Contacts of the helix formed by residues 29 - 47 (chain C) in PDB entry 5G04
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 LEU 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 5.5 1.8 - - + -
27C SER 5.3 2.5 - - - -
28C ASP* 1.3 89.2 + - - +
30C ARG* 1.3 57.2 + - - +
31C GLU 3.1 1.3 - - - -
32C ILE* 2.8 10.3 + - + +
33C LYS* 2.6 37.5 + - - +
62C LEU* 3.9 26.4 - - + +
63C PRO* 4.5 18.8 - - + -
257C VAL* 3.2 39.9 - - + +
258C GLY* 4.3 6.5 - - - -
259C PHE* 5.7 1.3 - - + -
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP* 2.9 10.8 + - - +
29C LEU* 1.3 77.7 - - - +
31C GLU* 1.3 56.1 + - - +
33C LYS* 4.0 5.6 - - - +
34C LYS* 3.0 30.3 + - - +
63C PRO* 5.4 13.8 - - + +
64C ALA 5.6 1.8 + - - -
65C LEU* 4.1 31.6 - - + +
66C PRO* 4.7 19.5 - - - +
69C GLU* 5.0 12.1 - - + +
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE 4.6 6.1 - - - +
27C SER* 5.5 0.2 + - - -
28C ASP* 3.1 39.6 + - + +
30C ARG* 1.3 72.9 - - - +
32C ILE* 1.3 76.3 + - - +
34C LYS* 3.4 17.5 + - - +
35C GLN* 2.8 58.6 + - - +
228C TRP* 4.9 1.1 + - - -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.0 31.2 - - + -
28C ASP 3.0 24.9 - - - +
29C LEU* 2.8 16.3 + - + +
31C GLU* 1.3 86.5 - - - +
33C LYS* 1.3 57.5 + - - +
35C GLN* 3.3 3.8 + - - +
36C LEU* 2.7 34.1 + - + +
62C LEU* 4.1 15.9 - - + -
228C TRP* 3.4 52.6 - - + +
259C PHE* 4.4 9.0 - - + -
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU 2.6 19.6 + - - +
30C ARG* 4.0 5.6 - - + +
32C ILE* 1.3 72.6 - - - +
34C LYS* 1.3 57.9 + - - +
36C LEU* 3.5 3.3 - - - +
37C LEU* 2.8 46.9 + - + +
59C ALA* 3.5 15.0 + - + +
62C LEU* 3.3 42.6 + - + -
63C PRO* 3.2 28.9 + - + +
64C ALA* 3.3 16.2 - - - +
65C LEU* 4.0 20.8 - - + +
85P ASP* 3.3 28.4 + - - +
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG 3.0 18.1 + - - +
31C GLU* 3.7 18.4 - - - +
33C LYS* 1.3 76.9 - - - +
35C GLN* 1.3 66.5 + - - +
37C LEU* 3.3 9.6 + - - +
38C LEU* 3.1 22.4 + - + +
65C LEU* 5.2 8.0 - - + +
69C GLU* 3.4 30.2 - - + +
70C LEU* 5.7 0.4 - - - -
71C GLN* 3.7 36.7 - - + +
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU* 2.8 45.7 + - + +
32C ILE 3.6 3.4 - - - +
34C LYS* 1.3 83.5 - - - +
36C LEU* 1.3 60.5 + - - +
38C LEU* 3.4 24.3 + - + +
39C ILE* 3.3 15.9 + - - +
200C PRO* 5.6 4.2 - - - +
201C LEU* 3.4 27.1 - - + +
227C THR* 5.5 6.8 - - - +
228C TRP* 4.6 11.8 + - - +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 2.7 20.6 + - + +
33C LYS 3.5 3.6 - - - +
35C GLN* 1.3 69.6 - - - +
37C LEU* 1.3 66.1 + - - +
39C ILE* 3.1 6.8 - - - +
40C ALA* 3.1 19.4 + - - +
55C SER* 3.1 44.1 + - - +
58C LEU* 3.5 19.1 - - + -
59C ALA* 3.5 30.5 - - + +
62C LEU* 4.1 14.4 - - + -
201C LEU* 3.7 27.7 - - + +
203C TRP* 6.0 1.3 - - + -
228C TRP* 4.1 14.8 - - + -
259C PHE* 4.6 0.7 - - + -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 2.8 41.9 + - + +
34C LYS* 3.6 9.0 - - - +
36C LEU* 1.3 77.2 - - - +
38C LEU* 1.3 60.7 + - - +
40C ALA* 3.3 12.3 + - + +
41C GLY* 3.1 18.7 + - - -
56C ALA* 6.2 0.7 - - - -
59C ALA* 4.1 17.3 - - + -
65C LEU* 6.3 1.8 - - + -
70C LEU* 6.5 1.6 - - + -
84P MET* 3.9 28.7 - - + +
85P ASP* 4.7 9.2 - - - +
88P THR* 3.8 27.4 - - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.1 9.7 + - + +
35C GLN* 3.5 28.7 - - + +
36C LEU 3.3 0.2 - - - -
