Contacts of the helix formed by residues 22 - 36 (chain D) in PDB entry 3L73
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 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D SER* 3.5 25.3 + - - +
14D HIS* 5.3 0.2 + - - -
21D LEU* 1.3 69.7 - - - +
23D HIS* 1.3 58.7 + - - +
24D SER* 3.4 17.5 + - - -
25D SER* 3.0 44.4 + - - -
26D VAL* 3.1 13.2 + - - +
28D ARG* 4.5 1.9 + - - -
184D LYS* 4.3 2.5 + - - +
188D THR* 4.2 3.2 - - + +
78H LYS 4.2 12.5 - - - +
49J GLY 4.1 12.5 - - - +
50J LYS* 4.0 16.3 - - + +
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Residues in contact with HIS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 3.2 29.1 - - + +
22D ASP* 1.3 70.8 - - - +
24D SER* 1.3 60.0 + - - +
26D VAL* 3.7 10.3 - - + +
27D ARG* 3.1 21.7 + - - +
53D GLY 5.3 0.4 - - - -
54D VAL* 3.0 45.3 + - + +
55D THR* 3.8 5.1 - - + +
192D TRP* 5.7 1.0 - + - -
199D ASP* 3.1 27.0 + - + -
50J LYS 2.8 22.6 + - - +
51J LEU* 4.6 3.3 - - + +
52J TRP* 3.5 20.6 + - + +
55J ILE* 4.1 15.6 - - + +
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.1 13.9 + - - -
23D HIS* 1.3 74.8 - - - +
25D SER* 1.3 65.7 + - - +
27D ARG* 3.2 9.1 + - - +
28D ARG* 3.2 38.3 + - - +
173D ASP* 5.7 0.9 - - - -
49J GLY 4.6 1.2 + - - -
50J LYS 4.5 0.4 + - - -
55J ILE* 3.3 35.7 - - - +
58J LYS* 4.1 11.5 + - - -
59J TYR* 5.1 1.3 + - - -
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.0 29.8 + - - -
24D SER* 1.3 79.1 - - - +
26D VAL* 1.3 58.2 + - - +
28D ARG* 3.6 14.5 + - - +
29D GLY 3.1 19.6 + - - -
184D LYS* 3.5 12.0 + - - -
185D ASP* 2.8 30.1 + - - +
188D THR* 3.4 22.1 + - - -
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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
----------------------------------------------------------
21D LEU* 4.2 19.7 - - + -
22D ASP 3.1 16.4 + - - +
23D HIS* 3.7 12.3 - - + +
24D SER 3.1 0.4 - - - -
25D SER* 1.3 76.9 - - - +
27D ARG* 1.3 65.4 + - - +
29D GLY* 3.1 2.3 + - - -
30D PHE* 2.9 19.1 + - - +
54D VAL* 5.7 0.2 - - + -
55D THR* 3.3 21.1 - - + -
188D THR* 3.2 31.6 - - + +
189D PHE* 3.7 27.6 - - + +
192D TRP* 4.3 16.2 - - + -
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D HIS 3.1 13.7 + - - +
24D SER* 3.2 11.9 + - - +
26D VAL* 1.3 77.9 - - - +
28D ARG* 1.3 65.6 + - - +
30D PHE* 3.1 19.4 + - - +
31D GLN* 3.3 23.0 + - - +
55D THR* 2.5 48.2 + - - +
56D HIS* 3.4 23.3 - - + -
60D GLU* 3.0 38.8 + - - -
172D ASP* 5.2 6.1 + - - -
173D ASP* 6.0 4.8 - - - +
55J ILE* 5.4 2.0 - - - -
59J TYR* 3.0 44.0 - - - -
63J GLU* 4.8 3.0 + - - -
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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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22D ASP* 4.5 1.6 + - - -
24D SER* 3.2 21.4 + - - +
25D SER* 3.6 18.5 - - - +
26D VAL 3.2 0.2 - - - -
27D ARG* 1.3 78.7 - - + +
29D GLY* 1.3 56.5 + - - +
31D GLN* 2.7 36.7 + - - +
32D VAL* 3.0 12.5 + - - +
171D TYR* 3.5 38.5 - - + -
173D ASP* 3.2 27.8 + - - +
175D THR* 3.6 15.3 + - - -
181D GLN* 3.7 4.3 - - - +
185D ASP* 2.7 39.2 + - - +
78H LYS* 2.7 39.2 + - - +
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Residues in contact with GLY 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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25D SER 3.1 8.1 + - - -
26D VAL 3.1 4.7 + - - -
28D ARG* 1.3 79.5 - - - +
