Contacts of the helix formed by residues 24 - 37 (chain D) in PDB entry 3SDL
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 24 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.3 0.3 - - - +
22D SER* 3.1 15.5 - - - -
23D MET* 1.3 80.3 - - - +
25D VAL* 1.3 65.4 + - - +
26D SER* 3.3 19.4 + - - -
27D GLU* 3.2 19.4 + - - +
28D LEU* 3.0 21.0 + - - +
56D ASP 5.6 2.9 - - - -
58D VAL 5.4 0.9 - - - -
59D PRO* 5.3 4.7 - - - -
60D LEU* 4.2 2.9 - - - +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D MET 4.1 0.6 + - - -
24D SER* 1.3 72.7 - - - +
26D SER* 1.3 58.4 + - - +
28D LEU* 3.1 8.0 + - - +
29D LYS* 2.9 57.9 + - + +
45D LEU* 4.6 8.3 - - + -
54D LEU* 4.1 17.7 - - + -
55D GLN 3.5 24.2 - - - +
56D ASP* 4.1 25.6 + - - +
58D VAL 4.3 5.0 + - - +
60D LEU* 3.5 24.7 - - + +
63D GLN* 4.4 0.2 - - - +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D SER* 3.3 16.6 + - - -
25D VAL* 1.3 79.0 - - - +
27D GLU* 1.3 61.2 + - - -
29D LYS* 3.4 9.1 + - - +
30D ALA* 3.1 22.7 + - - +
56D ASP 5.6 0.6 + - - -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.2 19.5 - - + +
20D SER* 2.7 38.2 + - - -
21D SER 3.6 3.3 + - - -
22D SER* 3.6 10.2 + - - -
23D MET 3.1 21.4 + - - -
24D SER* 3.2 18.1 + - - +
26D SER* 1.3 80.3 + - - +
28D LEU* 1.3 65.4 + - - +
30D ALA* 3.1 8.8 + - - +
31D GLN* 3.0 30.7 + - + +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.9 16.8 - - + -
7D VAL* 4.7 8.3 - - + -
17D VAL* 4.6 8.7 - - + -
19D LEU* 4.0 19.5 - - + -
24D SER 3.0 12.5 + - - +
25D VAL* 3.1 10.3 + - - +
27D GLU* 1.3 77.1 - - - +
29D LYS* 1.3 61.8 + - - +
31D GLN* 3.2 7.0 + - - +
32D ILE* 3.0 44.4 + - + +
45D LEU* 4.4 8.1 - - + -
54D LEU* 4.3 15.5 - - + -
60D LEU* 3.6 30.5 - - + -
71D VAL* 4.5 7.2 - - + -
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 2.9 40.2 + - + +
26D SER* 3.7 8.7 - - - +
28D LEU* 1.3 75.7 - - - +
30D ALA* 1.3 58.8 + - - +
32D ILE 3.1 0.7 + - - -
33D THR* 2.9 27.4 + - - -
40D ALA* 4.0 29.3 + - + +
43D GLN* 3.0 52.6 + - - +
45D LEU* 3.7 20.2 - - + +
56D ASP* 4.1 17.2 + - - -
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Residues in contact with ALA 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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26D SER 3.1 14.3 + - - +
27D GLU* 3.1 13.0 + - + +
29D LYS* 1.3 78.0 - - - +
31D GLN* 1.3 61.0 + - + +
33D THR* 3.5 8.2 + - - -
34D GLN* 3.2 28.0 + - - +
40D ALA* 5.4 2.0 - - - +
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Residues in contact with GLN 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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17D VAL* 3.0 30.5 - - + +
18D SER* 2.8 32.4 + - - +
19D LEU* 4.0 2.0 - - - +
20D SER* 3.9 9.1 - - - +
27D GLU* 3.0 35.5 + - + +
28D LEU 3.6 2.9 - - - +
30D ALA* 1.3 75.6 - - + +
32D ILE* 1.3 61.6 + - - +
34D GLN* 3.3 8.9 + - - +
35D LYS* 2.9 35.1 + - + +
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Residues in contact with ILE 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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7D VAL* 4.0 24.0 - - + -
15D PHE* 4.4 3.4 - - + -
17D VAL* 4.5 5.4 - - + -
28D LEU* 3.0 36.8 + - + +
29D LYS 3.1 1.1 + - - +
31D GLN* 1.3 74.0 - - - +
33D THR* 1.3 61.5 + - - +
35D LYS* 4.3 5.4 - - - -
36D ILE* 3.0 52.1 + - + +
38D VAL* 4.2 2.4 + - + -
43D GLN* 3.4 33.0 - - + +
45D LEU* 3.9 18.8 - - + -
73D LEU* 4.0 8.5 - - + -
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Residues in contact with THR 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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29D LYS 2.9 13.7 + - - -
30D ALA* 3.6 11.9 - - - -
32D ILE* 1.3 78.3 - - - +
34D GLN* 1.3 60.9 + - + +
37D GLY* 2.8 31.5 + - - -
38D VAL 2.8 31.7 + - - +
39D HIS* 4.4 13.0 - - + +
40D ALA* 3.6 9.9 + - - +
43D GLN* 3.3 2.8 + - - -
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Residues in contact with GLN 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 ALA 3.2 17.1 + - - +
31D GLN* 3.3 10.3 + - - +
33D THR* 1.3 79.4 - - + +
35D LYS* 1.3 62.8 + - + +
37D GLY 4.8 0.2 + - - -
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Residues in contact with LYS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.1 14.9 - - + +
16D GLN* 3.2 26.2 + - - +
17D VAL* 4.4 13.5 - - + +
31D GLN* 2.9 21.9 + - + +
32D ILE 3.8 3.6 - - - +
33D THR 3.2 0.2 - - - -
34D GLN* 1.3 81.5 - - + +
36D ILE* 1.3 71.1 + - + +
37D GLY 3.7 0.2 - - - -
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Residues in contact with ILE 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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38A ARG* 2.7 40.3 + - - +
9D MET* 3.9 15.0 - - + -
15D PHE* 3.7 42.0 - - + -
32D ILE* 3.0 20.2 + - + +
35D LYS* 1.3 81.6 - - + +
37D GLY* 1.3 58.8 + - - +
38D VAL* 3.8 19.1 - - + -
73D LEU* 3.8 22.0 - - + -
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Residues in contact with GLY 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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38A ARG* 4.1 4.8 + - - -
32D ILE 3.6 0.4 + - - -
33D THR* 2.8 23.8 + - - -
34D GLN 4.8 0.2 + - - -
35D LYS 3.7 0.6 - - - -
36D ILE* 1.3 78.9 - - - +
38D VAL* 1.3 63.4 + - - +
39D HIS* 3.5 18.4 + - - -
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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
------------------------------------------------------------
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