Contacts of the helix formed by residues 12 - 34 (chain D) in PDB entry 5DIR
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 TRP 12 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 1.3 92.5 - - + +
13D LEU* 1.3 59.0 + - - +
14D TRP* 3.0 10.8 + - - -
15D ILE* 3.2 42.6 + - + +
88D LEU* 4.8 18.1 - - + +
93D LYS* 6.3 1.6 - - - +
96D THR* 3.5 37.2 - - + +
99D ALA* 3.9 29.1 - - + +
100D ILE* 4.3 20.2 - - + -
103D ALA* 3.8 8.7 - - + +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PRO* 3.4 12.4 - - + -
12D TRP* 1.3 77.1 - - - +
14D TRP* 1.3 60.6 + - - +
15D ILE 3.1 0.4 - - - -
16D THR* 3.1 12.5 + - + +
17D VAL* 2.8 35.4 + - + +
85D VAL* 5.5 10.8 - - + -
88D LEU* 3.5 28.7 - - + -
89D LYS* 6.3 2.9 - - - -
106D LEU* 4.0 21.8 - - + -
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Residues in contact with TRP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PRO* 4.0 23.3 - - + +
12D TRP* 3.0 1.8 - - - +
13D LEU* 1.3 79.5 - - - +
15D ILE* 1.3 58.1 + - + +
17D VAL* 3.9 27.4 - - + +
18D LEU* 3.0 45.3 + - + +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TRP* 3.2 28.9 + - + +
13D LEU 3.1 0.2 - - - -
14D TRP* 1.3 79.9 - - + +
16D THR* 1.3 57.3 + - - +
18D LEU* 3.4 6.5 + - + +
19D VAL* 2.9 39.3 + - + +
100D ILE* 3.9 36.8 - - + -
103D ALA* 3.8 14.1 - - + -
104D LEU* 3.8 28.7 - - + +
201D OLC 4.3 13.9 - - + -
202D OLC 4.7 7.2 - - + -
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 3.1 20.9 + - + +
15D ILE* 1.3 80.0 - - - +
17D VAL* 1.3 58.9 + - + +
19D VAL 3.6 0.2 + - - -
20D PHE* 3.0 29.8 + - + +
103D ALA* 3.0 34.3 + - - +
106D LEU* 3.7 26.4 - - + +
107D GLY* 3.6 21.5 - - - +
110D LEU* 4.4 11.9 - - + -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 2.8 29.1 + - + +
14D TRP* 3.9 30.7 - - + +
16D THR* 1.3 75.4 - - + +
18D LEU* 1.3 67.7 + - + +
20D PHE* 3.4 5.8 + - + +
21D VAL* 3.0 35.6 + - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TRP* 3.0 33.6 + - + +
15D ILE* 3.9 6.5 - - + +
17D VAL* 1.3 77.5 - - + +
19D VAL* 1.3 66.0 + - - +
21D VAL* 4.0 5.3 - - + +
22D LEU* 3.0 44.2 + - + +
202D OLC 4.4 16.2 - - + -
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 2.9 23.0 + - + +
16D THR 3.9 3.4 - - - +
18D LEU* 1.3 74.8 - - - +
20D PHE* 1.3 64.1 + - - +
22D LEU* 4.0 2.3 - - - +
23D ASP* 2.9 27.6 + - + +
104D LEU* 3.9 25.8 - - + +
107D GLY* 3.7 4.3 - - - -
108D GLY* 3.7 20.0 - - - +
141D LEU* 4.9 6.4 - - + +
142D ALA* 5.1 2.7 - - - -
145D ALA* 3.6 26.0 - - + -
202D OLC 3.9 27.4 - - + -
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 3.0 20.7 + - + +
17D VAL* 3.7 5.6 - - - +
19D VAL* 1.3 78.8 - - - +
21D VAL* 1.3 71.8 + - + +
23D ASP* 3.4 4.0 - - - +
24D GLN* 3.0 47.4 + - + +
107D GLY* 3.8 12.3 + - - +
110D LEU* 3.3 33.2 - - + -
111D GLY* 3.5 22.0 - - - -
114D TYR* 3.8 29.6 - + + -
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL* 3.0 29.3 + - + +
18D LEU* 4.0 5.6 - - + +
20D PHE* 1.3 86.1 - - + +
22D LEU* 1.3 60.8 + - + +
24D GLN* 2.9 6.4 + - - +
25D VAL* 2.7 54.3 + - + +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 3.0 34.9 + - + +
19D VAL* 4.2 2.5 - - - +
21D VAL* 1.3 81.8 - - + +
23D ASP* 1.3 56.9 + - - +
25D VAL* 4.0 11.2 - - + +
26D SER* 2.7 35.0 + - - -
141D LEU* 3.8 14.1 - - + -
202D OLC 3.6 38.8 - - + -
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Residues in contact with ASP 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 2.9 21.3 + - + +
20D PHE* 3.4 5.6 - - - +
22D LEU* 1.3 78.9 - - - +
24D GLN* 1.3 60.3 + - - +
26D SER* 3.5 2.8 - - - -
27D LYS* 2.7 68.8 + - - +
107D GLY 5.5 0.2 - - - +
111D GLY* 3.4 18.2 - - - -
125D PHE* 5.3 0.2 - - - -
140D ASN* 4.0 0.2 - - - +
141D LEU* 3.5 20.9 + - + +
142D ALA* 2.7 33.6 + - + +
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.0 33.6 + - + +
21D VAL* 2.9 7.4 + - - +
23D ASP* 1.3 80.1 + - - +
25D VAL* 1.3 61.9 + - + +
