Contacts of the helix formed by residues 16 - 36 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 5.9 0.4 + - - -
278A LYS* 3.0 31.6 - - - +
14B LEU 4.9 0.8 + - - +
15B LEU* 1.3 74.4 - - - +
17B GLU* 1.3 65.3 + - - +
18B GLU* 3.2 13.1 + - - +
19B ASP* 2.7 39.5 + - - +
20B CYS* 3.6 2.1 + - - -
158B HIS* 4.2 4.9 - - - -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN* 1.3 69.2 - - - +
18B GLU* 1.3 63.4 + - - +
20B CYS* 3.1 8.3 + - - +
21B ARG* 2.7 61.8 + - - +
158B HIS* 4.6 4.5 - - - -
159B ILE* 3.9 38.6 - - + +
161B HIS* 5.4 10.6 - - + -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN* 2.7 16.2 + - - +
17B GLU* 1.3 77.1 - - - +
19B ASP* 1.3 56.6 + - - +
21B ARG* 3.2 20.9 + - - +
22B GLN* 2.5 57.1 + - + +
25B TYR* 4.4 6.1 + - - -
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.8 26.4 + - - +
121A HIS* 5.3 4.2 - - - -
14B LEU 4.2 1.6 - - - +
15B LEU* 3.2 33.3 - - + +
16B ASN* 2.7 47.6 + - - +
18B GLU* 1.3 73.2 - - - +
20B CYS* 1.3 60.6 + - - +
22B GLN* 3.1 21.0 + - - +
23B MET* 3.2 16.1 + - - +
155B TYR* 4.9 1.2 - - - -
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.4 8.5 - - - -
16B ASN 4.4 4.7 - - - -
17B GLU 3.1 8.2 + - - +
19B ASP* 1.3 79.7 - - - +
21B ARG* 1.3 61.6 + - - +
23B MET* 3.4 3.5 + - - +
24B ILE* 3.1 28.9 + - - +
155B TYR* 3.5 50.4 - - + +
158B HIS* 3.3 37.2 - - - -
159B ILE* 3.5 11.0 - - + -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 2.7 48.6 + - + +
18B GLU* 3.4 28.0 - - - +
19B ASP 3.1 0.2 - - - -
20B CYS* 1.3 75.6 - - - +
22B GLN* 1.3 59.1 + - - +
24B ILE* 3.1 9.5 + - + +
25B TYR* 2.9 61.6 + - + +
159B ILE* 4.4 17.7 - - + +
217B GLY 5.0 0.8 + - - -
218B VAL* 4.9 6.5 - - - +
221B SER* 2.9 44.1 + - - -
222B LEU* 4.1 14.5 - - - +
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 5.8 7.2 - - + +
18B GLU* 2.5 53.0 + - + +
19B ASP* 3.1 14.3 + - - +
21B ARG* 1.3 77.2 - - - +
23B MET* 1.3 60.3 + - + +
25B TYR* 3.3 25.7 + - - +
26B ARG* 3.0 26.6 + - - +
29B ARG* 4.6 6.8 + - - -
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.8 21.8 - - - +
121A HIS* 5.1 9.6 - - + +
152A PHE* 4.3 9.2 - - + -
19B ASP 3.2 7.4 + - - +
20B CYS 3.5 9.4 - - - +
22B GLN* 1.3 80.9 - - + +
24B ILE* 1.3 63.7 + - - +
26B ARG* 3.1 41.8 + - + +
27B SER 3.1 9.7 + - - -
147B CYS* 3.6 29.2 - - - -
152B LEU* 5.0 0.2 - - + -
155B TYR* 3.5 46.2 - - + +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B CYS 3.1 19.2 + - - +
21B ARG* 3.1 10.7 + - + +
23B MET* 1.3 75.5 - - - +
25B TYR* 1.3 68.3 + - + +
27B SER* 2.9 24.1 + - - -
28B GLU* 3.0 17.9 + - + +
152B LEU* 4.0 18.4 - - + -
155B TYR* 5.0 4.3 - - + -
156B ILE* 4.9 10.1 - - + -
159B ILE* 3.9 23.8 - - + -
193B VAL* 3.7 24.2 - - + -
222B LEU* 3.6 37.5 - - + -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 4.4 4.3 + - - -
21B ARG* 2.9 55.9 + - + +
22B GLN* 3.4 36.1 - - - +
24B ILE* 1.3 81.7 - - + +
26B ARG* 1.3 57.6 + - - +
28B GLU* 3.4 12.4 + - + +
29B ARG* 3.1 52.4 + - - +
221B SER 5.1 5.6 + - - -
222B LEU* 4.7 14.8 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 5.2 8.7 + - - -
57A GLU* 5.0 10.1 + - - +
152A PHE* 3.7 29.4 - - - -
22B GLN 3.0 13.5 + - - +
23B MET* 3.3 31.2 - - + +
24B ILE 3.0 0.4 - - - -
25B TYR* 1.3 77.3 - - - +
27B SER* 1.3 60.2 + - - +
29B ARG* 3.6 14.2 + - + +
30B GLU* 2.8 52.4 + - + +
143B VAL* 5.4 5.5 - - - +
