Contacts of the helix formed by residues 16 - 31 (chain D) in PDB entry 3P05
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 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D PRO* 5.2 1.2 - - - +
14D ALA 3.1 6.5 + - - -
15D ILE* 1.3 78.6 - - - +
17D PRO* 1.3 72.7 - - - +
18D ARG* 3.2 15.9 + - - +
19D THR* 3.3 20.4 + - - -
20D LEU* 3.1 21.3 + - - +
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Residues in contact with PRO 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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16C SER* 5.1 1.6 - - - +
18C ARG* 4.4 7.9 - - + +
19C THR* 3.2 45.1 - - + +
43C LEU* 4.2 24.0 - - + -
15D ILE 4.0 4.5 - - - +
16D SER* 1.3 85.2 - - - +
18D ARG* 1.3 58.3 + - - +
20D LEU* 4.4 2.7 - - + +
21D CYS* 2.7 42.9 + - - -
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Residues in contact with ARG 18 (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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18C ARG* 5.3 10.4 - - + +
16D SER* 3.2 8.1 + - - +
17D PRO* 1.3 76.3 - - - +
19D THR* 1.3 67.6 + - - +
21D CYS* 3.9 3.8 - - - +
22D CYS* 2.9 26.7 + - - +
17E PRO* 5.1 5.6 - - + -
18E ARG* 5.3 14.6 - - + -
21E CYS* 5.8 0.4 - - - -
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Residues in contact with THR 19 (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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15D ILE* 4.3 18.4 - - + -
16D SER* 3.3 24.3 + - - -
18D ARG* 1.3 78.6 - - - +
20D LEU* 1.3 57.9 - - - +
22D CYS* 3.4 3.2 + - - +
23D TRP* 2.9 30.8 + - + +
43D LEU* 3.7 35.5 - - + +
55D MET* 5.4 3.4 - - + -
17E PRO* 3.4 29.0 - - + +
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Residues in contact with LEU 20 (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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22C CYS* 5.2 0.4 - - - -
39C MET* 4.0 20.4 - - - -
42C ALA* 3.5 32.3 - - + -
43C LEU* 4.7 9.0 - - + -
15D ILE* 4.1 22.7 - - + +
16D SER 3.1 12.1 + - - +
17D PRO* 3.8 6.5 - - + +
18D ARG 3.3 0.2 - - - -
19D THR* 1.3 78.3 - - - +
21D CYS* 1.3 60.6 + - - +
23D TRP* 3.3 13.1 + - + +
24D VAL* 2.9 36.4 + - + +
54D THR* 3.8 15.5 - - + +
55D MET* 4.6 2.9 - - + -
58D THR* 3.6 24.2 - - + +
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Residues in contact with CYS 21 (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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18C ARG 5.1 0.4 - - - -
22C CYS* 2.0 59.7 - - + -
26C VAL* 6.2 0.4 - - - -
39C MET* 6.1 0.4 - - - -
17D PRO 2.7 34.7 + - - +
18D ARG* 4.1 3.4 - - - +
20D LEU* 1.3 72.5 - - - +
22D CYS* 1.3 67.6 + - - +
24D VAL* 3.8 5.5 - - - +
25D LYS* 2.9 26.5 + - - +
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Residues in contact with CYS 22 (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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18D ARG 2.9 17.9 + - - +
19D THR* 3.7 4.3 - - - +
21D CYS* 1.3 76.6 - - - +
23D TRP* 1.3 54.0 + - - +
25D LYS* 3.2 6.3 + - - +
26D VAL* 2.8 51.0 + - - +
39D MET* 5.0 2.5 - - - -
43D LEU* 4.3 9.2 - - + -
21E CYS* 2.0 56.1 - - + -
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Residues in contact with TRP 23 (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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19D THR* 2.9 18.3 + - + +
20D LEU* 3.6 7.9 - - + +
22D CYS* 1.3 76.3 - - - +
24D VAL* 1.3 68.0 + - + +
26D VAL* 3.3 8.0 + - + +
27D VAL* 3.1 48.9 + - + +
32D PHE* 6.2 0.7 - + - -
36D VAL* 4.4 12.8 - - + -
39D MET* 5.1 0.4 - - + -
40D PHE* 3.7 44.0 - + + -
