Contacts of the helix formed by residues 28 - 37 (chain H) in PDB entry 3HR4
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 THR 28 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ASP* 4.7 4.9 - - - +
24H ASP* 4.7 3.1 - - - +
26H THR* 4.2 12.3 + - - +
27H ILE* 1.3 75.6 - - - +
29H THR* 1.3 65.6 + - - +
30H LYS* 3.4 11.2 + - - +
31H GLU* 2.8 46.4 + - - +
32H LEU* 3.2 6.1 + - - +
62H THR* 4.1 17.5 - - + +
201H CA 4.6 0.9 - - - -
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Residues in contact with THR 29 (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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27H ILE 3.5 1.0 + - - -
28H THR* 1.3 71.7 - - - +
30H LYS* 1.3 59.2 + - - +
32H LEU* 3.0 6.2 + - - +
33H GLY* 2.9 26.3 + - - -
45H GLU* 5.4 5.1 + - - -
48H LEU* 4.1 11.0 - - - +
49H GLN* 3.3 44.4 - - + +
52H ILE* 3.3 29.1 - - + +
61H GLY 5.3 4.8 + - - +
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Residues in contact with LYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 2.9 11.1 + - - +
29H THR* 1.3 83.0 + - - +
31H GLU* 1.3 54.1 + - + +
33H GLY* 3.1 2.2 + - - +
34H THR* 2.7 49.3 + - - +
48H LEU* 5.9 0.9 - - - -
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H PHE* 3.6 14.6 - - - +
20H ASP* 3.9 0.7 - - - -
21H LYS* 3.1 30.0 + - + +
22H ASP* 2.8 20.4 + - - +
26H THR 3.0 2.9 - - - +
27H ILE* 4.0 7.4 - - + +
28H THR* 2.8 41.6 + - - +
30H LYS* 1.3 74.9 - - + +
32H LEU* 1.3 58.1 + - - +
34H THR* 4.0 6.6 - - - -
35H VAL* 3.1 31.5 + - - +
201H CA 2.2 32.5 - - - -
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Residues in contact with LEU 32 (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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524G PHE* 4.4 4.5 - - + -
528G LEU* 4.1 24.0 - - + -
19H PHE* 4.1 24.5 - - + -
27H ILE* 4.3 10.7 - - + +
28H THR 3.2 6.5 + - - +
29H THR* 3.0 13.5 + - - +
31H GLU* 1.3 76.9 - - - +
33H GLY* 1.3 59.8 + - - +
35H VAL* 3.4 1.1 + - - +
36H MET* 2.9 37.2 + - + +
48H LEU* 3.7 10.8 - - + +
51H MET* 3.4 32.8 - - + -
52H ILE* 4.0 21.5 - - + +
63H ILE* 5.3 2.9 - - + -
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Residues in contact with GLY 33 (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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29H THR 2.9 10.1 + - - -
30H LYS* 3.6 2.2 - - - -
32H LEU* 1.3 73.4 - - - +
34H THR* 1.3 61.8 + - - +
35H VAL 2.9 5.2 - - - -
36H MET* 4.5 0.4 - - - -
37H ARG* 2.9 43.0 + - - +
48H LEU* 3.3 31.4 - - - +
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Residues in contact with THR 34 (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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21H LYS* 4.3 20.7 - - + -
30H LYS* 2.7 39.5 + - - +
31H GLU* 4.2 7.9 - - - -
33H GLY* 1.3 71.1 - - - +
35H VAL* 1.3 50.6 + - - +
37H ARG* 4.4 5.6 - - - +
38H SER* 2.6 27.0 + - - -
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Residues in contact with VAL 35 (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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18H LEU 4.3 13.0 - - - +
19H PHE* 4.0 33.9 - - + +
21H LYS* 3.9 24.9 - - - +
31H GLU 3.1 20.6 + - - +
32H LEU 3.4 3.3 + - - +
33H GLY 2.9 0.8 - - - -
34H THR* 1.3 80.0 - - - +
36H MET* 1.3 60.4 + - - +
37H ARG 3.1 1.6 - - - -
38H SER* 2.7 33.4 + - - -
39H LEU* 3.3 14.5 - - + +
112H LEU* 4.2 18.4 - - + -
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Residues in contact with MET 36 (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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525G ALA* 3.3 37.5 - - + +
528G LEU* 4.5 3.4 - - - -
529G MET* 3.4 39.0 - - + +
32H LEU* 2.9 34.5 + - + +
33H GLY* 4.4 1.1 - - - +
35H VAL* 1.3 73.6 - - + +
37H ARG* 1.3 56.7 + - + +
38H SER 3.0 0.2 - - - -
39H LEU* 3.0 28.1 + - - +
41H GLN* 3.0 31.8 + - - +
43H PRO* 4.2 5.6 - - + -
48H LEU* 4.2 6.1 - - + -
51H MET* 3.4 33.7 - - - +
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Residues in contact with ARG 37 (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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33H GLY* 2.9 31.2 + - - +
34H THR* 4.8 4.7 - - - +
36H MET* 1.3 72.9 - - + +
38H SER* 1.3 56.8 + - - +
39H LEU 3.0 7.7 + - - -
40H GLY* 3.8 7.8 + - - -
41H GLN 3.4 12.3 - - - +
42H ASN* 4.1 15.2 + - + +
43H PRO* 3.0 32.0 + - + -
44H THR* 4.0 6.7 - - - +
45H GLU* 3.0 28.1 + - - +
48H LEU* 3.5 11.6 - - - +
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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