145B ASP* 3.2 36.4 + - - +
146B ARG 4.6 2.8 + - - -
147B CYS* 4.4 12.3 - - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET 3.1 3.8 + - - -
24B ILE* 2.9 19.8 + - - +
26B ARG* 1.3 76.1 - - - +
28B GLU* 1.3 60.6 + - - +
30B GLU* 3.6 10.2 - - - +
31B HIS* 2.9 29.8 + - - +
34B ARG* 5.5 0.2 + - - -
147B CYS* 3.6 36.3 - - - +
152B LEU* 3.7 15.3 - - - +
192B PRO* 4.1 18.3 - - - +
193B VAL* 4.7 3.3 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.0 24.8 + - + +
25B TYR* 3.4 15.9 - - + +
27B SER* 1.3 81.5 + - - +
29B ARG* 1.3 57.8 + - + +
31B HIS* 3.3 5.6 + - - +
32B ASP* 3.0 36.9 + - - +
191B ARG* 2.9 45.0 + - - +
192B PRO* 5.2 0.7 - - - +
193B VAL* 3.4 25.3 - - - +
222B LEU* 5.7 5.1 - - + +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 4.6 7.3 + - - -
25B TYR* 3.1 42.5 + - - +
26B ARG* 3.9 13.4 - - + +
28B GLU* 1.3 79.0 - - + +
30B GLU* 1.3 59.7 + - + +
32B ASP* 3.2 11.5 + - - +
33B ALA* 2.8 30.0 + - - +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG* 2.8 58.7 + - + +
27B SER* 3.6 11.9 - - - +
28B GLU 3.3 0.2 - - - -
29B ARG* 1.3 73.8 - - + +
31B HIS* 1.3 65.4 + - - +
33B ALA* 3.8 6.3 - - - +
34B ARG* 2.9 42.1 + - - +
79B GLU* 5.0 2.4 - - - +
145B ASP 3.8 1.0 - - - +
146B ARG* 3.6 28.5 + - - +
147B CYS* 2.9 24.1 + - - +
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER 2.9 18.2 + - - +
28B GLU* 3.4 7.6 - - - +
30B GLU* 1.3 77.3 - - - +
32B ASP* 1.3 65.5 + - - +
34B ARG* 3.2 19.7 + - - +
35B MET* 2.7 60.5 + - + +
189B MET 3.1 28.6 + - - -
190B LYS 3.6 2.8 + - - -
191B ARG* 3.5 44.4 + - + +
192B PRO* 3.7 16.7 - - + +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 3.0 19.7 + - - +
29B ARG* 3.4 13.6 - - + +
31B HIS* 1.3 79.7 - - - +
33B ALA* 1.3 58.8 + - - +
35B MET* 2.7 25.3 + - - +
36B VAL* 2.8 25.5 + - + +
191B ARG* 3.7 22.8 + - - -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG 2.8 19.7 + - - +
30B GLU* 3.8 7.4 - - - +
32B ASP* 1.3 73.7 - - - +
34B ARG* 1.3 60.3 + - - +
36B VAL* 4.1 11.8 + - - +
37B GLY* 4.9 0.9 + - - -
79B GLU* 4.6 16.8 - - - +
83B SER* 4.7 5.9 + - - -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 2.9 40.2 + - - +
31B HIS* 3.4 30.4 + - - +
32B ASP 3.0 0.2 - - - -
33B ALA* 1.3 76.9 - - - +
35B MET* 1.3 64.7 + - + +
37B GLY* 4.6 1.3 - - - -
44B PHE* 5.5 2.2 - - - -
75B ALA* 3.5 39.9 + - - +
78B ASP* 4.1 15.0 - - + -
79B GLU* 4.0 36.4 + - - +
82B LEU* 3.0 27.6 - - + +
83B SER* 5.7 0.2 - - - -
146B ARG* 4.0 15.4 - - - +
147B CYS 5.6 1.6 + - - -
192B PRO* 4.5 12.5 - - - +
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Residues in contact with MET 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B HIS* 2.7 47.4 + - + +
32B ASP* 2.7 9.9 + - - +
34B ARG* 1.3 94.5 - - + +
36B VAL* 1.3 52.9 + - + +
37B GLY 2.5 17.9 + - - +
40B VAL* 3.0 50.4 - - + +
44B PHE* 3.7 11.7 - - + -
82B LEU* 3.7 12.1 - - + -
189B MET* 3.9 14.8 - - - +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP* 2.8 27.4 + - + +
33B ALA* 4.1 8.4 + - - +
34B ARG 3.8 0.2 - - - -
35B MET* 1.3 70.5 - - + +
37B GLY* 1.3 64.3 + - - +
38B VAL* 5.4 0.3 - - - +
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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
------------------------------------------------------------
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