Contacts of the helix formed by residues 5 - 18 (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 GLN 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLU* 1.3 63.0 + - + +
7A PRO* 3.3 16.7 - - - +
8A VAL* 3.0 33.3 + - - +
9A GLN* 3.2 10.4 + - - +
31A LEU* 4.6 14.4 - - + +
35A VAL* 6.2 3.1 - - + -
465B ALA 6.0 2.2 - - - +
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Residues in contact with GLU 6 (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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5A GLN* 1.3 73.0 - - + +
7A PRO* 1.4 71.5 - - + +
9A GLN* 3.7 2.7 + - - +
10A ALA* 3.1 22.2 + - - +
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Residues in contact with PRO 7 (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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5A GLN 3.3 13.9 - - - +
6A GLU* 1.4 92.1 - - + +
8A VAL* 1.3 71.6 + - - +
10A ALA* 3.7 8.9 - - + +
11A ALA* 3.2 21.8 + - - +
465B ALA* 5.7 12.1 - - + +
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Residues in contact with VAL 8 (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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5A GLN* 3.0 19.7 + - - +
7A PRO* 1.3 86.8 - - + +
9A GLN* 1.3 57.6 + - - +
11A ALA* 3.2 17.2 + - - +
12A ILE* 3.2 18.5 + - + +
27A LEU* 4.7 13.0 - - + +
31A LEU* 4.7 16.2 - - + -
468B LEU* 6.1 5.4 - - + -
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Residues in contact with GLN 9 (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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5A GLN 3.2 7.7 + - - +
6A GLU* 4.0 2.7 - - - +
8A VAL* 1.3 74.6 - - - +
10A ALA* 1.3 64.9 + - - +
12A ILE* 4.0 14.9 - - + +
13A TRP* 4.0 19.9 + - - +
31A LEU* 3.7 23.8 - - + +
43A LEU* 5.6 7.4 - - + -
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Residues in contact with ALA 10 (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 GLU 3.1 18.3 + - - +
7A PRO* 3.7 9.9 - - + +
9A GLN* 1.3 78.8 - - - +
11A ALA* 1.3 60.5 + - - +
13A TRP* 3.3 8.6 + - - +
14A GLN* 3.3 18.4 + - - +
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Residues in contact with ALA 11 (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 PRO 3.2 11.0 + - - +
8A VAL* 3.3 13.7 - - - +
10A ALA* 1.3 77.0 - - - +
12A ILE* 1.3 61.4 + - - +
14A GLN* 3.4 11.1 + - - +
15A ALA* 3.2 19.4 + - - +
27A LEU* 4.7 6.7 - - + +
116B PHE* 5.2 1.7 - - - -
145B ASN* 5.7 6.0 + - - +
147B PHE* 4.8 19.3 - - + -
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Residues in contact with ILE 12 (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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8A VAL* 3.2 12.5 + - + +
9A GLN* 4.2 19.7 - - + +
10A ALA 3.4 0.4 - - - -
11A ALA* 1.3 72.8 - - - +
13A TRP* 1.3 64.7 + - + +
15A ALA* 2.8 24.6 + - - +
16A LEU* 2.9 16.4 + - + +
24A ALA* 3.9 9.6 - - + +
27A LEU* 3.5 28.9 - - + +
28A ALA* 3.4 32.5 - - + +
31A LEU* 4.3 12.8 - - + -
43A LEU* 5.6 7.0 - - + -
47A CYS* 3.7 27.8 - - - -
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Residues in contact with TRP 13 (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 4.0 12.2 + - - +
10A ALA* 3.3 10.4 + - - +
11A ALA 3.3 0.4 - - - -
12A ILE* 1.3 84.5 - - + +
14A GLN* 1.3 62.5 + - - +
16A LEU* 3.2 26.0 + - + +
17A ASN* 2.7 40.5 + - - +
42A PHE* 5.0 17.0 - + - -
43A LEU* 5.1 13.5 - - + +
46A THR* 5.0 11.5 - - + +
17B ASN* 5.2 15.0 - - - -
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Residues in contact with GLN 14 (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 3.3 8.6 + - - +
11A ALA* 3.5 15.7 - - - +
12A ILE 3.1 0.4 - - - -
13A TRP* 1.3 79.6 - - - +
15A ALA* 1.3 61.0 + - - +
17A ASN* 3.4 4.0 + - - +
18A HIS* 2.8 39.8 + - + +
116B PHE* 4.1 10.5 - - + -
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Residues in contact with ALA 15 (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 ALA 3.2 8.5 + - - +
12A ILE* 2.8 12.4 + - - +
14A GLN* 1.3 79.6 - - - +
16A LEU* 1.3 51.8 + - - +
18A HIS 3.3 1.7 + - - -
19A TYR 2.9 6.8 + - - -
20A ALA* 2.7 48.4 + - + +
23A ASP* 4.6 4.3 - - + -
24A ALA* 3.8 14.8 - - + +
27A LEU* 5.8 2.2 - - + -
116B PHE* 3.7 24.1 - - + -
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Residues in contact with LEU 16 (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* 2.9 12.2 + - + +
13A TRP* 3.2 37.6 + - + +
15A ALA* 1.3 72.2 - - - +
17A ASN* 1.3 58.8 + - - +
18A HIS 3.1 4.9 - - - -
19A TYR* 2.9 29.6 + - - +
20A ALA 4.7 0.4 - - - +
21A TYR* 3.7 30.9 - - + -
24A ALA* 3.8 15.7 - - + -
46A THR* 4.8 10.5 - - + -
47A CYS* 3.8 35.7 - - + -
50A ARG* 3.6 29.0 + - + +
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Residues in contact with ASN 17 (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* 2.7 29.7 + - - +
14A GLN* 4.1 5.2 - - - +
15A ALA 3.4 0.2 - - - -
16A LEU* 1.3 80.7 - - - +
18A HIS* 1.3 66.0 + - + +
19A TYR* 3.3 16.9 - - - -
50A ARG* 4.2 6.6 + - - -
13B TRP* 4.4 15.4 - - + -
42B PHE* 5.8 3.6 - - - -
50B ARG* 3.6 24.9 + - - +
73B TYR* 5.3 0.3 - - - -
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Residues in contact with HIS 18 (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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14A GLN* 2.8 30.9 + - + +
15A ALA 3.3 3.8 + - - +
16A LEU 3.1 0.6 - - - -
17A ASN* 1.3 82.7 - - + +
19A TYR* 1.3 73.3 + - - +
20A ALA 3.2 0.7 - - - -
73B TYR* 2.6 58.8 + + - +
112B ASP* 5.2 4.0 - - + -
113B SER* 2.7 37.3 + - - -
116B PHE* 3.5 30.5 - + + -
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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