Contacts of the helix formed by residues 16 - 36 (chain D) in PDB entry 1F5Q
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 ASN 16 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 5.2 1.2 + - - -
278C LYS* 5.0 11.7 - - - +
14D LEU 5.1 3.0 + - - -
15D LEU* 1.3 74.7 - - - +
17D GLU* 1.3 71.2 + - - +
18D GLU* 3.4 10.0 + - - +
19D ASP* 3.0 39.5 + - - +
20D CYS* 3.2 12.1 + - - -
158D HIS* 3.8 9.6 - - - -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN* 1.3 75.6 - - - +
18D GLU* 1.3 67.7 + - - +
20D CYS* 3.1 8.5 + - - +
21D ARG* 2.8 64.8 + - + +
158D HIS* 4.6 3.1 - - - -
159D ILE* 3.6 32.1 - - + +
161D HIS* 4.9 9.7 + - - +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN* 3.3 8.7 + - - +
17D GLU* 1.3 80.9 - - - +
19D ASP* 1.3 65.7 + - - +
21D ARG* 3.0 24.4 + - - +
22D GLN* 2.9 49.2 + - + +
25D TYR* 4.5 4.7 + - - -
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Residues in contact with ASP 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C SER* 3.2 29.6 + - - +
121C HIS* 5.4 4.7 - - + -
14D LEU 4.1 0.2 - - - +
15D LEU* 3.2 32.8 - - + -
16D ASN* 3.0 35.4 + - - +
18D GLU* 1.3 74.4 - - - +
20D CYS* 1.3 64.2 + - - +
22D GLN* 3.1 25.7 + - - +
23D MET* 3.3 9.7 + - - +
155D TYR* 6.1 0.2 - - - -
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Residues in contact with CYS 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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15D LEU* 4.2 10.1 - - - -
16D ASN 3.2 6.5 + - - -
17D GLU 3.1 8.9 + - - +
19D ASP* 1.3 79.6 - - - +
21D ARG* 1.3 62.9 + - - +
23D MET* 3.0 15.2 + - - +
24D ILE* 3.1 16.7 + - - +
155D TYR* 3.8 31.9 - - + +
158D HIS* 3.4 44.9 - - - -
159D ILE* 3.5 17.5 - - + -
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 2.8 48.0 + - - +
18D GLU* 3.0 31.4 + - - +
20D CYS* 1.3 75.3 - - - +
22D GLN* 1.3 57.7 + - - +
24D ILE* 3.1 11.3 + - + +
25D TYR* 2.8 68.3 + - + +
159D ILE* 3.9 19.7 - - + +
217D GLY 5.1 2.0 + - - -
218D VAL* 5.2 5.1 - - - +
221D SER* 3.3 35.4 + - - -
222D LEU* 4.9 10.1 - - - +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 2.9 52.6 + - + +
19D ASP* 3.1 12.1 + - - +
21D ARG* 1.3 75.4 - - - +
23D MET* 1.3 59.5 + - + +
25D TYR* 3.2 22.7 + - - +
26D ARG* 2.8 27.8 + - - +
29D ARG* 4.2 9.6 + - - +
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 6.5 0.7 - - + -
121C HIS* 5.3 17.0 - - + +
122C ARG* 6.0 0.7 - - + -
152C PHE* 3.5 32.3 - - + -
15D LEU* 6.2 2.2 - - + -
19D ASP 3.3 7.5 + - - +
20D CYS 3.0 11.1 + - - +
22D GLN* 1.3 79.3 - - + +
24D ILE* 1.3 65.9 + - - +
26D ARG* 3.0 29.9 + - - +
27D SER 2.9 17.5 + - - -
147D CYS* 3.8 18.9 - - - -
155D TYR* 3.7 44.2 - - + +
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Residues in contact with ILE 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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20D CYS 3.5 14.8 - - - +
21D ARG* 3.1 13.8 + - + +
23D MET* 1.3 76.0 - - - +
25D TYR* 1.3 58.4 + - + +
27D SER* 2.6 35.8 + - - +
28D GLU* 3.0 10.1 + - + +
152D LEU* 3.7 18.6 - - + -
155D TYR* 4.8 8.3 - - + -
156D ILE* 5.1 9.9 - - + -
159D ILE* 3.8 25.1 - - + -
193D VAL* 3.4 26.5 - - + -
222D LEU* 3.5 37.2 - - + -
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Residues in contact with TYR 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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18D GLU* 4.5 4.6 + - - -
21D ARG* 2.8 61.2 + - + -
22D GLN* 3.3 28.3 - - - +
24D ILE* 1.3 79.8 - - + +
26D ARG* 1.3 62.1 + - - +
28D GLU* 3.1 21.8 + - + +
29D ARG* 3.1 33.4 + - - +
221D SER* 4.8 7.4 + - - -
222D LEU* 4.2 20.4 - - + -
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Residues in contact with ARG 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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53C SER* 5.4 6.3 + - - -
57C GLU* 5.1 9.1 - - - +
152C PHE* 4.3 22.6 - - - -
22D GLN 2.8 13.8 + - - +
23D MET* 3.0 29.3 + - - +
25D TYR* 1.3 76.9 - - - +
27D SER* 1.3 60.5 + - - +
29D ARG* 3.3 23.8 + - + +
30D GLU* 2.9 61.3 + - + +
143D VAL* 5.4 5.7 - - - +
145D ASP* 3.4 32.3 + - - +
146D ARG* 4.1 3.3 - - - +
