + - - +
38A GLU* 3.7 9.4 - - - +
40A ALA* 1.3 77.5 - - - +
42A PHE* 1.3 63.1 + - - +
44A LEU* 3.3 5.5 + - - +
45A ALA* 3.0 24.2 + - - +
64A HIS* 5.0 4.7 - - + +
66A CYS* 5.6 4.0 - - + -
71A CYS* 5.1 6.1 - - - -
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Residues in contact with PHE 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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13A TRP* 5.0 16.8 - + - -
38A GLU 3.1 16.7 + - - +
39A GLU* 3.6 8.1 - - + +
41A LEU* 1.3 79.5 - - - +
43A LEU* 1.3 53.2 + - + +
45A ALA* 3.2 4.8 + - - +
46A THR* 2.6 59.9 + - + -
70A GLN* 3.1 57.0 - - + +
71A CYS* 3.9 15.8 - - - -
74A LEU* 4.0 16.8 - - + -
17B ASN 5.9 2.9 - - - -
19B TYR* 5.6 3.1 - + - -
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Residues in contact with LEU 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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9A GLN* 5.6 6.1 - - + -
12A ILE* 5.6 9.2 - - + -
13A TRP* 5.1 13.2 + - + +
28A ALA* 5.4 3.8 - - + -
31A LEU* 5.6 4.7 - - + -
39A GLU 3.0 17.4 + - - +
40A ALA* 3.6 8.7 - - - +
41A LEU 3.3 0.2 - - - -
42A PHE* 1.3 80.3 - - + +
44A LEU* 1.3 57.5 + - - +
46A THR* 3.2 9.7 - - - -
47A CYS* 2.8 37.6 + - - -
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Residues in contact with LEU 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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25A VAL* 4.1 3.1 - - + +
28A ALA* 3.6 29.9 - - + +
29A GLU* 3.9 24.5 - - + +
32A TYR* 4.2 22.9 - - + -
40A ALA 3.0 14.0 + - - +
41A LEU* 3.6 9.0 - - - +
43A LEU* 1.3 76.1 - - - +
45A ALA* 1.3 57.7 + - - +
47A CYS* 2.9 5.9 + - + +
48A TYR* 2.8 69.9 + - + +
60A LEU* 6.0 2.9 - - + -
537B TYR* 4.8 6.5 - - - +
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Residues in contact with ALA 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 LEU 3.0 16.5 + - - +
42A PHE* 3.6 6.3 - - - +
44A LEU* 1.3 75.3 - - - +
46A THR* 1.3 62.7 + - - +
48A TYR* 3.4 10.6 + - - -
49A TYR* 3.0 23.9 + - - +
57A ALA* 3.5 24.0 - - + +
60A LEU* 5.2 5.8 - - + -
61A LEU* 4.9 11.0 - - + +
71A CYS* 6.3 1.1 - - - -
74A LEU* 3.7 17.2 - - + +
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Residues in contact with THR 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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13A TRP* 5.0 9.2 - - + +
16A LEU* 4.8 9.6 - - + -
42A PHE* 2.6 54.0 + - + -
43A LEU* 3.2 12.8 - - - -
45A ALA* 1.3 72.8 - - - +
47A CYS* 1.3 63.5 + - - +
49A TYR* 3.1 5.6 + - - +
50A ARG* 3.0 34.4 + - - +
74A LEU* 3.7 7.8 - - - +
19B TYR* 3.1 24.6 + - - +
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Residues in contact with CYS 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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12A ILE* 3.7 29.6 - - - -
16A LEU* 3.8 28.4 - - + +
21A TYR* 4.9 0.2 - - - -
24A ALA* 4.3 4.5 - - - -
25A VAL* 3.7 23.7 - - + +
28A ALA* 3.9 13.0 - - + -
43A LEU* 2.8 26.6 + - - -
44A LEU* 2.9 9.2 + - + +
46A THR* 1.3 74.0 - - - +
48A TYR* 1.3 62.4 + - - +
50A ARG* 3.4 0.9 + - - +
51A SER* 3.0 26.0 + - - -
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Residues in contact with TYR 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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25A VAL* 3.4 30.1 - - + -
29A GLU* 2.7 32.2 + - - +
44A LEU* 2.8 42.4 + - + +
45A ALA* 3.7 10.3 - - - +
47A CYS* 1.3 72.7 - - - +
49A TYR* 1.3 60.1 + - - +
51A SER* 2.6 21.9 + - - -
53A LYS* 3.2 19.3 + - + +
56A LYS* 4.1 23.1 - - + -
57A ALA* 3.9 14.4 - - + +
60A LEU* 4.5 5.8 - - + -
535B GLU* 4.8 0.9 + - - -
537B TYR* 3.5 42.1 + + - -
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Residues in contact with TYR 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 ALA 3.0 17.4 + - - +
46A THR* 3.1 5.1 + - - +
48A TYR* 1.3 78.0 - - - +
50A ARG* 1.3 64.0 + - + +
52A GLY* 3.2 13.7 + - - -
53A LYS 4.0 5.8 + - - -
54A ALA* 4.0 17.1 + - + -
57A ALA* 4.2 4.0 - - + +
74A LEU* 4.0 12.6 - - + -
77A LYS* 3.6 18.8 + - + +
78A CYS* 3.3 31.0 - - - -
81A ASP* 2.4 35.8 + - - -
19B TYR* 3.7 45.7 - + + +
21B TYR* 5.0 5.6 - + - -
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Residues in contact with ARG 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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16A LEU* 3.6 44.8 + - + +
17A ASN* 4.2 4.9 + - - -
19A TYR* 4.3 3.8 - - - -
21A TYR* 3.3 37.2 + - + +
46A THR* 3.0 24.5 + - - +
47A CYS 4.3 1.8 - - - +
49A TYR* 1.3 73.5 - - - +
51A SER* 1.3 57.5 + - - +
52A GLY* 2.9 10.1 + - - -
16B LEU 5.7 1.9 + - - -
17B ASN* 5.2 7.9 + - - -
19B TYR* 3.4 42.1 - - + +
21B TYR* 5.0 5.4 + - - +
50B ARG* 2.8 52.9 - - - +
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Residues in contact with SER 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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21A TYR* 3.9 32.6 - - - -
25A VAL* 4.6 7.5 - - - +
47A CYS 3.0 14.0 + - - -
48A TYR* 2.6 28.3 + - - -
50A ARG* 1.3 76.7 - - - +
52A GLY* 1.3 57.4 + - - +
53A LYS* 3.8 9.5 + - - +
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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