Contacts of the strand formed by residues 24 - 33 (chain D) in PDB entry 3KDO
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 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D TYR* 2.7 28.5 + - - -
19D PRO* 3.4 10.0 - - + +
20D SER* 2.7 35.5 + - - +
23D ARG* 1.3 84.4 - - - +
25D ILE* 1.3 65.9 + - - +
26D ILE* 4.4 2.0 - - + +
90D ALA* 4.2 13.8 - - + +
91D TYR 3.3 15.7 - - - +
92D PRO* 3.7 6.6 - - - +
127D TYR* 3.5 17.3 - - - -
129D PRO* 3.4 16.5 - - - +
23I ARG* 5.7 2.1 + - - -
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Residues in contact with ILE 25 (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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24D ASP* 1.3 73.8 - - - +
26D ILE* 1.3 68.3 + - - +
90D ALA* 3.3 3.5 - - - -
91D TYR* 2.7 58.6 + - + +
93D PHE* 3.3 39.5 - - + +
96D PHE* 4.2 14.4 - - + -
104D LEU* 4.9 11.0 - - + -
108D ILE* 5.4 0.9 - - + -
126D LEU* 4.5 8.5 - - + -
127D TYR 3.4 11.4 - - - +
128D PHE* 4.3 13.2 - - + -
129D PRO* 3.9 7.0 - - + -
132D LEU* 3.5 32.1 - - + -
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Residues in contact with ILE 26 (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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19D PRO* 3.8 23.8 - - + -
20D SER 5.6 1.3 - - - +
21D LYS* 6.4 0.2 - - - -
24D ASP* 3.9 5.4 + - + +
25D ILE* 1.3 83.7 - - - +
27D ALA* 1.3 69.7 + - - +
28D VAL* 4.1 0.6 + - + -
75D TYR* 3.3 33.7 - - + +
88D ARG* 4.2 5.8 - - + -
89D ILE 3.2 9.4 - - - +
90D ALA* 4.6 4.0 - - - -
125D ASP 4.0 0.5 - - - +
126D LEU* 3.4 3.1 - - - -
127D TYR* 2.7 60.5 + - + +
352D LEU* 3.6 22.6 - - + +
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Residues in contact with ALA 27 (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 ILE 4.2 0.4 - - - -
26D ILE* 1.3 73.9 - - - +
28D VAL* 1.3 61.2 + - - +
29D PHE* 3.5 28.4 + - + -
87D VAL 3.6 2.4 - - - +
88D ARG* 3.6 1.4 - - - -
89D ILE* 3.0 31.7 + - - -
91D TYR* 4.0 17.6 - - + +
108D ILE* 4.5 3.8 - - + -
123D LEU* 4.1 5.8 - - + -
125D ASP 3.6 4.7 - - - -
126D LEU* 3.7 17.9 - - + -
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Residues in contact with VAL 28 (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 ILE* 4.5 0.4 - - + -
27D ALA* 1.3 72.3 - - - +
29D PHE* 1.3 55.3 + - - +
86D ILE* 3.5 30.7 - - + -
87D VAL 3.6 4.3 - - - +
88D ARG* 4.2 14.6 - - + +
123D LEU* 3.6 3.6 - - - +
124D GLU* 2.7 37.9 + - + -
125D ASP* 3.0 19.4 + - + +
349D VAL 4.5 0.9 - - - +
350D PHE 3.3 26.2 - - - +
352D LEU* 3.6 37.9 - - + -
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Residues in contact with PHE 29 (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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27D ALA* 3.5 27.1 - - + -
28D VAL* 1.3 74.4 - - - +
30D ARG* 1.3 59.3 - - - +
31D VAL* 3.5 20.0 + - + +
46D VAL* 4.1 4.3 - - + -
85D TRP 3.4 1.2 - - - +
86D ILE* 3.3 4.5 - - - +
87D VAL* 2.8 41.2 + - + +
89D ILE* 3.9 29.8 - - + -
91D TYR* 4.1 7.2 - - - -
108D ILE 3.5 23.1 - - - -
112D ILE* 3.5 27.1 - - + -
113D PHE* 5.1 2.0 - + - -
121D LEU* 3.5 25.4 - - + -
122D ARG 3.2 9.9 - - - -
123D LEU* 3.9 21.1 - - + -
124D GLU* 4.5 2.0 - - - -
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D PHE* 1.3 70.6 - - - +
31D VAL* 1.3 58.6 + - - +
32D THR* 4.0 0.6 + - - +
80D MET* 3.5 23.6 - - - +
82D ASP* 2.6 29.7 + - - -
84D SER* 3.1 23.2 + - - +
85D TRP 3.3 4.0 - - - +
86D ILE* 3.9 15.7 - - + -
120D GLY 3.8 1.4 - - - +
121D LEU* 3.6 4.3 + - - -
122D ARG* 2.8 38.8 + - + +
124D GLU* 3.5 22.7 + - - +
292D PRO* 3.4 27.9 + - - +
293D TYR* 3.4 24.6 + - + +
350D PHE* 3.5 24.0 - - - -
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Residues in contact with VAL 31 (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 PHE* 3.6 27.8 - - + +
30D ARG* 1.3 76.3 - - - +
32D THR* 1.3 65.0 + - - +
33D PRO* 3.4 5.0 - - - +
39D ILE* 3.9 14.6 - - + -
42D ALA* 4.0 31.2 - - + -
43D ALA* 4.9 2.0 - - - +
46D VAL* 4.9 6.3 - - + -
84D SER* 3.2 2.4 - - - -
85D TRP* 2.6 38.2 + - - +
87D VAL* 3.9 17.3 - - + -
118D VAL* 4.3 14.1 - - + -
120D GLY 3.9 2.5 - - - +
121D LEU* 4.0 9.0 - - + -
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Residues in contact with THR 32 (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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30D ARG* 4.0 1.2 + - - +
31D VAL* 1.3 72.9 - - - +
33D PRO* 1.3 62.7 - - - +
83D GLY* 3.6 17.0 - - - +
84D SER* 3.2 18.5 - - - -
118D VAL* 3.4 3.1 - - - -
119D LYS* 2.6 56.4 + - + +
120D GLY* 2.9 27.5 + - - +
293D TYR* 4.2 14.7 + - - +
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Residues in contact with PRO 33 (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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31D VAL* 3.4 11.2 - - - +
32D THR* 1.3 96.4 - - - +
34D ALA* 1.3 63.2 + - - +
35D GLU 3.9 0.9 + - - -
37D TYR* 3.5 24.7 - - + +
39D ILE* 3.9 33.0 - - + +
42D ALA* 3.9 18.8 - - + -
83D GLY 3.6 15.0 - - - +
85D TRP* 4.7 4.0 - - + +
117D ARG 3.8 7.2 - - - +
118D VAL* 4.2 0.2 - - - -
119D LYS* 3.8 3.7 - - - +
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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