Contacts of the strand formed by residues 46 - 52 (chain D) in PDB entry 4KZX
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 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D PHE* 5.7 4.3 - - + -
39D VAL* 3.8 25.4 - - + -
40D ARG 4.1 5.8 - - - +
41D VAL* 5.3 5.3 - - + +
45D ARG* 1.3 76.1 + - - +
47D GLU* 1.3 57.9 + - - +
48D ILE* 6.1 0.2 - - + -
79D PHE* 1.8 55.6 - - + -
83D SER 3.0 7.1 + - - -
84D VAL* 3.1 12.5 - - + +
85D GLU* 2.4 35.6 + - - +
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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 GLU 3.8 0.7 - - - +
39D VAL* 3.5 6.1 - - - +
40D ARG* 3.0 49.3 + - + +
42D THR* 5.0 12.9 - - + +
45D ARG* 4.1 6.1 - - + +
46D THR* 1.3 75.3 - - - +
48D ILE* 1.3 60.1 + - - +
49D ILE* 4.0 13.5 - - + +
85D GLU* 1.8 46.3 - - + +
87D TYR* 3.5 21.3 + - + -
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Residues in contact with ILE 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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21D LEU* 2.4 52.0 - - + -
25D LEU* 4.5 1.3 - - + -
37D VAL* 4.3 7.4 - - + -
38D GLU 3.6 7.9 - - - +
39D VAL* 4.6 4.3 - - + +
47D GLU* 1.3 73.9 - - - +
49D ILE* 1.3 65.2 + - - +
50D ILE* 3.7 23.4 + - + +
73D VAL* 4.7 8.7 - - + -
84D VAL* 5.0 5.8 - - + -
85D GLU 2.6 14.9 + - - +
86D LEU* 2.8 40.6 - - + +
87D TYR 2.9 21.9 + - - +
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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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37D VAL* 3.5 2.8 - - - +
38D GLU* 2.9 52.0 + - + +
40D ARG* 3.1 40.6 - - + +
47D GLU* 4.7 13.7 - - + +
48D ILE* 1.3 80.0 - - - +
50D ILE* 1.4 63.6 + - - +
51D LEU* 3.5 5.5 + - + +
87D TYR* 3.3 25.4 - - + +
88D ALA 4.4 0.9 - - - +
89D GLU* 3.7 33.2 - - + -
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Residues in contact with ILE 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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25D LEU* 3.6 21.3 - - + -
29D LEU* 3.4 28.5 - - + -
34D TYR* 3.5 16.6 - - + -
36D GLY 3.9 1.6 - - - -
37D VAL* 3.4 24.0 - - + -
48D ILE* 3.7 23.8 - - + +
49D ILE* 1.4 71.5 - - - +
51D LEU* 1.3 57.7 + - - +
52D ALA* 2.9 18.1 + - + +
58D VAL* 5.3 3.4 - - + -
69D LEU* 5.3 3.6 - - + -
86D LEU* 5.2 9.0 - - + -
87D TYR 2.8 19.9 + - - +
88D ALA* 3.8 5.4 - - + +
89D GLU 3.1 18.9 + - - -
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Residues in contact with LEU 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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34D TYR* 4.3 0.3 - - - -
35D SER* 2.8 27.4 + - - -
36D GLY* 2.8 23.9 + - - +
37D VAL* 5.5 0.9 - - - -
38D GLU* 5.1 11.4 - - + +
49D ILE* 3.5 6.6 + - + +
50D ILE* 1.3 70.5 - - - +
52D ALA* 1.3 58.2 + - - +
89D GLU* 3.1 43.7 - - + +
90D LYS 3.7 8.7 - - - +
91D VAL* 3.4 25.8 - - + -
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Residues in contact with ALA 52 (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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29D LEU* 4.9 0.2 - - + -
32D ASP* 4.0 9.2 - - + +
33D GLY 3.4 6.3 - - - +
34D TYR* 3.6 21.8 - - + -
35D SER 3.9 0.2 - - - +
50D ILE* 2.9 22.4 + - + +
51D LEU* 1.3 74.3 - - - +
53D THR* 1.3 70.9 + - - +
54D ARG 3.3 1.6 - - - +
55D THR* 3.5 5.4 - - + +
58D VAL* 4.5 15.5 - - + -
89D GLU 3.1 14.8 + - - +
90D LYS* 3.5 3.6 - - - -
91D VAL* 3.8 1.3 - - - +
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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