Contacts of the helix formed by residues 35 - 47 (chain H) in PDB entry 4HHM
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 ASP 35 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H ALA 4.0 2.2 + - - -
34H LEU* 1.3 77.9 - - - +
36H PRO* 1.3 69.7 - - - +
37H VAL* 3.1 26.0 - - - +
38H GLU* 2.7 37.6 + - + +
39H ALA 2.9 10.4 + - - -
74H ARG* 3.1 26.1 + - - -
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Residues in contact with PRO 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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15H LEU* 4.4 17.3 - - + +
34H LEU 3.4 8.3 - - - +
35H ASP* 1.3 92.3 - - - +
37H VAL* 1.3 62.6 + - + +
39H ALA* 3.1 10.1 + - + +
40H VAL* 3.0 29.6 + - - +
57H ASP 3.8 22.0 - - - +
58H LEU* 4.7 11.9 - - + +
71H HIS* 6.2 1.3 - - - +
74H ARG* 5.2 6.1 - - - +
75H PHE* 4.3 18.6 - - + -
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Residues in contact with VAL 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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35H ASP* 3.1 13.8 + - - +
36H PRO* 1.3 77.0 - - + +
38H GLU* 1.3 60.6 + - - +
40H VAL* 3.3 3.7 + - - +
41H GLN* 3.2 46.1 + - - +
74H ARG* 3.3 45.8 - - + +
75H PHE* 4.6 3.6 - - - +
78H ALA* 4.0 29.3 - - + +
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Residues in contact with GLU 38 (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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34H LEU* 3.8 22.0 - - + -
35H ASP* 2.7 33.6 + - + +
37H VAL* 1.3 75.7 - - - +
39H ALA* 1.3 58.6 + - - -
41H GLN* 3.4 12.3 + - - +
42H ARG* 2.6 69.1 + - + +
300H TRP* 5.0 1.1 + - + -
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Residues in contact with ALA 39 (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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15H LEU* 4.1 20.4 - - + +
18H VAL* 4.4 14.8 - - + -
34H LEU* 3.4 23.1 - - + +
35H ASP 2.9 6.3 + - - +
36H PRO* 3.4 10.8 - - + +
38H GLU* 1.3 74.1 - - - +
40H VAL* 1.3 67.2 + - - +
42H ARG 3.4 0.5 + - - -
43H LEU* 2.9 34.2 + - + +
300H TRP* 4.2 6.7 - - - -
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 4.9 1.3 - - + -
36H PRO 3.0 15.2 + - - +
37H VAL* 3.6 9.0 - - - +
39H ALA* 1.3 74.5 - - - +
41H GLN* 1.3 58.8 + - + +
43H LEU* 3.5 2.0 + - - +
44H ALA* 2.9 28.2 + - - +
51H VAL* 4.4 10.3 - - + -
75H PHE* 3.5 30.1 - - + -
78H ALA* 4.0 15.5 - - + +
79H LEU* 4.3 9.6 - - + -
82H THR* 3.4 26.5 - - + +
84H MET* 3.8 23.0 - - + +
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Residues in contact with GLN 41 (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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37H VAL* 3.2 33.9 + - - +
38H GLU* 3.6 24.4 + - - +
39H ALA 3.2 0.4 - - - -
40H VAL* 1.3 75.3 - - + +
42H ARG* 1.3 84.8 + - - +
44H ALA* 3.3 3.3 + - - +
45H GLU* 3.1 27.4 + - - +
78H ALA* 5.5 4.1 - - + +
82H THR* 4.3 19.7 - - + -
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Residues in contact with ARG 42 (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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38H GLU* 2.6 63.3 + - - +
41H GLN* 1.3 94.4 - - - +
43H LEU* 1.3 63.4 + - - +
45H GLU* 2.8 45.2 + - - +
46H LEU* 3.2 26.3 + - + +
300H TRP* 3.5 50.7 - - + +
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Residues in contact with LEU 43 (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* 3.8 48.2 - - + +
14H GLY 5.7 1.1 - - - +
15H LEU* 5.7 1.3 - - + -
18H VAL* 4.4 15.0 - - + -
39H ALA* 2.9 26.5 + - + +
40H VAL 3.8 2.9 - - - +
42H ARG* 1.3 78.0 - - - +
44H ALA* 1.3 60.4 + - - +
46H LEU* 3.1 15.3 + - + +
47H GLY 3.3 0.2 + - - -
48H ALA* 3.0 32.5 + - + +
51H VAL* 3.5 28.5 - - + -
84H MET* 3.9 4.5 - - + -
300H TRP* 4.1 19.5 - - + -
303H ALA* 4.6 5.4 - - + -
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Residues in contact with ALA 44 (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 PRO* 5.8 1.6 - - - +
40H VAL 2.9 19.3 + - - +
41H GLN 3.6 4.7 - - - +
43H LEU* 1.3 74.6 - - - +
45H GLU* 1.3 62.8 + - + +
47H GLY* 3.0 15.6 + - - -
48H ALA 4.1 4.5 + - - +
82H THR* 4.0 30.5 - - + +
84H MET* 4.0 16.3 - - + -
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Residues in contact with GLU 45 (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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4H GLN* 5.0 5.2 + - - -
41H GLN* 3.1 12.6 + - - +
42H ARG* 2.8 46.9 + - - +
44H ALA* 1.3 76.9 - - + +
46H LEU* 1.3 63.6 + - + +
47H GLY 3.5 0.2 + - - -
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Residues in contact with LEU 46 (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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4H GLN* 3.7 9.4 + - - +
5H PRO* 3.2 22.7 - - - +
42H ARG 3.2 15.3 + - - +
43H LEU* 3.1 14.2 + - + +
44H ALA 3.1 1.4 - - - -
45H GLU* 1.3 80.1 - - + +
47H GLY* 1.3 58.7 + - - +
48H ALA 3.6 0.2 - - - -
300H TRP* 3.6 39.7 - - + +
303H ALA* 4.1 17.0 - - + -
304H ALA* 4.2 19.3 - - + +
307H MET* 3.7 13.7 - - + +
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Residues in contact with GLY 47 (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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4H GLN* 4.6 1.1 - - - -
5H PRO* 3.6 17.7 - - - +
6H THR* 3.3 28.3 + - - +
7H PRO* 4.3 5.4 - - - -
11H PHE* 4.9 2.1 - - - +
44H ALA 3.0 11.1 + - - -
45H GLU 3.3 1.0 + - - -
46H LEU* 1.3 79.8 - - - +
48H ALA* 1.3 66.8 + - - +
49H TYR 3.7 0.5 + - - -
307H MET* 4.2 8.4 - - - +
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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