Contacts of the helix formed by residues 20 - 35 (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 ALA 20 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 2.7 20.7 + - + +
18A HIS 3.2 2.5 - - - +
19A TYR* 1.3 69.9 - - - +
21A TYR* 1.3 63.4 + - - +
22A ARG 3.5 2.2 - - - -
23A ASP* 3.3 11.7 + - + -
24A ALA* 3.1 21.7 + - - +
73B TYR* 5.1 1.8 - - - +
116B PHE* 3.7 31.6 - - + -
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 26.5 - - + -
19A TYR* 3.1 53.5 + + + -
20A ALA* 1.3 74.9 - - - +
22A ARG* 1.3 58.6 + - - +
24A ALA* 3.2 4.0 + - - +
25A VAL* 2.8 36.8 + - + +
47A CYS 4.9 0.4 - - - -
50A ARG* 3.3 40.6 + - + +
51A SER* 3.9 33.0 - - - -
49B TYR* 4.9 6.0 - + - -
50B ARG* 5.6 2.1 - - - +
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.5 0.6 - - - -
21A TYR* 1.3 78.1 - - - +
23A ASP* 1.3 61.3 + - - +
25A VAL* 4.2 5.5 - - - +
26A PHE* 3.3 24.2 + - + +
149B TRP* 5.4 4.4 - - + -
150B SER* 4.4 16.4 - - - -
153B GLU* 3.4 33.6 + - - +
157B GLU* 5.8 0.4 + - - -
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 4.6 5.8 - - + -
20A ALA* 3.3 20.0 + - + +
21A TYR 3.2 0.6 - - - -
22A ARG* 1.3 76.5 - - - +
24A ALA* 1.3 65.8 + - - +
26A PHE* 3.6 4.6 + - - +
27A LEU* 3.4 28.3 + - + +
116B PHE* 5.5 2.7 - - + -
147B PHE 4.8 2.1 - - - +
148B LEU* 4.4 24.2 - - + -
149B TRP 4.5 8.9 + - - +
150B SER* 4.5 15.2 - - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.9 17.0 - - + +
15A ALA* 3.8 17.9 - - + +
16A LEU* 3.8 30.5 - - + -
20A ALA 3.1 13.2 + - - +
21A TYR 3.6 5.8 - - - +
23A ASP* 1.3 75.8 - - - +
25A VAL* 1.3 60.5 + - - +
27A LEU* 3.2 6.4 + - - +
28A ALA* 2.9 28.1 + - - +
47A CYS* 4.3 3.8 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 2.8 27.3 + - - +
22A ARG* 4.2 5.4 - - - +
24A ALA* 1.3 71.1 - - + +
26A PHE* 1.3 57.8 + - - +
28A ALA* 3.6 2.5 - - - +
29A GLU* 2.9 40.8 + - - +
44A LEU* 4.7 0.7 - - + -
47A CYS* 3.7 38.3 - - + +
48A TYR* 3.4 31.2 - - + -
51A SER* 4.6 8.3 - - - -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.3 18.4 + - + +
23A ASP 3.7 5.2 - - - +
24A ALA 3.2 0.8 - - - -
25A VAL* 1.3 79.3 - - - +
27A LEU* 1.3 66.4 + - + +
29A GLU* 3.2 11.7 + - - +
30A ARG* 3.1 50.5 + - + +
149B TRP* 3.5 61.5 - + + -
153B GLU* 5.8 0.2 - - - -
472B LEU* 4.3 13.9 - - + -
475B MET* 4.1 17.0 - - + -
506B TRP* 3.5 44.6 - + - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.7 14.6 - - + +
11A ALA* 4.7 5.2 - - + +
12A ILE* 3.5 39.7 - - + +
15A ALA* 5.8 1.8 - - + -
23A ASP* 3.4 14.1 + - + +
24A ALA 3.2 3.0 + - - +
26A PHE* 1.3 80.1 - - + +
28A ALA* 1.3 58.3 + - - +
30A ARG* 3.1 9.0 + - + +
31A LEU* 2.8 29.6 + - - +
147B PHE* 3.6 45.5 - - + +
148B LEU* 5.6 0.2 - - - -
468B LEU* 5.9 6.1 - - + -
472B LEU* 5.2 13.2 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.4 14.3 - - + +
24A ALA 2.9 17.0 + - - +
