Contacts of the helix formed by residues 46 - 51 (chain D) in PDB entry 4G7H
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 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PRO* 4.3 3.3 - - - +
40D GLU 3.8 8.8 + - - +
41D ARG* 3.7 7.5 + - - +
42D ASP* 2.5 30.6 + - - +
43D GLY 3.3 17.5 + - - +
44D LEU 3.5 0.8 - - - -
45D PHE* 1.3 74.6 - - - +
47D GLU* 1.3 68.9 + - - +
48D ARG* 2.9 46.8 + - - +
49D ILE* 3.3 14.1 + - + +
50D PHE* 3.1 31.6 + - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 5.4 3.8 - - - +
39D PRO* 4.1 21.6 - - + +
45D PHE 3.3 0.8 + - - -
46D ASP* 1.3 72.3 + - - +
48D ARG* 1.3 64.1 + - + +
49D ILE 3.1 2.5 - - - -
51D GLY* 3.2 39.6 + - - +
52D PRO* 3.7 4.4 - - - +
53D ILE* 2.8 47.6 + - + +
54D LYS* 4.7 2.6 + - - -
57D GLU 5.1 1.4 - - - +
58D CYS 5.3 0.2 - - - -
59D ALA* 3.5 28.4 + - + +
78D VAL* 3.7 23.6 - - + +
79D GLU 5.1 0.9 + - - -
86D ARG* 4.5 2.2 - - - +
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR* 4.5 5.0 - - - +
41D ARG* 3.4 40.7 - - - +
42D ASP* 2.5 36.6 + - - +
46D ASP* 2.9 25.0 + - - +
47D GLU* 1.3 78.1 - - + +
49D ILE* 1.3 68.0 + - - +
76D CYS 3.5 26.0 - - - +
77D GLY* 3.8 25.0 - - - +
78D VAL* 4.5 4.0 - - + +
79D GLU 5.8 0.7 + - - -
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR* 3.2 34.9 - - + +
24D GLY* 3.9 30.7 - - - +
25D GLU 3.5 31.4 - - - +
26D VAL* 4.3 4.0 - - + -
42D ASP* 4.6 3.8 - - - -
43D GLY 4.3 9.6 - - - +
46D ASP* 3.3 27.1 + - + +
47D GLU 3.1 0.4 - - - -
48D ARG* 1.3 89.9 - - - +
50D PHE* 1.3 94.6 + - + +
51D GLY 3.4 1.4 + - - -
89D ARG* 4.3 2.1 + - - -
91D GLY* 4.4 2.9 - - - -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 3.8 20.0 - - + -
43D GLY 4.0 4.7 - - - -
44D LEU 3.0 33.0 - - - -
45D PHE 4.1 0.2 - - - -
46D ASP 3.1 28.3 + - - +
49D ILE* 1.3 98.1 - - + +
51D GLY* 1.3 58.5 + - - +
85D VAL* 3.7 7.3 - - - +
86D ARG* 3.4 27.3 + - - +
89D ARG* 3.4 30.0 - - - +
90D MET 4.4 0.2 - - - -
91D GLY 3.5 23.1 - - - -
519D VAL* 4.1 13.7 - - + -
520D LEU 4.4 1.6 - - - -
522D PRO* 3.4 33.9 - - + -
525D ARG* 4.5 0.2 - - - -
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLU* 3.2 28.7 + - - +
49D ILE 3.4 2.8 + - - -
50D PHE* 1.3 79.2 - - - +
52D PRO* 1.3 73.4 - - - +
78D VAL* 5.0 0.2 - - - -
79D GLU* 6.0 1.3 - - - -
85D VAL* 3.9 7.6 - - - -
86D ARG* 3.1 20.8 + - - -
89D ARG* 4.7 7.6 - - - +
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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