Contacts of the helix formed by residues 7 - 21 (chain F) in PDB entry 7CR3
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 GLU 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F THR* 1.3 77.5 + - - +
8F GLU* 1.3 57.7 + - - +
10F ILE* 3.6 25.2 - - - +
11F ALA* 2.9 35.3 + - + +
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Residues in contact with GLU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F THR* 3.2 17.0 + - + +
7F GLU* 1.3 78.6 - - - +
9F GLN* 1.3 84.0 + - - +
11F ALA* 3.5 4.0 + - - +
12F GLU* 2.9 36.4 + - - +
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Residues in contact with GLN 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 3.5 30.5 - - + +
541A ARG* 5.7 3.8 - - - +
6F THR* 3.5 19.6 + - + +
7F GLU 3.4 0.2 - - - -
8F GLU* 1.3 93.9 + - - +
10F ILE* 1.3 62.5 + - + +
12F GLU* 3.4 21.2 - - - +
13F PHE* 2.9 59.5 + - + -
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F THR 3.2 19.7 + - - +
7F GLU* 3.6 28.3 - - - +
8F GLU 3.2 0.2 - - - -
9F GLN* 1.3 78.3 - - + +
11F ALA* 1.3 58.7 + - - +
13F PHE* 3.3 7.7 + - + +
14F LYS* 2.9 25.5 + - + +
66F PHE* 3.8 11.9 - - + -
70F LEU* 3.6 29.6 - - + -
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Residues in contact with ALA 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLU* 2.9 24.2 + - + +
8F GLU* 4.0 3.8 - - - +
10F ILE* 1.3 75.5 - - - +
12F GLU* 1.3 60.1 + - - +
14F LYS* 3.3 12.6 - - + +
15F GLU* 2.9 27.4 + - - +
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Residues in contact with GLU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A GLY* 3.2 27.3 + - - -
538A VAL* 3.1 35.7 - - - +
541A ARG* 6.3 0.4 - - - -
8F GLU* 2.9 28.0 + - - +
9F GLN* 3.4 22.3 - - - +
10F ILE 3.2 0.2 - - - -
11F ALA* 1.3 76.3 - - - +
13F PHE* 1.3 61.9 + - - +
15F GLU* 3.2 9.7 + - - +
16F ALA* 3.0 22.0 + - - +
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Residues in contact with PHE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 6.6 0.2 - - + -
538A VAL* 3.6 30.3 - - + -
541A ARG* 6.5 0.2 - - - -
9F GLN* 2.9 47.4 + - + +
10F ILE* 3.8 6.1 - - + +
12F GLU* 1.3 74.8 - - - +
14F LYS* 1.3 61.3 + - - +
16F ALA* 3.6 4.3 - - - -
17F PHE 2.8 22.3 + - - -
66F PHE* 3.4 4.7 - - - -
69F PHE* 3.2 20.9 - + + -
70F LEU* 3.8 28.3 - - + -
73F MET* 3.6 51.8 - - + -
74F ALA* 5.1 2.5 - - + -
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Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 2.9 15.1 + - + +
11F ALA* 3.3 16.2 - - + +
12F GLU 3.2 0.2 - - - -
13F PHE* 1.3 75.0 - - - +
15F GLU* 1.3 60.6 + - - +
17F PHE* 3.1 18.3 + - + -
18F SER* 2.9 34.2 + - - +
66F PHE* 3.6 27.8 - - + -
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Residues in contact with GLU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A GLY* 4.3 21.0 + - - +
11F ALA 2.9 13.2 + - - +
12F GLU* 3.2 13.9 + - - +
14F LYS* 1.3 71.9 - - - +
16F ALA* 1.3 62.7 + - - +
18F SER* 3.3 7.3 + - - +
19F LEU* 2.9 39.4 + - - +
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Residues in contact with ALA 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 3.6 32.5 - - + +
539A SER* 5.2 1.8 - - - +
12F GLU 3.0 10.1 + - - +
13F PHE* 3.5 10.8 - - - +
14F LYS 3.2 0.2 - - - -
15F GLU* 1.3 78.1 + - - +
17F PHE* 1.3 57.9 + - - +
19F LEU* 3.8 6.9 - - - +
20F PHE* 2.9 40.7 + - + -
69F PHE* 3.6 21.3 - - + -
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Residues in contact with PHE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE 2.8 14.7 + - - +
14F LYS* 3.2 22.0 - - + +
16F ALA* 1.3 77.5 - - - +
18F SER* 1.3 55.1 + - - +
20F PHE* 3.4 2.4 + - - -
21F ASP* 2.7 40.9 + - - +
26F GLY* 3.2 40.4 - - - -
27F THR* 3.5 7.9 - - - -
28F ILE* 3.3 34.6 - - + +
64F ILE 3.6 0.2 - - - -
65F ASP 3.4 6.1 - - - -
66F PHE* 3.3 54.1 - + + -
69F PHE* 4.0 12.1 - + + -
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 2.9 25.3 + - - +
15F GLU* 3.3 8.5 + - - -
17F PHE* 1.3 76.6 - - - +
19F LEU* 1.3 58.0 + - - +
21F ASP* 2.9 28.1 + - - +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A GLY* 4.4 7.6 - - - +
536A LEU* 5.3 0.9 - - - +
539A SER* 3.4 27.8 - - - +
15F GLU* 2.9 34.3 + - - +
16F ALA* 3.8 6.5 - - - +
18F SER* 1.3 76.5 - - - +
20F PHE* 1.3 68.2 + - + +
21F ASP 3.2 1.8 + - - +
22F LYS* 3.3 25.1 - - - +
36F VAL* 4.3 5.3 - - + +
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Residues in contact with PHE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A SER* 4.3 19.7 - - - -
542A ALA* 3.7 31.0 - - + -
543A VAL* 4.2 13.2 - - + -
546A MET* 3.8 21.8 - - + -
16F ALA* 2.9 29.2 + - + +
17F PHE* 3.6 1.3 - - - +
19F LEU* 1.3 79.4 - - + +
21F ASP* 1.3 59.1 + - - +
22F LYS* 3.5 4.9 + - - +
28F ILE* 3.6 36.8 - - + -
32F GLU* 2.9 29.7 - - - +
33F LEU* 3.7 16.2 - - + -
36F VAL* 4.6 22.7 - - + -
64F ILE* 5.7 2.7 - - + -
69F PHE* 5.1 8.5 - + - -
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PHE* 2.7 27.8 + - + +
18F SER* 2.9 27.2 + - - +
19F LEU 3.2 1.1 - - - +
20F PHE* 1.3 72.1 - - - +
22F LYS* 1.3 68.4 + - - +
24F GLY* 3.2 30.3 + - - -
25F ASP* 3.6 6.2 + - - +
26F GLY* 3.9 6.8 + - - -
27F THR 2.9 23.6 + - - +
28F ILE* 3.4 2.9 - - + +
32F GLU* 2.8 18.4 - - - +
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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