147D CYS* 4.7 8.6 - - + +
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D MET 2.9 10.0 + - - -
24D ILE* 2.6 23.6 + - - +
26D ARG* 1.3 73.0 - - - +
28D GLU* 1.3 59.7 + - - +
30D GLU* 3.7 12.4 - - - +
31D HIS* 3.1 27.0 + - - +
34D ARG* 5.3 0.2 + - - -
147D CYS* 3.9 24.9 - - - -
152D LEU* 3.9 11.3 - - - +
192D PRO* 3.9 14.1 - - - +
193D VAL* 3.7 18.2 - - - +
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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
----------------------------------------------------------
24D ILE* 3.0 21.3 + - + +
25D TYR* 3.1 18.1 + - + +
27D SER* 1.3 80.3 + - - +
29D ARG* 1.3 59.2 + - + +
31D HIS* 3.5 5.6 + - - +
32D ASP* 3.0 35.8 + - - +
191D ARG* 2.5 47.8 + - - +
192D PRO* 4.7 1.6 - - - +
193D VAL* 4.6 14.3 - - - +
222D LEU* 4.5 15.8 - - + +
223D TYR* 6.0 1.2 - - - -
224D ILE* 5.9 0.9 - - - +
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Residues in contact with ARG 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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22D GLN* 4.2 10.7 + - - +
25D TYR* 3.1 24.8 + - - +
26D ARG* 3.3 36.7 + - + +
28D GLU* 1.3 74.9 - - + +
30D GLU* 1.3 68.0 + - + +
32D ASP* 3.0 12.2 + - - +
33D ALA* 2.9 24.4 + - - +
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Residues in contact with GLU 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 ARG* 2.9 50.3 + - + +
27D SER* 3.7 6.5 - - - +
29D ARG* 1.3 76.6 - - + +
31D HIS* 1.3 62.5 + - - +
33D ALA* 3.3 7.8 + - - +
34D ARG* 3.0 34.0 + - - +
79D GLU* 5.3 1.6 - - - +
145D ASP 3.7 1.2 - - - +
146D ARG* 3.3 43.0 + - - +
147D CYS* 2.8 34.1 + - - +
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Residues in contact with HIS 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 SER 3.1 19.8 + - - +
28D GLU* 3.5 6.5 - - - +
30D GLU* 1.3 76.9 - - - +
32D ASP* 1.3 59.8 + - - +
34D ARG* 3.0 21.5 + - - +
35D MET* 2.8 58.9 + - + +
189D MET* 3.1 28.5 + - - -
190D LYS 3.7 12.9 + - - -
191D ARG* 3.5 42.6 + - + +
192D PRO* 3.8 20.7 - - + +
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Residues in contact with ASP 32 (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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28D GLU* 3.0 23.2 + - - +
29D ARG* 3.0 10.9 + - - +
31D HIS* 1.3 78.6 - - - +
33D ALA* 1.3 57.5 + - - +
35D MET* 4.0 4.8 - - - +
36D VAL* 3.1 39.4 + - + +
191D ARG* 2.7 27.5 + - - -
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Residues in contact with ALA 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 ARG 2.9 15.7 + - - +
30D GLU* 3.7 7.9 - - - +
32D ASP* 1.3 75.7 - - - +
34D ARG* 1.3 62.3 + - - +
35D MET 3.3 0.2 - - - -
36D VAL* 3.9 13.9 - - - +
79D GLU* 4.1 18.5 - - - +
83D SER* 5.7 3.3 - - - -
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Residues in contact with ARG 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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27D SER 5.3 0.4 + - - -
30D GLU* 3.0 37.9 + - - +
31D HIS* 3.0 32.9 + - - +
33D ALA* 1.3 79.7 - - - +
35D MET* 1.3 61.2 + - + +
36D VAL 4.8 1.0 - - - +
44D PHE* 5.6 4.9 - - - -
75D ALA* 3.6 39.7 + - - +
78D ASP* 4.5 10.5 - - + -
79D GLU* 3.9 39.0 + - + +
82D LEU* 3.0 34.7 - - + +
146D ARG* 4.0 14.3 - - - +
147D CYS 5.2 3.8 + - - -
148D LEU* 6.0 0.6 - - - +
190D LYS 5.8 0.2 + - - -
192D PRO* 4.1 16.0 - - - +
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Residues in contact with MET 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 HIS* 2.8 45.0 + - + +
32D ASP* 4.2 5.6 - - - +
34D ARG* 1.3 85.7 - - + +
36D VAL* 1.3 61.4 + - + +
37D GLY 3.1 2.1 + - - -
40D VAL* 3.0 48.1 - - + +
44D PHE* 4.1 23.1 - - - -
82D LEU* 5.0 0.2 - - - -
189D MET* 3.6 34.5 - - + +
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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 ASP* 3.1 22.8 + - + +
33D ALA* 3.9 12.2 + - - +
34D ARG 3.6 1.7 - - - +
35D MET* 1.3 75.3 - - + +
37D GLY* 1.3 60.5 + - - +
82D LEU* 4.8 1.0 - - - +
83D SER* 5.7 2.8 - - - -
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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