30D PHE* 1.3 60.2 + - - +
32D VAL* 3.3 5.9 + - - +
33D TYR* 2.9 23.0 + - - +
185D ASP* 3.4 31.2 - - - +
186D VAL* 3.7 5.8 - - - +
189D PHE* 3.6 12.9 - - - -
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Residues in contact with PHE 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 VAL* 2.9 11.8 + - + +
27D ARG* 3.2 13.7 - - - +
28D ARG 3.0 0.2 - - - -
29D GLY* 1.3 76.0 - - - +
31D GLN* 1.3 60.8 + - + +
33D TYR* 3.2 6.3 + + - +
34D LYS* 2.7 59.3 + - + +
48D PHE* 5.1 4.7 - + - -
51D LEU* 3.7 28.5 - - + -
55D THR* 5.2 0.7 - - - +
56D HIS* 3.4 22.7 - + + -
64D LEU* 3.7 37.0 - - + -
91D PHE* 3.9 18.8 - + - -
189D PHE* 3.8 32.3 - + + -
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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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27D ARG* 3.7 33.4 + - - +
28D ARG* 2.7 22.9 + - - +
30D PHE* 1.3 79.4 - - + +
32D VAL* 1.3 59.4 + - - +
34D LYS* 3.1 6.8 + - + -
35D GLN* 2.6 56.9 + - - +
56D HIS* 5.5 2.5 + - - +
169D LEU* 5.1 0.4 - - + -
170D GLU 4.4 3.5 - - - +
171D TYR* 4.3 13.8 - - + +
172D ASP* 3.4 44.7 + - - +
173D ASP* 6.0 2.0 - - - +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG 3.0 10.4 + - - +
29D GLY* 3.4 11.4 - - - +
31D GLN* 1.3 75.9 - - - +
33D TYR* 1.3 56.0 + - - +
36D VAL* 2.7 45.4 + - + +
164D ILE* 4.8 0.2 - - + -
169D LEU* 3.9 13.6 - - + +
171D TYR* 3.6 30.3 - - + +
182D ILE* 3.8 28.0 - - + +
186D VAL* 3.8 21.1 - - + -
501D HEC 4.1 16.4 - - + -
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Residues in contact with TYR 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 GLY 2.9 8.9 + - - +
30D PHE* 3.4 10.1 - + - +
32D VAL* 1.3 78.7 - - - +
34D LYS* 1.3 65.1 + - + +
37D CYS* 3.1 27.4 + - + -
38D SER* 2.6 52.1 + - - -
41D HIS* 2.7 34.1 + - + -
42D SER* 3.8 0.9 - - - -
43D MET* 3.4 29.5 + - + +
91D PHE* 3.9 30.1 - + + +
92D PRO 4.8 3.6 + - - -
113D LEU* 4.5 10.8 - - + -
186D VAL* 4.3 2.9 - - + +
189D PHE* 3.6 34.3 - + + -
190D LEU* 5.7 2.0 - - + -
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Residues in contact with LYS 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 PHE* 2.7 48.6 + - + +
31D GLN* 3.6 6.3 - - + +
33D TYR* 1.3 77.4 - - + +
35D GLN* 1.3 74.1 + - + +
38D SER* 2.4 23.9 + - - +
48D PHE* 5.6 4.0 - - - -
64D LEU* 3.8 23.6 + - + +
67D GLU* 3.4 28.5 + - - +
68D VAL* 5.6 4.2 - - - +
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Residues in contact with GLN 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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31D GLN* 2.6 35.7 + - - +
32D VAL 4.2 0.7 - - - +
34D LYS* 1.3 89.3 - - + +
36D VAL* 1.3 65.3 + - + +
39D ALA* 5.7 2.1 - - - +
169D LEU* 3.5 32.6 - - + +
170D GLU 4.9 6.4 + - - +
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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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32D VAL* 2.7 26.3 + - + +
33D TYR 3.4 1.2 + - - -
35D GLN* 1.3 80.9 - - + +
37D CYS* 1.3 67.9 + - - +
38D SER 3.4 0.9 - - - -
39D ALA* 3.5 13.1 - - - +
163D PRO* 3.7 24.0 - - + +
164D ILE* 4.3 8.1 - - + -
168D ILE* 4.1 21.5 - - + +
169D LEU* 4.2 22.7 - - + -
501D HEC 3.3 29.9 - - + +
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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