Contacts of the helix formed by residues 30 - 40 (chain D) in PDB entry 5SY1
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D THR* 1.3 77.2 - - - +
31D LYS* 1.3 60.0 + - - +
33D LEU* 2.9 6.0 + - + +
34D GLY* 2.8 25.8 + - - -
46D GLU* 4.8 17.9 - - + +
49D LEU* 4.6 24.4 - - + +
50D GLN* 5.1 7.8 - - + +
53D ILE* 3.3 24.2 - - + +
62D GLY 5.1 3.0 + - - -
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Residues in contact with LYS 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 THR* 3.6 4.9 + - - +
30D THR* 1.3 80.2 - - - +
32D GLU* 1.3 60.8 + - - +
33D LEU 3.3 0.7 + - - -
34D GLY* 4.3 2.5 - - - +
35D THR* 3.3 32.9 + - + +
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Residues in contact with GLU 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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20D PHE* 3.9 20.9 - - - +
21D ASP* 2.4 19.6 - - - +
22D LYS* 4.8 3.8 - - + +
23D ASP* 1.8 40.2 - - - +
27D THR 2.7 9.9 - - - +
28D ILE* 3.3 8.3 - - + +
29D THR* 3.2 33.1 + - - +
31D LYS* 1.3 76.5 - - - +
33D LEU* 1.3 59.0 + - - +
35D THR* 3.7 9.9 + - - -
36D VAL* 4.1 7.6 - - - +
203D CA 2.3 16.4 - - - -
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Residues in contact with LEU 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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563B PHE* 5.1 5.6 - - + -
567B LEU* 4.6 19.1 - - + -
20D PHE* 4.2 24.2 - - + -
28D ILE* 4.0 12.1 - - + -
29D THR 3.4 12.0 + - - +
30D THR* 2.9 9.4 + - + +
32D GLU* 1.3 77.2 - - - +
34D GLY* 1.3 60.4 + - - +
35D THR 3.1 2.5 - - - -
36D VAL* 3.0 20.5 + - + +
37D MET* 3.4 30.9 + - + +
49D LEU* 4.7 17.0 - - + +
52D MET* 5.3 1.1 - - + -
53D ILE* 3.8 28.9 - - + +
64D ILE* 5.3 6.5 - - + -
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Residues in contact with GLY 34 (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 THR 2.8 17.6 + - - -
31D LYS* 3.7 3.5 + - - -
33D LEU* 1.3 72.9 - - - +
35D THR* 1.3 59.8 + - - +
37D MET* 4.1 5.8 - - - +
38D ARG* 3.2 38.2 + - - +
44D PRO* 5.7 1.4 - - - +
49D LEU* 4.0 23.7 - - - +
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Residues in contact with THR 35 (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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483A LEU* 4.7 22.3 - - + +
31D LYS* 3.3 28.3 + - + +
32D GLU* 3.7 10.6 + - - -
34D GLY* 1.3 77.6 - - - +
36D VAL* 1.3 66.1 + - - +
38D ARG* 3.5 21.4 + - - +
39D SER* 3.1 25.2 + - - -
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Residues in contact with VAL 36 (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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483A LEU* 6.4 1.3 - - + -
560B MET* 4.6 17.9 - - + -
564B CYS* 4.4 12.1 - - - -
19D LEU 4.4 12.8 - - - +
20D PHE* 3.7 42.4 - - + +
22D LYS* 6.3 1.3 - - - -
32D GLU 4.1 7.9 - - - +
33D LEU* 3.0 7.9 + - + +
35D THR* 1.3 83.4 + - - +
37D MET* 1.3 60.5 + - - +
39D SER* 2.4 34.4 + - - +
40D LEU* 3.2 13.0 + - + +
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Residues in contact with MET 37 (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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219B ASP* 5.3 5.4 - - - +
564B CYS* 3.6 43.5 - - + +
567B LEU* 3.9 19.7 - - + -
568B LEU* 5.6 8.1 - - - -
33D LEU* 3.4 23.8 + - + +
34D GLY* 4.2 6.1 - - - +
35D THR 3.4 0.2 - - - -
36D VAL* 1.3 76.8 - - - +
38D ARG* 1.3 60.6 + - - +
39D SER 3.5 0.2 + - - -
40D LEU* 3.5 8.8 + - - +
41D GLY 3.6 0.2 + - - -
42D GLN* 2.9 32.2 + - + +
44D PRO* 4.2 20.0 - - + -
49D LEU* 4.4 16.2 - - + -
52D MET* 3.7 26.7 - - + -
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Residues in contact with ARG 38 (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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65B SER* 5.4 0.5 + - - -
66B ASP* 5.6 2.3 - - - +
34D GLY* 3.2 42.8 + - - +
35D THR* 3.5 26.6 - - - +
36D VAL 3.2 0.4 - - - -
37D MET* 1.3 79.4 - - - +
39D SER* 1.3 62.9 + - - +
41D GLY* 3.2 14.2 + - - +
42D GLN 3.3 9.8 + - - +
43D ASN* 3.8 19.8 + - - +
44D PRO* 5.2 1.1 - - + +
49D LEU* 6.0 2.2 - - - +
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Residues in contact with SER 39 (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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483A LEU* 6.6 0.4 - - - -
486A ARG* 3.8 45.0 + - - +
66B ASP* 4.4 6.2 - - - +
560B MET* 5.9 1.6 - - - +
35D THR 3.1 11.9 + - - -
36D VAL* 2.4 33.8 + - - +
38D ARG* 1.3 79.6 - - - +
40D LEU* 1.3 65.8 + - - +
41D GLY 3.2 1.1 + - - -
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Residues in contact with LEU 40 (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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486A ARG* 5.4 5.4 - - - +
81B LEU 6.1 0.4 - - - +
218B GLU* 2.9 25.3 + - + +
219B ASP* 4.2 17.7 + - + +
555B GLN 4.7 12.6 - - - +
556B SER* 6.0 0.7 - - - -
560B MET* 4.8 7.2 - - + +
561B LYS* 4.1 48.9 - - + +
564B CYS* 4.4 21.3 - - + -
36D VAL* 3.2 16.1 + - + +
37D MET* 3.5 3.8 + - - +
38D ARG 3.3 0.4 - - - -
39D SER* 1.3 85.4 + - - +
41D GLY* 1.3 56.8 + - - +
42D GLN* 3.1 22.3 + - - +
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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