43D LEU* 3.7 26.4 - - + +
55D MET* 2.7 60.9 + - + -
56D LEU* 5.0 7.4 - - + -
58D THR* 4.2 8.1 - - - -
59D VAL* 3.9 13.6 - - + +
138D LEU* 5.4 7.6 - - + -
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Residues in contact with VAL 24 (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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26C VAL* 5.4 6.5 - - + -
29C GLU* 6.2 0.2 - - - +
30C LYS* 4.1 20.6 - - - +
39C MET* 3.6 28.7 - - + -
20D LEU* 2.9 20.3 + - + +
21D CYS* 3.8 5.8 - - - +
23D TRP* 1.3 82.4 - - + +
25D LYS* 1.3 64.1 + - - +
27D VAL* 3.4 4.0 + - - +
28D GLU* 3.1 26.1 + - + +
58D THR* 3.7 25.4 - - - +
59D VAL* 4.9 2.7 - - - +
60D GLY 5.8 2.2 - - - +
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Residues in contact with LYS 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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25C LYS* 5.7 4.0 - - - +
29C GLU* 3.9 25.9 + - - -
21D CYS 2.9 17.5 + - - +
22D CYS* 3.4 8.1 - - - +
24D VAL* 1.3 77.2 - - - +
26D VAL* 1.3 67.6 + - + +
28D GLU* 3.2 15.1 + - - +
29D GLU* 3.0 62.4 + - + +
25E LYS* 4.5 10.5 - - - +
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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
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22D CYS* 2.8 41.4 + - - +
23D TRP* 3.8 9.0 - - + +
25D LYS* 1.3 75.3 - - + +
27D VAL* 1.3 67.8 + - + +
29D GLU* 4.9 5.4 - - - +
30D LYS* 3.0 46.8 + - + +
36D VAL* 4.7 8.7 - - + -
39D MET* 3.9 37.5 - - + -
21E CYS* 5.9 0.2 - - - -
24E VAL* 4.9 10.8 - - + -
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Residues in contact with VAL 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 TRP* 3.1 59.5 + - + +
24D VAL* 4.0 3.1 - - - +
26D VAL* 1.3 77.3 - - - +
28D GLU* 1.3 65.2 + - - +
31D ALA* 3.2 25.3 + - - +
32D PHE* 4.6 15.3 - - + -
36D VAL* 4.5 11.7 - - + -
59D VAL* 3.8 33.9 - - + -
60D GLY 5.5 0.2 - - - +
62D HIS* 4.1 11.1 + - + -
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Residues in contact with GLU 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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29C GLU* 5.2 4.2 - - - +
24D VAL* 3.1 20.3 + - + +
25D LYS* 3.9 15.0 + - - +
27D VAL* 1.3 82.1 - - + +
29D GLU* 1.3 68.8 + - - +
31D ALA* 3.5 6.2 + - - +
60D GLY* 4.8 15.5 - - - +
62D HIS* 4.4 11.3 + - + +
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Residues in contact with GLU 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 LYS* 3.0 46.1 + - + +
26D VAL* 4.2 4.5 - - - +
28D GLU* 1.3 80.5 - - - +
30D LYS* 1.3 67.1 + - + +
31D ALA* 3.3 2.0 + - - +
24E VAL* 6.1 0.7 - - - +
25E LYS* 2.7 33.7 + - - -
28E GLU* 3.3 17.3 - - - +
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Residues in contact with LYS 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* 3.0 34.1 + - + +
29D GLU* 1.3 81.6 - - + +
31D ALA* 1.3 68.9 + - - +
32D PHE 3.1 0.5 + - - -
33D SER* 3.1 19.7 + - - -
35D GLU* 2.9 37.9 - - + +
36D VAL* 3.9 13.2 - - + -
39D MET* 3.5 19.4 - - - +
24E VAL* 3.5 17.6 - - - +
28E GLU* 6.1 4.9 - - - -
58E THR 3.0 26.7 + - - -
60E GLY* 4.2 7.6 - - - +
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Residues in contact with ALA 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 VAL* 3.2 20.8 + - - +
28D GLU 3.5 2.3 + - - +
29D GLU 3.3 5.0 + - - +
30D LYS* 1.3 78.8 - - - +
32D PHE* 1.3 75.9 + - - +
33D SER 4.7 0.2 - - - +
36D VAL* 3.4 14.7 - - - +
62D HIS* 4.0 26.0 - - + -
145D TYR* 4.3 12.3 - - + -
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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