Contacts of the helix formed by residues 14 - 34 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.8 14.1 - - + +
11A SER* 3.1 19.5 + - - +
12A GLU 3.3 0.2 - - - -
13A GLY* 1.3 77.4 - - - +
15A PRO* 1.4 59.7 - - + -
16A ASP* 3.1 53.4 + - + +
17A LYS* 2.9 8.7 + - + -
18A ILE* 2.8 32.5 + - - +
163A ASP* 3.5 6.1 - - - +
164A ALA 4.4 1.1 - - - +
165A LYS* 3.6 17.1 - - + +
238A ASP* 4.8 0.9 - - - -
245A LYS* 3.8 11.1 + - - +
384A ANP 2.9 60.3 + - - -
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Residues in contact with PRO 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 3.7 4.4 - - - +
14A HIS* 1.4 83.8 - - + +
16A ASP* 1.3 62.3 + - - +
18A ILE* 3.1 23.8 + - + +
19A ALA* 3.1 9.9 + - - +
45A VAL* 4.7 2.1 - - + +
163A ASP* 3.8 10.5 - - - +
234A GLY* 3.6 19.3 - - - +
235A PRO* 4.4 5.8 - - + -
238A ASP* 3.0 30.3 - - + +
239A CYS 3.9 2.5 - - - +
240A GLY* 3.3 21.8 - - - +
384A ANP 3.3 25.1 - - - +
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.1 15.4 + - + +
15A PRO* 1.3 77.4 - - - +
17A LYS* 1.3 64.8 + - - +
19A ALA* 3.2 6.9 - - - +
20A ASP* 3.1 21.6 + - - +
239A CYS 3.6 3.4 - - - +
240A GLY* 3.5 4.7 - - - -
241A LEU* 3.0 31.7 + - - +
244A ARG* 3.7 15.6 - - + +
245A LYS* 3.3 20.2 + - + +
384A ANP 3.1 13.9 + - - -
388A MG 2.2 30.6 - - - -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.9 16.2 - - + +
11A SER 3.7 22.0 - - - +
12A GLU 4.3 4.5 - - - +
14A HIS* 2.9 12.0 + - + +
16A ASP* 1.3 78.1 - - - +
18A ILE* 1.3 61.2 + - - +
20A ASP* 3.2 18.3 + - - +
21A GLN* 2.6 39.6 + - - +
245A LYS* 3.8 21.8 - - + -
248A VAL* 4.5 5.9 - - - +
249A ASP* 2.6 30.0 + - - -
355A ALA* 2.7 34.2 + - - +
356A ALA* 3.8 15.7 - - + +
357A TYR 4.3 4.3 - - - +
358A GLY 5.0 1.0 - - - +
359A HIS* 4.9 0.2 + - - -
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.9 13.2 + - - +
13A GLY 3.8 17.9 - - - +
14A HIS 2.8 16.5 + - - +
15A PRO* 3.1 19.7 + - + +
17A LYS* 1.3 71.8 - - - +
19A ALA* 1.3 65.4 + - - +
21A GLN* 3.2 7.9 + - - +
22A ILE* 2.9 35.8 + - + +
45A VAL* 4.4 15.3 - - + -
72A VAL* 4.0 26.7 - - + -
75A ILE* 4.2 12.8 - - + -
77A TYR* 3.9 22.2 - - + -
84A PHE* 6.1 1.6 - - + -
235A PRO* 4.1 15.5 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 3.1 7.7 + - - +
16A ASP 3.2 11.0 - - - +
18A ILE* 1.3 79.3 - - - +
20A ASP* 1.3 53.6 + - - +
22A ILE* 2.9 5.8 + - - +
23A SER* 2.7 34.8 + - - -
43A THR* 3.7 17.2 + - - +
45A VAL* 4.2 10.1 - - + +
241A LEU* 3.4 28.7 - - - +
242A THR* 3.5 12.6 - - - +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.1 9.4 + - - +
17A LYS* 3.3 26.9 + - - +
19A ALA* 1.3 78.1 - - - +
