Contacts of the strand formed by residues 46 - 51 (chain D) in PDB entry 4JHN
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 HIS 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY* 2.8 27.4 + - - -
44D ASP 3.8 0.2 - - - -
45D GLU* 1.3 83.7 + - - +
47D SER* 1.3 60.9 + - - +
58D MET* 3.8 12.8 - - + -
59D PHE 3.5 12.3 - - - +
60D GLY* 4.2 0.4 - - - -
61D SER 3.7 8.1 - - - +
66D GLN* 3.7 28.2 + - + +
67D LEU* 3.6 10.8 - - + -
94D CYS* 3.4 24.9 - - + +
95D GLY 3.2 27.5 + - - -
96D ARG 4.4 2.2 + - - -
98D HIS 3.4 12.5 + - - -
99D THR* 2.8 28.5 + - - -
360D HIS* 3.2 10.0 + - - -
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Residues in contact with SER 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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20D SER* 5.0 0.7 + - - -
41D SER 3.3 11.2 - - - -
42D CYS* 3.6 7.6 - - - -
46D HIS* 1.3 71.0 - - - +
48D ALA* 1.3 60.6 + - - +
49D VAL* 5.8 0.4 - - - -
58D MET* 3.5 9.7 - - - +
59D PHE* 2.9 61.3 + - - +
94D CYS* 4.0 4.5 - - - -
360D HIS* 2.9 31.4 + - - -
362D VAL* 3.7 5.9 - - - +
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Residues in contact with ALA 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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39D HIS* 4.6 0.6 - - - -
40D LEU* 3.5 6.2 - - - +
41D SER* 2.8 34.8 + - - +
47D SER* 1.3 75.2 - - - +
49D VAL* 1.3 67.2 + - - +
50D VAL 4.2 0.2 - - - -
56D LEU* 4.1 1.6 - - + -
57D TYR 3.4 5.2 - - - -
58D MET* 3.5 19.7 - - - -
92D ALA* 3.9 24.5 - - + -
94D CYS* 3.6 17.5 - - - -
99D THR* 4.9 0.2 - - + -
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Residues in contact with VAL 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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14D VAL* 4.9 0.9 - - + -
30D PHE* 4.3 13.7 - - + -
32D PHE* 3.9 26.7 - - + -
37D PRO* 4.0 21.8 - - + -
39D HIS 3.6 4.9 - - - +
40D LEU* 3.8 20.0 - - + -
47D SER* 5.8 0.4 - - - -
48D ALA* 1.3 78.3 - - - +
50D VAL* 1.3 67.1 + - - +
51D THR* 4.1 1.1 + - + -
55D LYS 3.7 0.7 - - - +
56D LEU* 3.5 4.0 - - - -
57D TYR* 2.8 49.4 + - + +
59D PHE* 4.1 22.4 - - + -
362D VAL* 5.1 0.2 - - + -
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Residues in contact with VAL 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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37D PRO* 3.5 4.3 - - - +
38D VAL* 2.8 28.7 + - + -
39D HIS* 2.9 27.4 + - + +
48D ALA 5.6 0.4 - - - -
49D VAL* 1.3 76.0 - - - +
51D THR* 1.3 68.5 + - - +
55D LYS 3.4 4.9 - - - +
56D LEU* 4.0 10.5 - - + -
89D VAL* 3.5 45.5 - - + +
90D LYS 3.6 13.2 - - - +
91D LEU 4.1 1.6 - - - -
92D ALA* 4.0 24.9 - - + +
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Residues in contact with THR 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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32D PHE* 3.9 24.9 - - + -
35D ASP* 2.7 29.8 + - - +
36D VAL 3.3 8.5 - - - +
37D PRO* 4.6 0.7 - - + -
38D VAL* 3.6 11.2 - - - +
49D VAL* 4.5 2.5 - - + -
50D VAL* 1.3 79.2 - - - +
52D GLY* 1.3 59.0 + - - +
53D ASN 3.5 1.4 + - - -
54D ASN* 2.9 21.7 + - - -
55D LYS* 2.9 27.2 + - - +
57D TYR* 3.7 31.6 - - + -
89D VAL 4.6 0.2 - - - +
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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