Contacts of the helix formed by residues 14 - 34 (chain D) in PDB entry 1P7L
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 HIS 14 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885C SAM 3.2 31.1 + - - -
10D VAL* 3.7 20.0 - - + +
11D SER* 3.1 18.9 + - - +
12D GLU 3.3 0.4 - - - -
13D GLY* 1.3 77.7 - - - +
15D PRO* 1.3 73.1 - - + -
16D ASP* 3.0 43.3 + - + +
17D LYS* 2.7 16.8 + - + -
18D ILE* 2.8 12.5 + - - +
163D ASP* 3.5 6.1 - - - +
164D ALA 4.5 0.9 - - - +
165D LYS* 3.7 14.8 - - + +
238D ASP* 4.6 1.6 - - - -
245D LYS* 3.9 7.2 - - - +
884D PPK 2.8 39.5 + - - -
888D MG 4.6 0.2 - - - -
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Residues in contact with PRO 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C SAM 3.7 17.9 - - - +
13D GLY 3.6 4.4 - - - +
14D HIS* 1.3 92.5 - - + +
16D ASP* 1.3 63.6 + - - +
18D ILE* 3.1 24.6 + - + +
19D ALA* 3.1 9.9 + - - +
45D VAL* 4.6 2.0 - - + +
163D ASP* 3.8 10.5 - - - +
234D GLY* 3.8 18.6 - - - +
235D PRO* 4.6 4.9 - - + -
238D ASP* 3.1 29.6 - - + +
239D CYS 3.9 2.2 - - - +
240D GLY* 3.4 23.0 - - - +
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Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D HIS* 3.0 14.7 + - + +
15D PRO* 1.3 76.5 - - - +
17D LYS* 1.3 64.9 + - - +
19D ALA* 3.0 20.1 + - - +
20D ASP* 3.1 8.7 + - - +
239D CYS 3.7 1.5 - - - +
240D GLY* 3.5 4.2 - - - -
241D LEU* 2.9 35.5 + - - +
244D ARG* 3.8 12.4 - - + +
245D LYS* 3.4 21.9 + - + +
884D PPK 2.7 14.7 + - - -
888D MG 2.1 32.0 - - - -
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Residues in contact with LYS 17 (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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10D VAL* 3.7 24.9 - - + +
11D SER 3.7 17.0 - - - +
12D GLU 4.3 6.1 - - - +
14D HIS* 2.7 16.2 + - + +
16D ASP* 1.3 73.5 - - - +
18D ILE* 1.3 57.6 + - - +
20D ASP* 3.2 14.0 + - - +
21D GLN* 2.7 39.1 + - - +
245D LYS* 3.9 22.9 - - + -
248D VAL* 4.4 6.4 - - - +
249D ASP* 2.5 30.4 + - - -
354D THR 4.9 0.2 + - - -
355D ALA* 2.6 34.7 + - - +
356D ALA* 3.7 12.4 - - + +
357D TYR 4.2 5.5 - - - +
358D GLY 4.9 1.4 - - - +
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU 4.0 12.8 - - - +
13D GLY 3.9 16.6 - - - +
14D HIS 2.8 12.6 + - - +
15D PRO* 3.2 18.6 - - + +
17D LYS* 1.3 75.4 - - - +
19D ALA* 1.3 64.6 + - - +
21D GLN* 3.4 2.3 + - - +
22D ILE* 2.9 36.9 + - + +
45D VAL* 4.3 13.7 - - + -
72D VAL* 4.0 26.7 - - + -
75D ILE* 4.0 18.6 - - + -
77D TYR* 4.0 21.1 - - + -
84D PHE* 6.0 1.3 - - + -
235D PRO* 4.1 17.7 - - + -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PRO 3.1 5.8 + - - +
16D ASP 3.0 12.0 + - - +
18D ILE* 1.3 79.1 - - - +
20D ASP* 1.3 53.7 + - - +
22D ILE* 2.8 7.0 + - - +
23D SER* 2.7 34.1 + - - -
43D THR* 3.7 13.4 + - - +
45D VAL* 4.1 14.3 - - + +
241D LEU* 3.4 28.9 - - - +
242D THR* 3.5 12.8 - - - +
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP 3.1 10.4 + - - +
