Contacts of the helix formed by residues 7 - 21 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6H THR* 1.3 76.2 + - - +
8H GLU* 1.3 58.5 + - - +
10H ILE* 3.6 26.6 - - - +
11H ALA* 2.9 34.3 + - + +
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Residues in contact with GLU 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H THR* 3.2 16.1 + - + +
7H GLU* 1.3 79.6 - - - +
9H GLN* 1.3 84.0 + - - +
11H ALA* 3.5 4.3 + - - +
12H GLU* 2.9 36.9 + - - +
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Residues in contact with GLN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351G LEU* 3.5 31.4 - - + +
541G ARG* 5.7 3.8 - - - +
6H THR* 3.5 20.7 + - + +
7H GLU 3.4 0.2 - - - -
8H GLU* 1.3 95.5 + - - +
10H ILE* 1.3 60.7 + - + +
12H GLU* 3.4 20.5 - - - +
13H PHE* 2.9 60.4 + - + -
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Residues in contact with ILE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H THR 3.2 20.3 + - - +
7H GLU* 3.6 28.9 - - - +
8H GLU 3.2 0.4 - - - -
9H GLN* 1.3 78.8 - - + +
11H ALA* 1.3 57.5 + - - +
13H PHE* 3.3 7.8 + - + +
14H LYS* 2.9 24.5 + - + +
66H PHE* 3.8 12.1 - - + -
70H LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU* 2.9 22.6 + - + +
8H GLU* 4.0 3.6 - - - +
10H ILE* 1.3 75.7 - - - +
12H GLU* 1.3 59.7 + - - +
14H LYS* 3.2 11.2 + - + +
15H GLU* 2.9 27.5 + - - +
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Residues in contact with GLU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G GLY* 3.2 27.7 + - - -
538G VAL* 3.1 35.4 - - - +
541G ARG* 6.3 0.2 - - - -
8H GLU* 2.9 28.3 + - - +
9H GLN* 3.4 22.2 - - - +
10H ILE 3.2 0.2 - - - -
11H ALA* 1.3 77.6 - - - +
13H PHE* 1.3 61.2 + - - +
15H GLU* 3.2 10.3 + - - +
16H ALA* 3.0 21.3 + - - +
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Residues in contact with PHE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351G LEU* 6.6 0.2 - - + -
538G VAL* 3.6 30.5 - - + -
9H GLN* 2.9 47.2 + - + +
10H ILE* 3.8 6.3 - - + +
12H GLU* 1.3 74.9 - - - +
14H LYS* 1.3 60.2 + - - +
16H ALA* 4.0 3.4 - - - -
17H PHE 2.8 22.7 + - - -
66H PHE* 3.4 5.0 - - - -
69H PHE* 3.2 19.0 - + + -
70H LEU* 3.8 27.1 - - + -
73H MET* 3.6 51.1 - - + -
74H ALA* 5.1 3.6 - - + -
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Residues in contact with LYS 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ILE* 2.9 15.6 + - + +
11H ALA* 3.3 16.6 - - + +
12H GLU 3.2 0.2 - - - -
13H PHE* 1.3 75.1 - - - +
15H GLU* 1.3 60.5 + - - +
17H PHE* 3.1 18.4 + - + +
18H SER* 2.9 34.0 + - - +
66H PHE* 3.6 28.6 - - + -
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Residues in contact with GLU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G GLY* 4.3 20.6 - - - -
11H ALA 2.9 12.8 + - - +
12H GLU* 3.6 12.8 - - - +
14H LYS* 1.3 73.3 - - - +
16H ALA* 1.3 62.7 + - - +
18H SER* 3.3 6.6 + - - +
19H LEU* 2.9 39.9 + - - +
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538G VAL* 3.6 33.0 - - + +
539G SER* 5.2 1.6 - - - +
12H GLU 3.0 9.3 + - - +
13H PHE* 3.5 10.5 - - - +
14H LYS 3.2 0.2 - - - -
15H GLU* 1.3 79.4 + - - +
17H PHE* 1.3 57.8 + - - +
19H LEU* 3.8 6.5 - - - -
20H PHE* 2.9 40.3 + - + -
69H PHE* 3.6 21.3 - - + -
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Residues in contact with PHE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H PHE 2.8 15.3 + - - +
14H LYS* 3.1 22.4 + - + +
16H ALA* 1.3 77.3 - - - +
18H SER* 1.3 54.8 + - - +
20H PHE* 3.4 2.4 + - - -
21H ASP* 2.7 40.7 + - - +
26H GLY* 3.2 41.3 - - - -
27H THR* 3.5 7.0 - - - -
28H ILE* 3.3 34.7 - - + +
64H ILE 3.6 0.4 - - - -
65H ASP 3.4 5.4 - - - -
66H PHE* 3.3 53.2 - + + -
69H PHE* 4.0 11.4 - + + -
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Residues in contact with SER 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LYS* 2.9 24.6 + - - +
15H GLU* 4.0 8.5 - - - -
17H PHE* 1.3 77.9 - - - +
19H LEU* 1.3 59.1 + - - +
21H ASP* 2.9 28.0 + - - +
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G GLY* 4.4 7.2 - - - +
536G LEU* 5.3 0.9 - - - +
539G SER* 3.4 28.5 - - - +
15H GLU* 2.9 33.4 + - - +
16H ALA* 3.8 6.3 - - - +
17H PHE 3.2 0.2 - - - -
18H SER* 1.3 75.5 - - - +
20H PHE* 1.3 65.9 + - + +
21H ASP 3.2 1.3 - - - +
22H LYS* 3.3 25.2 - - - -
36H VAL* 4.3 5.7 - - + +
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Residues in contact with PHE 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539G SER* 4.3 20.0 - - - -
542G ALA* 3.7 31.0 - - + -
543G VAL* 4.2 12.8 - - + -
546G MET* 3.8 22.9 - - + -
16H ALA* 2.9 28.9 + - + +
17H PHE* 3.6 1.6 - - - +
19H LEU* 1.3 79.3 - - + +
21H ASP* 1.3 59.6 + - - +
22H LYS* 3.5 5.5 + - - +
28H ILE* 3.6 35.9 - - + -
32H GLU* 2.9 30.3 - - - +
33H LEU* 3.7 15.7 - - + -
36H VAL* 4.6 24.2 - - + +
64H ILE* 5.7 2.2 - - + -
69H PHE* 5.0 9.0 - + - -
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Residues in contact with ASP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H PHE* 2.7 28.2 + - + +
18H SER* 2.9 26.5 + - - +
19H LEU 3.2 0.5 - - - +
20H PHE* 1.3 74.2 - - - +
22H LYS* 1.3 66.8 + - - +
24H GLY* 3.2 31.2 + - - -
25H ASP* 3.6 6.2 + - - +
26H GLY* 3.9 7.3 + - - -
27H THR 2.9 23.3 + - - +
28H ILE* 3.6 2.0 - - + -
32H GLU* 2.8 17.5 - - - +
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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