21A GLN* 1.3 54.8 + - - +
23A SER* 3.1 4.7 + - - -
24A ASP* 2.7 37.6 + - - +
242A THR* 3.4 7.4 + - - +
243A GLY* 3.1 29.3 + - - -
244A ARG 5.1 0.2 + - - -
245A LYS* 4.5 6.2 + - - +
249A ASP* 3.7 16.6 - - - +
263A SER* 3.4 23.7 + - - +
355A ALA* 3.9 13.2 - - + +
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.0 50.3 + - - +
17A LYS 2.6 32.7 + - - +
18A ILE* 3.4 6.3 - - - +
20A ASP* 1.3 72.0 - - - +
22A ILE* 1.3 52.1 + - - +
24A ASP* 3.3 1.4 + - - +
25A ALA* 2.7 38.6 + - - +
71A THR* 4.0 14.8 - - + +
75A ILE* 3.8 12.7 - - + +
352A LYS* 4.2 15.5 - - + +
355A ALA* 3.7 19.9 - - + +
356A ALA* 3.8 19.0 + - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 2.9 28.1 + - + +
19A ALA* 2.9 8.5 + - - +
21A GLN* 1.3 74.6 - - - +
23A SER* 1.3 65.3 + - - +
25A ALA* 2.9 19.3 + - + +
26A VAL* 2.9 16.0 + - + +
43A THR* 3.9 20.9 - - + +
45A VAL* 4.9 0.9 - - + -
50A VAL* 3.6 15.5 - - + -
52A VAL* 4.2 11.0 - - + -
67A ILE* 5.8 0.4 - - + -
68A THR* 3.5 43.3 - - + +
71A THR* 4.1 14.6 - - + -
72A VAL* 4.1 17.9 - - + -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.7 12.4 + - - -
20A ASP* 3.4 8.3 - - - -
22A ILE* 1.3 74.2 - - - +
24A ASP* 1.3 62.4 + - - +
26A VAL* 3.3 10.9 + - - +
27A LEU* 3.3 12.0 + - - +
41A CYS* 3.0 30.6 + - - +
43A THR* 2.7 23.3 + - - -
242A THR* 2.9 22.3 + - - -
263A SER 4.3 0.2 - - - -
264A GLY* 3.8 15.8 - - - -
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP 2.7 16.2 + - - +
21A GLN 3.6 1.1 - - - +
23A SER* 1.3 71.5 - - - +
25A ALA* 1.3 62.9 + - - +
26A VAL 3.3 0.2 - - - -
27A LEU* 3.8 8.6 - - - +
28A ASP* 3.2 28.8 + - - +
263A SER* 3.0 21.1 + - - -
264A GLY* 2.6 25.6 + - - -
272A ARG* 2.5 38.3 + - - -
351A TYR* 3.6 11.4 - - + +
352A LYS* 3.7 20.2 - - - +
354A THR* 3.8 1.9 - - - +
355A ALA* 4.1 3.5 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN 2.7 22.9 + - - +
22A ILE 2.9 6.9 + - - +
24A ASP* 1.3 71.7 - - - +
26A VAL* 1.3 65.6 + - - +
28A ASP* 3.9 3.3 - - - +
29A ALA* 3.3 22.3 + - - +
67A ILE* 3.8 13.0 - - + +
71A THR* 3.3 26.9 - - - +
352A LYS* 3.7 20.0 - - + +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.9 18.8 + - + +
23A SER 3.3 8.0 + - - +
25A ALA* 1.3 77.6 - - - +
27A LEU* 1.3 58.0 + - - +
29A ALA* 3.3 5.6 + - - +
30A ILE* 2.9 48.4 + - + +
39A VAL* 5.0 0.4 - - + -
41A CYS* 4.2 9.6 - - + -
52A VAL* 4.2 21.5 - - + -
56A ILE* 4.1 14.4 - - + -
62A VAL* 5.3 1.3 - - + -
64A ILE* 4.3 26.0 - - + -
67A ILE* 4.1 19.2 - - + +
68A THR* 5.1 0.2 - - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER 3.3 9.4 + - - +
24A ASP* 3.8 21.1 - - - +
25A ALA 3.3 0.2 - - - -