27D LYS* 3.8 10.0 - - - +
28D ALA* 3.0 28.6 + - - +
111D GLY* 2.5 38.4 + - - -
114D TYR* 3.5 26.3 - - + +
115D ASP* 3.4 18.4 + - - +
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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
----------------------------------------------------------
21D VAL* 2.7 40.0 + - + +
22D LEU* 4.0 12.6 - - + +
24D GLN* 1.3 70.2 - - + +
26D SER* 1.3 66.4 + - - +
28D ALA* 3.4 6.5 + - + +
29D PHE* 3.0 23.8 + - + +
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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
----------------------------------------------------------
22D LEU 2.7 23.5 + - - -
23D ASP 3.5 4.9 - - - -
24D GLN 3.3 0.2 - - - -
25D VAL* 1.3 76.9 - - - +
27D LYS* 1.3 61.6 + - - -
29D PHE* 3.0 17.7 + - - +
30D PHE* 3.0 23.8 + - - -
125D PHE* 3.4 26.5 - - - -
141D LEU* 3.5 17.1 - - - +
202D OLC 4.6 9.6 - - - +
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Residues in contact with LYS 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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23D ASP* 2.7 47.4 + - - +
24D GLN* 3.8 19.1 - - - +
25D VAL 3.4 0.2 - - - -
26D SER* 1.3 78.9 - - - +
28D ALA* 1.3 62.8 + - - +
30D PHE* 3.5 1.3 + - - +
31D GLN* 3.0 33.1 + - - +
111D GLY 3.4 5.9 + - - -
112D ASN* 3.0 22.4 + - - -
115D ASP* 2.6 31.3 + - - +
123D VAL* 3.8 27.2 - - + +
125D PHE* 4.1 15.0 - - + -
140D ASN* 3.3 18.4 - - - +
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Residues in contact with ALA 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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24D GLN 3.0 17.9 + - - +
25D VAL* 3.6 8.3 - - + +
26D SER 3.2 0.2 - - - -
27D LYS* 1.3 77.1 - - - +
29D PHE* 1.3 62.7 + - - +
31D GLN* 3.5 10.5 + - - +
32D ALA* 3.2 23.0 + - - +
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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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25D VAL* 3.0 15.9 + - + +
26D SER* 3.0 11.9 + - - +
28D ALA* 1.3 76.8 - - - +
30D PHE* 1.3 83.4 + + - +
32D ALA* 3.2 6.9 + - - +
33D GLU* 3.0 45.2 + - + +
202D OLC 3.8 57.4 - - + -
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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
----------------------------------------------------------
26D SER* 3.0 28.8 + - - +
27D LYS* 4.4 1.8 - - - +
29D PHE* 1.3 93.7 - + - +
31D GLN* 1.3 63.9 + - - +
32D ALA 3.2 0.7 - - - -
33D GLU* 3.9 2.9 - - - +
34D LEU* 3.1 52.2 + - + +
49D TRP* 3.4 52.0 - + + -
50D THR 4.4 4.0 - - - +
51D LEU* 4.0 9.3 - - + +
123D VAL* 5.8 0.2 - - + -
125D PHE* 3.5 46.9 - + + -
202D OLC 3.7 26.7 - - + -
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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 LYS* 3.0 26.8 + - - +
28D ALA* 3.8 9.0 + - - +
30D PHE* 1.3 78.0 - - - +
32D ALA* 1.3 59.2 + - - +
34D LEU 3.4 11.6 - - - +
51D LEU* 4.0 19.9 - - + +
53D TYR* 3.3 29.2 + - - +
119D LEU* 4.0 17.9 - - - +
121D HIS* 4.7 1.4 + - - -
123D VAL* 3.5 27.9 - - + +
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA 3.2 15.0 + - - +
29D PHE* 3.2 7.0 + - - +
30D PHE 3.2 0.6 - - - -
31D GLN* 1.3 79.1 - - - +
33D GLU* 1.3 66.4 + - - +
34D LEU 3.5 0.6 - - - +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.0 35.6 + - + +
32D ALA* 1.3 83.4 - - - +
34D LEU* 1.3 73.4 + - + +
38D GLN* 4.5 6.2 + - - +
40D ILE* 5.4 1.7 - - + +
202D OLC 3.2 29.6 + - - +
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.1 31.9 + - + +
31D GLN 3.4 11.8 - - - +
32D ALA 3.5 0.8 - - - -
33D GLU* 1.3 99.6 - - + +
35D SER* 1.3 65.7 + - - +
38D GLN* 3.7 18.8 - - - +
40D ILE* 3.7 29.8 - - + -
49D TRP* 4.2 5.8 - - + +
50D THR* 3.5 43.5 - - - +
51D LEU* 3.3 17.6 - - + +
202D OLC 4.6 1.1 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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