Contacts of the helix formed by residues 19 - 24 (chain C) in PDB entry 1H5R
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 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C TYR* 1.3 79.5 - - + +
20C VAL* 1.3 65.0 + - - +
21C THR 3.2 3.1 - - - -
22C MET* 3.2 35.1 + - + +
23C ALA 3.6 3.1 + - - -
33D ASP 3.5 21.1 - - - +
34D LYS* 4.4 0.2 - - + -
35D PRO* 3.9 12.2 - - + +
38D TYR* 3.8 29.2 - - + +
67D LEU* 4.9 0.5 - - - +
255D GLU* 5.9 0.4 - - - +
276D LEU* 4.7 6.3 - - + -
281D TYR* 3.6 40.8 - - + -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.0 11.2 + - + +
19C PRO* 1.3 77.4 - - - +
21C THR* 1.3 61.6 + - + +
23C ALA* 3.1 17.8 + - - +
24C VAL* 3.2 18.6 - - + +
29C LEU* 3.9 31.6 - - + -
230C HIS* 3.6 17.5 - - + +
233C LEU* 5.7 1.6 - - + -
28D LEU 5.0 1.0 - - - +
30D PRO* 3.8 30.3 - - + -
32D TYR 3.9 0.4 - - - +
33D ASP 3.4 30.1 - - - -
34D LYS* 3.5 7.4 - - - +
35D PRO* 4.5 7.6 - - - -
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Residues in contact with THR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER 4.5 4.5 - - - +
14C GLY* 2.6 34.3 + - - +
17C LEU* 3.2 30.9 - - + -
18C TYR* 3.3 10.2 - - - -
19C PRO 3.2 0.2 - - - -
20C VAL* 1.3 80.9 - - + +
22C MET* 1.3 62.4 + - - +
23C ALA 3.2 0.7 - - - -
24C VAL 3.3 22.7 + - - +
25C SER* 5.5 0.7 - - - -
26C LYS* 4.0 27.1 - - + +
29C LEU* 4.7 0.9 - - + -
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Residues in contact with MET 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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18C TYR* 3.7 39.0 - - + +
19C PRO* 3.2 31.0 - - + +
21C THR* 1.3 79.1 + - - +
23C ALA* 1.3 61.3 + - - +
38D TYR* 6.0 0.2 - - - -
66D GLN* 6.0 1.9 - - - +
67D LEU* 3.8 22.1 - - + +
276D LEU* 4.1 17.0 - - - -
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Residues in contact with ALA 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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19C PRO 3.6 1.0 + - - -
20C VAL 3.1 10.8 + - - +
22C MET* 1.3 81.9 - - - +
24C VAL* 1.3 59.3 + - - +
28D LEU* 3.7 47.0 - - + +
35D PRO* 3.9 19.3 - - + -
63D ARG* 5.5 7.1 - - - +
67D LEU* 4.0 10.8 - - + -
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Residues in contact with VAL 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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20C VAL* 3.2 15.5 + - + +
21C THR* 3.3 22.7 - - - +
22C MET 3.7 0.4 - - - -
23C ALA* 1.3 81.4 - - + +
25C SER* 1.3 78.7 + - - +
26C LYS 3.4 0.3 + - - -
28C LEU* 3.9 7.4 - - + +
29C LEU* 3.1 29.8 - - + -
60C ASP* 5.2 0.7 - - - -
24D VAL* 3.8 40.8 - - + -
28D LEU* 4.1 15.3 - - + +
29D LEU* 5.6 0.9 - - + -
30D PRO* 5.0 0.7 - - + -
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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