Contacts of the helix formed by residues 21 - 31 (chain C) in PDB entry 6R7H
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 MET 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C LEU 4.3 9.2 - - - +
16C SER* 4.4 4.7 - - - +
18C GLN 3.9 16.4 - - - +
19C GLY* 3.3 11.4 + - - +
20C GLN* 1.3 75.1 - - - +
22C THR* 1.3 64.1 + - - +
23C GLN 3.4 2.0 - - - -
24C LEU* 3.6 21.9 + - + +
25C CYS* 4.2 2.6 + - - +
92C HIS* 3.3 42.4 - - + +
95C TYR* 3.6 62.3 - - + +
96C ALA* 5.2 0.9 + - - +
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 3.5 11.7 - - - +
21C MET* 1.3 78.0 + - - +
23C GLN* 1.3 66.8 + - - +
24C LEU 3.1 1.0 + - - -
25C CYS* 3.4 16.9 + - - +
26C GLU* 3.9 5.0 + - - +
95C TYR* 5.3 5.1 - - - -
173C ASN* 4.2 26.6 + - + +
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Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.7 29.1 - - + +
20C GLN* 4.5 25.8 + - + +
21C MET* 3.4 0.6 - - - +
22C THR* 1.3 76.7 - - - +
24C LEU* 1.3 63.3 + - - +
25C CYS 3.3 0.4 - - - -
26C GLU* 3.4 25.7 + - - +
27C LEU* 3.2 19.9 + - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.0 23.1 - - + +
15C LEU* 3.8 28.6 - - + +
16C SER* 3.4 31.9 - - - +
21C MET* 3.6 18.7 + - + +
22C THR 3.1 1.2 - - - -
23C GLN* 1.3 79.0 - - - +
25C CYS* 1.3 61.1 + - - +
27C LEU* 3.5 1.8 + - + +
28C ILE* 3.3 38.1 + - + +
53C GLU* 4.5 16.4 - - + -
92C HIS* 4.4 23.1 - - + +
96C ALA* 5.6 5.8 - - + -
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C MET 4.2 1.7 + - - +
22C THR 3.4 10.5 + - - +
23C GLN 3.3 0.8 - - - -
24C LEU* 1.3 79.4 - - - +
26C GLU* 1.3 59.5 + - - +
27C LEU 3.5 0.2 - - - -
28C ILE* 3.4 18.4 - - - +
29C ASN* 3.5 13.0 + - - +
95C TYR 4.6 4.5 - - - +
96C ALA* 3.7 24.8 - - + +
98C ASP* 3.7 17.7 - - - +
99C THR* 3.3 40.1 - - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR 3.9 3.9 + - - +
23C GLN* 3.4 29.0 + - - +
24C LEU 3.2 0.4 - - - -
25C CYS* 1.3 80.1 - - - +
27C LEU* 1.3 63.7 + - - +
29C ASN* 3.5 23.0 + - - +
30C LYS* 3.6 30.5 + - + +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 5.8 10.3 - - + +
11C SER* 3.8 34.8 - - - +
12C VAL* 4.5 11.7 - - + +
15C LEU* 3.8 22.9 - - + -
23C GLN* 3.2 16.0 + - + +
24C LEU* 3.5 4.9 + - + +
25C CYS 3.5 0.2 - - - -
26C GLU* 1.3 80.0 - - - +
28C ILE* 1.3 58.7 + - + +
30C LYS* 3.7 6.1 + - + +
31C SER* 3.2 24.9 + - - -
32C GLY* 5.3 8.3 - - - +
54C HIS* 4.5 3.8 + - + +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.6 5.4 - - + -
24C LEU* 3.3 34.5 + - + +
25C CYS* 3.4 12.1 - - - +
27C LEU* 1.3 76.3 - - - +
29C ASN* 1.3 65.2 + - - +
30C LYS 3.4 0.2 - - - -
31C SER* 3.5 7.5 + - - -
53C GLU* 3.8 24.7 - - + +
54C HIS* 3.9 26.5 - - + -
56C LEU* 3.7 17.9 - - + -
57C GLY* 3.4 27.1 - - - +
96C ALA* 4.5 9.0 - - + -
99C THR* 3.3 27.3 - - + +
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C CYS 3.5 15.0 - - - +
26C GLU* 3.5 21.2 + - - +
27C LEU 3.3 0.8 - - - -
28C ILE* 1.3 83.3 - - - +
30C LYS* 1.3 61.6 + - - +
31C SER* 4.8 0.2 - - - -
61C VAL* 4.6 12.0 - - - +
99C THR* 3.6 20.3 - - + +
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLU* 3.6 35.7 + - + +
27C LEU* 4.5 6.1 - - + +
29C ASN* 1.3 85.8 - - - +
31C SER* 1.3 70.1 - - - +
32C GLY* 4.2 6.5 - - - +
33C GLU* 2.8 62.3 + - - +
34C LEU 3.9 4.3 + - - +
61C VAL* 5.2 2.8 - - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 4.7 4.0 - - - -
27C LEU 3.2 15.2 + - - -
28C ILE 3.5 14.2 + - - -
29C ASN 3.7 0.2 - - - -
30C LYS* 1.3 79.1 - - - +
32C GLY* 1.3 60.3 + - - +
33C GLU 3.4 0.3 + - - -
34C LEU* 3.6 25.9 + - - +
39C LEU* 3.9 25.2 - - - +
54C HIS* 3.9 18.3 + - - -
57C GLY 3.9 16.3 + - - -
58C VAL* 4.3 3.0 + - - +
61C VAL* 4.4 7.0 - - - +
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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