26A VAL* 1.3 80.6 - - - +
28A ASP* 1.3 52.3 + - - +
30A ILE* 3.0 5.5 + - - +
31A LEU* 2.6 53.6 + - + +
39A VAL* 3.4 43.7 - - + -
264A GLY 4.9 2.0 - - - -
265A LYS 3.7 16.4 - - - +
266A ASP* 3.7 21.3 - - + +
351A TYR* 3.5 35.0 - - + -
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP 3.2 14.8 + - - +
25A ALA* 3.9 5.4 - - - +
26A VAL 3.4 0.2 - - - -
27A LEU* 1.3 77.6 - - - +
29A ALA* 1.3 63.2 + - - +
31A LEU* 3.1 1.6 + - - -
32A GLU* 2.8 24.2 + - - +
349A PRO* 3.1 40.1 - - + +
350A ILE* 3.1 0.9 + - - -
351A TYR* 3.0 29.2 + - - +
352A LYS* 2.8 31.1 + - + +
353A GLU 4.6 0.3 + - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.3 9.6 + - - +
26A VAL 3.5 8.5 - - - +
28A ASP* 1.3 79.5 - - - +
30A ILE* 1.3 65.0 + - - +
32A GLU* 3.5 15.5 + - - +
33A GLN* 3.6 8.0 + - - +
62A VAL* 4.1 10.8 - - + +
67A ILE* 3.5 32.5 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 2.9 24.6 + - + +
27A LEU 3.3 7.0 - - - +
29A ALA* 1.3 75.8 - - - +
31A LEU* 1.3 54.9 + - - +
33A GLN* 2.8 28.1 + - - +
34A ASP 2.9 9.2 + - - -
37A ALA* 3.6 17.0 - - + -
39A VAL* 3.9 12.6 - - + -
56A ILE* 3.6 42.4 - - + -
58A THR* 3.6 30.7 - - + +
60A ALA* 3.8 3.1 - - + +
62A VAL* 3.9 29.4 - - + -
64A ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 2.6 48.4 + - + +
28A ASP 3.6 3.6 - - - +
30A ILE* 1.3 73.6 - - + +
32A GLU* 1.3 65.4 + - - +
34A ASP 2.9 27.8 + - - +
35A PRO* 3.1 41.5 - - + +
37A ALA* 4.4 13.9 - - + +
266A ASP* 5.2 2.7 - - + -
267A PRO* 4.7 8.3 - - + -
346A LEU 4.7 0.4 - - - +
348A HIS* 3.7 26.9 - - - +
349A PRO* 4.3 13.4 - - + +
351A TYR* 4.0 13.2 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP 2.8 20.5 + - - +
29A ALA* 3.5 9.8 - - - +
31A LEU* 1.3 74.5 - - - +
33A GLN* 1.3 60.7 + - - +
35A PRO* 5.2 2.1 - - - +
349A PRO* 3.9 24.2 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 4.1 5.4 - - - +
30A ILE 2.8 10.2 + - - +
31A LEU 3.6 0.2 - - - -
32A GLU* 1.3 85.1 - - - +
34A ASP* 1.3 59.0 + - - +
35A PRO* 4.3 2.9 - - - +
59A SER* 4.5 3.0 + - - -
60A ALA* 3.2 14.0 - - + +
61A TRP* 2.5 55.5 + - - +
62A VAL* 4.3 5.2 - - - +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE 2.9 5.9 + - - +
31A LEU* 2.9 20.3 + - - +
33A GLN* 1.3 81.3 - - - +
35A PRO* 1.3 66.3 - - - +
36A LYS* 2.9 20.3 + - - +
37A ALA* 3.0 22.0 + - - +
58A THR* 2.8 28.9 + - - +
59A SER* 3.6 23.3 + - - +
60A ALA* 4.3 2.9 - - + -
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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
------------------------------------------------------------
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