17D LYS* 3.2 22.7 + - + +
19D ALA* 1.3 77.8 - - - +
21D GLN* 1.3 54.2 + - - +
23D SER* 3.2 3.5 + - - -
24D ASP* 2.8 37.6 + - - +
241D LEU 5.2 0.2 - - - -
242D THR* 3.3 8.7 - - - +
243D GLY* 3.0 31.2 + - - -
244D ARG 5.1 0.4 + - - -
245D LYS* 4.5 5.9 + - - +
249D ASP* 3.7 19.3 - - - +
263D SER* 3.3 23.5 + - - +
355D ALA* 3.9 13.0 - - - +
359D HIS* 5.7 0.2 + - - -
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU* 2.9 51.9 + - - +
17D LYS* 2.7 26.6 + - - +
18D ILE* 3.6 6.1 - - - +
20D ASP* 1.3 71.8 - - - +
22D ILE* 1.3 53.4 - - - +
24D ASP* 3.5 1.0 - - - +
25D ALA* 2.6 38.5 + - - +
71D THR* 4.0 15.2 - - + +
75D ILE* 3.8 12.5 - - + +
352D LYS* 4.2 15.8 - - + +
355D ALA* 3.7 19.3 - - + +
356D ALA* 3.8 16.6 + - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 2.9 28.6 + - + +
19D ALA* 2.8 7.9 + - - +
21D GLN* 1.3 74.8 - - - +
23D SER* 1.3 65.3 + - - +
25D ALA* 2.8 18.1 + - + +
26D VAL* 2.9 17.0 + - + +
43D THR* 3.9 19.1 - - + +
45D VAL* 5.0 0.4 - - + -
50D VAL* 3.6 14.6 - - + -
52D VAL* 4.2 11.2 - - + -
67D ILE* 5.8 0.4 - - + -
68D THR* 3.5 43.3 - - + +
71D THR* 4.1 13.9 - - + -
72D VAL* 4.1 18.4 - - + -
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA 2.7 12.3 + - - -
20D ASP* 3.4 10.8 - - - -
22D ILE* 1.3 76.9 - - - +
24D ASP* 1.3 62.0 + - - +
26D VAL* 3.2 11.4 + - - +
27D LEU* 3.3 12.3 + - - +
41D CYS* 3.0 31.4 + - - +
43D THR* 2.8 21.4 + - - -
242D THR* 2.9 21.9 + - - -
264D GLY* 3.9 15.7 - - - -
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASP 2.8 15.7 + - - +
21D GLN 4.1 0.9 - - - +
23D SER* 1.3 70.4 - - - +
25D ALA* 1.3 62.9 + - - +
26D VAL 3.3 0.2 - - - -
27D LEU* 3.9 9.2 - - - +
28D ASP* 3.2 29.1 + - - +
263D SER* 3.0 21.7 + - - -
264D GLY* 2.6 25.3 + - - -
272D ARG* 2.6 38.1 + - - -
351D TYR* 3.7 10.6 - - + +
352D LYS* 3.7 20.6 - - - +
354D THR* 3.8 1.9 - - - +
355D ALA* 4.1 3.4 - - + +
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Residues in contact with ALA 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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21D GLN 2.6 22.0 + - - +
22D ILE* 2.8 9.4 + - - +
24D ASP* 1.3 75.2 - - - +
26D VAL* 1.3 60.7 + - - +
28D ASP* 3.8 2.9 - - - +
29D ALA* 3.3 21.3 + - - +
67D ILE* 3.7 12.5 - - + +
71D THR* 3.3 26.7 - - - +
352D LYS* 3.7 21.1 - - + +
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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
----------------------------------------------------------
22D ILE* 2.9 17.4 + - + +
23D SER 3.6 8.1 - - - +
25D ALA* 1.3 75.0 - - - +
27D LEU* 1.3 67.9 + - - +
29D ALA* 3.3 6.1 + - - +
30D ILE* 2.9 42.9 + - + +
41D CYS* 4.5 8.7 - - + -
52D VAL* 4.3 16.8 - - + -
56D ILE* 4.1 14.4 - - + -
62D VAL* 5.2 1.6 - - + -
64D ILE* 4.2 30.3 - - + -
67D ILE* 4.0 19.2 - - + +
68D THR* 5.2 0.2 - - - +
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Residues in contact with LEU 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 SER 3.3 9.8 + - - +