25A VAL 3.6 1.8 - - - +
27A LEU* 1.3 76.0 - - - +
29A GLU* 1.3 62.2 + - - +
31A LEU* 3.7 3.8 - - - +
32A TYR* 2.9 28.6 + - - +
40A ALA 5.0 1.7 - - - +
43A LEU* 4.7 1.8 - - + -
44A LEU* 3.6 38.0 - - + +
47A CYS* 3.9 12.3 - - - -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 2.9 31.7 + - - +
26A PHE* 3.5 5.0 - - - +
28A ALA* 1.3 76.4 - - - +
30A ARG* 1.3 92.7 + - - +
32A TYR* 4.3 1.6 - - - +
33A ALA* 3.2 23.9 + - - +
44A LEU* 3.9 14.3 - - + +
48A TYR* 2.7 32.5 + - + +
504B THR* 4.8 2.7 + - - +
506B TRP* 3.9 18.2 - - - +
535B GLU* 4.3 8.8 - - - +
538B ARG* 4.3 14.5 + - - -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.1 46.8 + - + +
27A LEU* 3.1 7.4 + - + +
29A GLU* 1.3 118.1 + - - +
31A LEU* 1.3 64.1 + - - +
33A ALA* 3.4 3.8 + - - +
34A GLU* 3.0 21.7 + - - +
472B LEU* 5.1 7.6 - - + -
475B MET* 3.5 35.1 - - - +
501B HIS* 3.3 24.4 + - + +
504B THR* 2.6 46.6 + - - +
506B TRP* 4.4 4.4 - - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 4.6 19.5 - - + +
8A VAL* 4.7 9.9 - - + -
9A GLN* 3.7 33.0 - - + +
12A ILE* 4.3 11.9 - - + -
27A LEU 2.8 16.4 + - - +
28A ALA* 3.7 4.9 - - - +
30A ARG* 1.3 77.1 - - - +
32A TYR* 1.3 64.5 + - - +
34A GLU* 3.1 7.4 + - + +
35A VAL* 2.9 44.6 + - + +
40A ALA* 4.0 22.0 - - + +
43A LEU* 5.6 2.7 - - + -
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Residues in contact with TYR 32 (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 2.9 17.4 + - - +
29A GLU 4.3 1.3 - - - +
31A LEU* 1.3 76.8 - - - +
33A ALA* 1.3 63.6 + - - +
35A VAL 2.8 23.5 - - - +
36A HIS* 3.5 44.1 + + + +
37A SER 3.8 3.4 - - - -
40A ALA* 4.0 9.8 - - - +
41A LEU* 3.4 38.8 - - + +
44A LEU* 4.2 21.1 - - + -
64A HIS* 2.1 49.1 + + - -
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Residues in contact with ALA 33 (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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29A GLU 3.2 19.3 + - - +
30A ARG* 3.7 11.4 - - - +
31A LEU 3.2 0.6 - - - -
32A TYR* 1.3 77.6 - - + +
34A GLU* 1.3 64.5 + - - +
36A HIS* 3.2 22.0 - - - -
500B HIS* 3.5 31.3 - - - +
501B HIS* 3.7 12.8 - - + -
504B THR* 4.9 5.4 - - - -
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Residues in contact with GLU 34 (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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30A ARG 3.0 11.9 + - - +
31A LEU* 3.7 6.8 - - + +
33A ALA* 1.3 80.8 - - - +
35A VAL* 1.3 88.6 + - - +
36A HIS* 3.8 8.3 + - - -
500B HIS* 5.7 1.5 - - - +
501B HIS* 3.4 27.8 + - + +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 6.2 3.4 - - + -
31A LEU* 2.9 34.4 + - + +
32A TYR* 2.8 19.4 - - - +
34A GLU* 1.3 91.1 + - - +
36A HIS* 1.3 60.0 + - - +
37A SER* 3.1 29.6 + - - +
40A ALA* 4.0 2.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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