Contacts of the strand formed by residues 22 - 30 (chain D) in PDB entry 3LON
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 SER 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C SER 3.9 5.2 - - - +
38C THR* 4.4 5.5 - - - -
39C ALA 5.4 0.3 + - - -
62C ARG* 3.8 9.7 + - - +
63C THR* 3.0 35.1 + - - +
64C ILE 3.6 0.3 - - - -
65C ALA* 3.5 20.2 + - - -
70C PRO* 4.1 4.6 - - - +
21D GLY* 1.3 74.8 - - - -
23D VAL* 1.3 62.0 + - - +
24D VAL* 3.7 10.1 + - - +
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Residues in contact with VAL 23 (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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36C VAL* 3.6 35.7 - - + -
37C SER 3.5 9.2 - - - +
38C THR* 3.9 13.0 - - + -
43C PHE* 4.7 2.2 - - + -
59C ALA* 3.9 11.2 - - + -
62C ARG* 3.9 16.4 - - + -
63C THR 2.7 16.1 + - - +
64C ILE* 3.4 9.1 - - + +
65C ALA* 2.8 26.9 + - - +
85C TRP* 3.7 33.2 - - + -
22D SER* 1.3 72.9 - - - +
24D VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 3.2 6.2 - - - -
37C SER* 2.9 42.7 + - - +
65C ALA* 3.7 22.9 - - + -
22D SER* 4.1 12.1 - - - +
23D VAL* 1.3 77.9 - - - +
25D ILE* 1.3 63.9 + - - +
26D VAL* 3.6 17.4 + - + -
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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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34C GLN* 4.3 12.1 - - + -
35C ILE 3.7 5.2 - - - +
36C VAL* 4.3 13.2 - - + -
64C ILE* 4.3 17.9 - - + -
65C ALA* 5.1 7.2 - - - +
88C PRO* 3.6 37.9 - - + -
89C GLN 5.3 3.8 - - - +
24D VAL* 1.3 75.3 - - - +
26D VAL* 1.3 60.1 + - - +
27D GLY 3.4 26.5 - - - +
28D ARG* 4.4 11.2 - - + -
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Residues in contact with VAL 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 2.7 43.2 + - + +
37C SER* 3.4 29.8 - - - +
42C THR* 4.6 2.0 - - + -
109C ARG* 5.0 1.1 - - - +
24D VAL* 3.9 17.7 - - + +
25D ILE* 1.3 75.7 - - - +
27D GLY* 1.3 54.3 + - - -
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Residues in contact with GLY 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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37B ILE* 5.3 3.4 - - - -
38B ILE 5.8 0.9 - - - -
34C GLN* 3.7 0.5 - - - -
35C ILE* 2.9 35.8 + - - -
25D ILE* 3.4 10.3 - - - +
26D VAL* 1.3 79.2 - - - +
28D ARG* 1.3 73.7 + - - +
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Residues in contact with ARG 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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37B ILE* 3.1 11.4 - - - +
38B ILE* 2.7 79.5 + - + +
39B PRO 5.2 1.6 + - - -
40B LYS* 6.3 0.8 - - - +
29C VAL 2.9 28.3 + - - -
31C GLY* 4.7 4.3 - - - -
33C VAL 3.4 9.4 - - - +
34C GLN* 4.5 8.5 - - + +
35C ILE* 4.2 3.1 - - - +
89C GLN 5.0 1.7 + - - +
90C GLY* 3.3 38.0 + - - +
25D ILE* 4.4 12.1 - - + -
27D GLY* 1.3 81.6 - - - +
29D ILE* 1.3 59.6 + - - +
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Residues in contact with ILE 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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35B PRO* 4.3 6.1 - - + -
36B ALA 3.1 15.9 - - - +
37B ILE* 3.8 15.5 - - + +
38B ILE* 4.5 0.2 - - - -
31C GLY* 3.3 4.3 - - - -
32C GLU* 3.3 23.4 + - - +
33C VAL* 2.9 33.5 + - + +
35C ILE* 4.1 9.6 - - + -
107C VAL* 4.5 3.8 - - + -
108C THR 3.4 25.6 - - - +
109C ARG* 4.1 13.0 - - - +
111C ALA* 3.8 13.9 - - + +
28D ARG* 1.3 78.1 - - - +
30D VAL* 1.3 69.5 + - - +
31D LEU* 3.9 18.1 + - + -
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Residues in contact with VAL 30 (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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36B ALA* 2.7 33.6 + - + +
38B ILE* 3.9 22.4 - - + +
29C VAL* 3.9 11.9 - - + -
30C GLU 3.6 19.5 - - - +
31C GLY* 4.4 1.6 - - - -
32C GLU* 3.8 6.7 - - - +
92C ARG* 5.7 1.3 - - - -
29D ILE* 1.3 73.2 - - - +
31D LEU* 1.3 64.4 + - - +
32D SER* 3.7 21.1 - - - +
33D GLY* 3.1 10.2 + - - -
34D LYS* 3.8 28.3 - - + +
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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