24D ASP* 4.0 17.5 - - - +
25D ALA 3.4 0.2 - - - -
26D VAL* 1.3 79.8 - - - +
28D ASP* 1.3 52.5 + - - +
30D ILE* 3.0 5.9 + - - +
31D LEU* 2.6 55.6 + - + +
39D VAL* 3.5 43.5 - - + -
264D GLY 4.9 2.2 - - - -
265D LYS 3.9 15.3 - - - +
266D ASP* 3.8 17.7 - - + +
351D TYR* 3.4 39.5 - - + -
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP 3.2 15.3 + - - +
25D ALA* 3.8 5.4 - - - +
27D LEU* 1.3 76.7 - - - +
29D ALA* 1.3 66.2 + - - +
31D LEU* 3.0 2.6 + - - -
32D GLU* 2.8 23.6 + - - +
349D PRO* 3.0 47.2 - - + +
350D ILE 3.1 0.9 + - - -
351D TYR* 3.1 18.5 + - - +
352D LYS* 2.9 33.8 + - + +
353D GLU 4.6 0.3 + - - -
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Residues in contact with ALA 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 ALA 3.3 9.0 + - - +
26D VAL 3.4 7.6 - - - +
28D ASP* 1.3 79.6 - - - +
30D ILE* 1.3 65.7 + - - +
32D GLU* 3.3 16.8 + - - +
33D GLN* 3.6 7.4 + - - +
62D VAL* 4.1 11.0 - - + +
67D ILE* 3.4 33.4 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D VAL* 2.9 25.0 + - + +
27D LEU 3.3 7.0 - - - +
29D ALA* 1.3 77.4 - - - +
31D LEU* 1.3 56.8 + - - +
33D GLN* 2.8 23.4 + - - +
34D ASP 2.8 10.6 + - - -
37D ALA* 3.6 17.5 - - + -
39D VAL* 3.8 12.6 - - + -
56D ILE* 3.6 42.0 - - + -
58D THR* 3.6 28.9 - - + +
60D ALA* 3.7 2.6 - - + +
62D VAL* 3.9 29.8 - - + -
64D ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 2.6 48.4 + - + +
28D ASP* 3.6 4.3 - - - +
30D ILE* 1.3 69.9 - - + +
32D GLU* 1.3 67.7 + - - +
34D ASP 2.9 34.3 + - - +
35D PRO* 3.1 34.5 - - + +
37D ALA* 4.4 12.1 - - + +
266D ASP* 5.2 2.5 - - + -
267D PRO* 4.7 9.2 - - + -
346D LEU 4.7 0.2 - - - +
347D LEU 5.4 0.8 - - - +
348D HIS 3.8 24.7 - - - +
349D PRO* 4.3 13.7 - - + +
351D TYR* 4.1 12.3 - - + -
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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
----------------------------------------------------------
28D ASP 2.8 15.4 + - - +
29D ALA* 3.4 14.5 - - - +
31D LEU* 1.3 73.6 - - - +
33D GLN* 1.3 60.0 + - - +
35D PRO* 5.3 1.6 - - - +
349D PRO* 3.9 24.6 - - + +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ALA 3.6 4.9 + - - +
30D ILE 2.8 8.8 + - - +
31D LEU 3.7 0.2 - - - -
32D GLU* 1.3 83.8 - - + +
34D ASP* 1.3 60.3 + - - +
35D PRO* 4.3 3.3 - - - +
59D SER* 4.5 2.7 + - - -
60D ALA* 3.2 14.8 - - + +
61D TRP* 2.6 53.7 + - - +
62D VAL* 4.4 4.9 - - - +
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ILE 2.8 6.2 + - - +
31D LEU* 2.9 24.8 + - - +
33D GLN* 1.3 81.7 - - - +
35D PRO* 1.3 64.8 - - - +
36D LYS* 2.9 20.4 + - - +
37D ALA* 3.1 22.0 + - - +
58D THR* 2.9 27.6 + - - +
59D SER* 3.6 23.7 + - - +
60D ALA* 4.3 2.5 - - + -
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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) + - + + + + + -
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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