37C LEU* 1.3 75.3 - - - +
39C ILE* 1.3 64.8 - - + +
41C GLY* 3.3 3.5 + - - +
42C LEU* 2.9 43.3 + - + +
71C GLN* 3.8 28.3 - - - +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLN 3.3 4.7 + - - +
36C LEU 3.1 13.3 + - - +
38C LEU* 1.3 80.1 - - + +
40C ALA* 1.3 64.0 + - - +
42C LEU* 3.3 9.4 + - + +
43C THR* 2.9 38.1 + - + -
55C SER* 2.9 29.4 - - - +
170C PHE* 4.9 4.9 - - + -
199C LEU* 3.8 17.0 - - + -
200C PRO 3.5 24.5 - - - +
201C LEU* 3.3 45.1 - - + +
202C HIS* 3.6 4.7 - - + +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU 3.1 12.3 + - - +
37C LEU* 3.5 19.1 - - + +
39C ILE* 1.3 75.8 - - - +
41C GLY* 1.3 57.0 + - - +
43C THR* 3.0 9.3 + - - -
44C ARG* 3.0 34.4 + - - +
52C SER* 3.1 14.4 + - - +
55C SER* 4.1 17.5 - - - -
56C ALA* 4.3 17.7 - - + +
59C ALA* 6.1 0.2 - - + -
88P THR* 5.8 1.1 - - - -
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU 3.1 10.7 + - - -
38C LEU* 3.6 4.3 - - - -
39C ILE 3.3 0.4 - - - -
40C ALA* 1.3 78.2 - - - +
42C LEU* 1.4 54.5 + - - +
44C ARG* 3.4 24.4 + - - +
45C GLU* 3.0 39.2 + - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 2.9 29.0 + - + +
39C ILE* 3.3 10.5 + - + +
41C GLY* 1.4 72.8 - - - +
43C THR* 1.3 61.7 + - - +
45C GLU* 3.5 13.5 + - + +
46C ARG* 3.3 38.0 + - + +
113C LYS* 5.4 11.0 - - + -
170C PHE* 3.6 30.5 - - + -
199C LEU* 5.7 4.0 - - + -
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 2.9 26.2 + - + +
40C ALA* 3.0 15.2 + - - -
42C LEU* 1.3 71.3 - - - +
44C ARG* 1.3 59.8 + - - +
46C ARG* 3.1 3.4 + - - +
47C GLY 2.8 23.9 + - - -
48C LEU* 3.0 23.5 + - + +
51C SER* 3.5 22.3 - - - +
52C SER* 3.3 19.2 + - - -
55C SER* 5.5 0.6 - - - -
170C PHE* 3.7 24.9 - - + -
202C HIS* 3.9 11.0 - - + -
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA* 3.0 32.3 + - - +
41C GLY* 3.5 20.2 + - - +
43C THR* 1.3 72.2 + - - +
45C GLU* 1.3 73.8 + - + +
47C GLY* 3.1 15.0 + - - +
48C LEU 5.0 0.4 - - - +
49C LEU* 5.3 8.5 - - + +
52C SER* 3.7 16.9 + - - +
56C ALA* 6.3 0.4 - - - +
91C LYS* 3.9 5.4 + - - +
84P MET* 6.0 0.4 - - - +
87P TYR* 5.8 4.7 - - - -
88P THR* 3.7 40.9 + - - +
91P LYS* 4.6 22.9 - - - +
92P ALA* 5.9 4.6 - - - +
95P ASP* 5.2 8.7 - - - +
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLY* 3.0 33.2 + - - +
42C LEU* 3.5 17.9 - - + +
43C THR 3.3 0.2 - - - -
44C ARG* 1.3 82.1 + - - +
46C ARG* 1.3 59.4 + - + +
87C TYR* 2.6 33.3 + - - +
91C LYS* 3.1 23.7 + - - +
44P ARG* 5.6 6.9 + - - -
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.3 24.3 + - + +
43C THR 3.1 6.7 + - - +
45C GLU* 1.3 81.1 - - + +
47C GLY* 1.3 59.9 + - - +
48C LEU* 3.2 16.4 - - + +
87C TYR* 4.4 3.6 - - + +
91C LYS* 3.6 2.2 + - - -
94C PHE* 3.5 13.0 - - - -
112C LYS 4.8 3.2 + - - -
113C LYS* 5.0 19.7 + - + +
116C PHE* 3.0 75.7 - - + +
117C LEU* 4.0 11.4 - - - +
120C TYR* 4.2 1.7 - - - -
170C PHE* 2.6 73.2 - - - +
171C GLY 5.0 0.2 - - - +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR 2.8 3.4 + - - -
44C ARG* 3.1 11.4 + - - -
45C GLU 3.3 0.2 - - - -
46C ARG* 1.3 79.9 - - - +
48C LEU* 1.3 63.6 + - - +
49C LEU* 3.1 26.4 + - - +
91C LYS* 3.4 15.7 - - - +
94C PHE* 3.6 10.7 - - - -
95C ASP* 5.3 0.4 - - - -
120C TYR* 3.7 13.9 + - - -
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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