Contacts of the helix formed by residues 43 - 53 (chain B) in PDB entry 3E7H
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 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ARG* 4.6 2.0 - - - -
41B ARG* 3.8 9.9 - - + +
42B VAL* 1.3 75.4 - - - +
44B ALA* 1.3 64.3 + - - +
45B ARG* 3.3 12.7 + - - +
46B HIS* 2.9 52.8 + - + +
47B ILE* 3.1 17.5 + - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.3 33.6 + - - +
43B THR* 1.3 75.1 - - - +
45B ARG* 1.3 57.1 + - - +
47B ILE* 3.2 4.0 + - - +
48B ARG* 2.9 47.9 + - - +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 3.4 11.4 - - - +
44B ALA* 1.3 77.9 - - - +
46B HIS* 1.3 66.8 + - + +
48B ARG* 3.3 34.6 + - - +
49B GLN* 3.0 47.4 + - - +
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.4 25.5 + - + -
36B VAL* 3.3 29.7 - - + +
40B ARG* 5.9 1.3 - - + -
41B ARG 3.5 18.2 - - - -
42B VAL* 3.6 7.5 - - + -
43B THR* 2.9 44.3 + - + +
45B ARG* 1.3 75.1 - - + +
47B ILE* 1.3 68.1 + - - +
49B GLN* 3.1 22.1 + - - +
50B LEU* 3.0 29.0 + - + +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO* 3.7 38.0 - - + +
19B LEU* 4.2 12.1 - - + -
20B ARG* 3.8 47.3 - - + +
42B VAL* 3.8 19.1 - - + -
43B THR 3.1 11.4 + - - +
44B ALA 3.4 7.4 - - - +
46B HIS* 1.3 76.8 - - - +
48B ARG* 1.3 65.1 + - + +
50B LEU* 3.4 10.2 + - + +
51B GLU* 3.1 27.9 + - + +
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 2.9 23.8 + - - +
45B ARG* 3.6 71.7 - - - +
46B HIS 3.2 0.2 - - - -
47B ILE* 1.3 79.1 - - + +
49B GLN* 1.3 56.6 + - + +
51B GLU* 3.3 14.3 + - - +
52B LYS* 2.9 31.0 + - - +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 5.5 5.7 - - - +
35B TYR* 4.0 26.1 - - + +
45B ARG* 3.0 45.4 + - + +
46B HIS* 3.1 24.4 + - - +
48B ARG* 1.3 75.5 - - + +
50B LEU* 1.3 62.0 + - - +
52B LYS* 3.8 11.5 - - - +
53B ASP* 3.0 30.2 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.0 20.2 - - + -
16B PRO* 5.9 2.0 - - + -
19B LEU* 4.1 20.0 - - + -
28B ILE* 4.3 13.2 - - + -
35B TYR* 3.5 40.6 - - + -
36B VAL* 6.0 0.7 - - + -
46B HIS* 3.0 22.5 + - + +
47B ILE* 3.7 17.5 - - + +
49B GLN* 1.3 76.0 - - - +
51B GLU* 1.3 57.4 + - - +
53B ASP* 3.3 2.1 + - - -
54B GLY 3.0 7.8 + - - -
55B VAL* 2.9 59.0 + - + +
58B ILE* 4.8 0.4 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.1 20.6 + - + +
48B ARG* 3.5 14.3 - - - +
50B LEU* 1.3 76.6 - - - +
52B LYS* 1.3 66.0 + - - +
54B GLY* 3.0 14.8 + - - +
55B VAL 5.0 1.3 - - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 6.0 1.3 - - - +
48B ARG 2.9 16.4 + - - +
49B GLN* 3.8 11.7 - - - +
50B LEU 3.4 0.2 - - - -
51B GLU* 1.3 79.6 - - - +
53B ASP* 1.3 73.4 + - - +
54B GLY* 3.2 1.3 + - - -
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 2.7 30.2 + - - +
35B TYR* 2.5 32.1 + - - +
49B GLN* 3.0 16.6 + - - +
50B LEU 3.9 3.4 - - - +
52B LYS* 1.3 92.8 - - - +
54B GLY* 1.3 63.0 + - - +
55B VAL* 3.5 5.5 + - + +
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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