Contacts of the helix formed by residues 7 - 18 (chain B) 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 PRO 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A PHE* 4.8 17.1 - - + -
462A LYS 5.3 5.4 - - - +
464A ALA* 3.7 31.9 - - + +
465A ALA* 4.9 6.1 - - + +
6B GLU* 1.3 96.1 - - + +
8B VAL* 1.3 57.9 + - + +
10B ALA* 3.8 4.8 - - + +
11B ALA* 2.9 30.9 + - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 4.8 11.9 - - + -
464A ALA* 5.1 13.0 - - + +
465A ALA 5.6 0.2 - - - +
468A LEU* 4.3 24.5 - - + -
6B GLU 3.3 3.1 - - - +
7B PRO* 1.3 80.5 - - + +
9B GLN* 1.3 62.6 + - - +
11B ALA* 3.4 6.6 + - - +
12B ILE* 3.1 27.5 + - + +
27B LEU* 4.3 20.6 - - + +
30B ARG* 6.1 1.1 - - + -
31B LEU* 3.9 37.0 - - + -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.5 16.1 + - - +
7B PRO 3.3 0.6 - - - -
8B VAL* 1.3 79.4 - - - +
10B ALA* 1.3 61.6 + - - +
12B ILE* 3.2 13.8 + - - +
13B TRP* 3.3 24.7 + - + +
31B LEU* 4.9 10.8 - - + +
43B LEU* 4.3 18.6 - - + +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU 3.1 14.7 + - - +
7B PRO* 4.0 4.5 - - + +
9B GLN* 1.3 79.5 - - - +
11B ALA* 1.3 60.7 + - - +
13B TRP* 3.7 9.4 + - - +
14B GLN* 3.4 20.8 + - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 5.6 0.2 - - - -
145A ASN* 5.9 2.8 + - - +
147A PHE* 4.2 31.2 - - + -
7B PRO 2.9 19.2 + - - +
8B VAL* 3.6 7.4 - - - +
9B GLN 3.2 0.2 - - - -
10B ALA* 1.3 76.1 - - - +
12B ILE* 1.3 63.6 + - - +
14B GLN* 3.5 12.9 + - - +
15B ALA* 3.2 20.1 + - - +
27B LEU* 4.2 11.0 - - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.1 21.6 + - + +
9B GLN* 3.2 6.9 + - - +
11B ALA* 1.3 76.3 - - - +
13B TRP* 1.3 57.4 + - - +
15B ALA* 2.8 25.6 + - - +
16B LEU* 2.8 20.4 + - + +
24B ALA* 3.9 8.9 - - + +
27B LEU* 3.5 24.7 - - + +
28B ALA* 3.6 29.8 - - + +
31B LEU* 4.6 4.3 - - + -
43B LEU* 3.6 28.9 - - + -
47B CYS* 3.8 26.7 - - - -
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Residues in contact with TRP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN* 4.4 16.6 - - + -
9B GLN* 3.3 27.7 + - + +
10B ALA* 4.1 7.6 - - - +
11B ALA 3.5 0.2 - - - -
12B ILE* 1.3 78.7 - - - +
14B GLN* 1.3 59.1 + - - +
16B LEU* 3.8 14.7 - - + +
17B ASN* 2.6 45.5 + - - +
42B PHE* 4.9 15.3 - + - -
43B LEU* 3.8 30.4 - - + +
46B THR* 4.4 10.1 - - + -
50B ARG* 3.3 41.7 - - - -
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 3.9 34.2 + - - +
115A CYS* 5.1 1.2 - - - -
116A PHE* 3.6 20.7 - - + -
145A ASN* 4.3 12.6 + - - -
10B ALA 3.4 11.9 + - - +
11B ALA* 3.5 16.0 - - - +
12B ILE 3.1 0.8 - - - -
13B TRP* 1.3 78.6 - - - +
15B ALA* 1.3 61.6 + - - +
17B ASN* 3.3 4.8 + - - +
18B HIS* 2.8 39.6 + - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.4 18.8 - - + -
11B ALA 3.2 9.7 + - - +
12B ILE* 2.8 9.3 + - - +
14B GLN* 1.3 79.9 - - - +
16B LEU* 1.3 56.7 + - - +
18B HIS* 3.4 1.7 + - - -
19B TYR 3.2 2.8 + - - -
20B ALA* 2.7 50.7 + - + +
23B ASP* 4.4 7.0 - - + -
24B ALA* 3.8 15.5 - - + +
27B LEU* 5.6 2.5 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ARG* 5.7 1.6 + - - -
12B ILE* 2.8 24.2 + - + +
13B TRP* 3.8 35.4 - - + +
15B ALA* 1.3 72.5 - - - +
17B ASN* 1.3 55.3 + - - +
18B HIS 3.0 4.5 - - - -
19B TYR* 2.7 33.5 + - - +
20B ALA 4.7 0.4 - - - +
21B TYR* 4.3 22.6 - - + -
24B ALA* 3.6 26.9 - - + -
43B LEU* 4.8 1.1 - - + -
46B THR* 4.0 20.2 - - + -
47B CYS* 3.8 17.7 - - - -
50B ARG* 4.0 24.0 + - - +
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Residues in contact with ASN 17 (chain B).
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* 5.2 16.0 - - - -
42A PHE* 5.9 2.8 - - - -
50A ARG* 5.2 7.3 + - - -
73A TYR* 5.4 0.5 - - - -
13B TRP* 2.6 41.8 + - - +
14B GLN* 3.3 6.8 + - - +
16B LEU* 1.3 79.7 - - - +
18B HIS* 1.3 69.3 + - + +
19B TYR* 3.4 20.3 + - - -
50B ARG* 5.0 6.9 + - - -
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 2.9 51.5 + + + -
77A LYS* 3.5 2.3 - - - +
112A ASP* 5.1 4.9 - - - -
113A SER* 3.3 25.9 + - - -
116A PHE* 3.2 55.4 - + + -
14B GLN* 2.8 31.3 + - + -
15B ALA 3.4 0.2 + - - -
16B LEU 3.0 0.8 - - - -
17B ASN* 1.3 85.6 - - + +
19B TYR* 1.3 74.9 + - - +
20B ALA 3.2 1.9 + - - -
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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