Contacts of the helix formed by residues 48 - 62 (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 48 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR* 3.0 19.4 + - + +
44C ARG* 5.0 0.2 - - - +
46C ARG* 3.2 33.2 - - + +
47C GLY* 1.3 74.7 - - - +
49C LEU* 1.3 64.0 - - - +
50C HIS 3.4 2.2 - - - -
51C SER* 3.2 24.0 + - - +
52C SER* 3.2 12.4 + - - -
116C PHE* 3.2 31.0 - - + -
120C TYR* 3.6 27.8 - - + +
170C PHE* 4.0 5.4 - - + -
173C TYR* 4.8 11.0 - - + +
202C HIS* 4.0 23.1 - - + +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 5.3 10.3 - - + +
47C GLY* 3.1 29.2 + - - +
48C LEU* 1.3 71.7 - - - +
50C HIS* 1.3 70.1 + - + +
52C SER* 3.2 11.3 + - - -
53C LYS* 2.9 29.5 + - - +
94C PHE* 5.7 2.7 - - + -
95C ASP* 5.3 8.1 - - - +
97C LYS* 5.8 11.2 - - + -
120C TYR* 5.1 1.4 + - - -
92P ALA* 4.7 7.4 - - - +
95P ASP* 3.4 51.8 - - + +
96P VAL* 4.7 9.5 - - + +
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Residues in contact with HIS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 4.2 22.1 + - + +
48A LEU* 3.3 49.7 - - + +
48C LEU 3.4 0.2 - - - -
49C LEU* 1.3 88.4 - - + +
51C SER* 1.3 61.7 + - - +
53C LYS* 3.4 30.9 + - - +
54C TRP* 3.1 24.1 + - - +
96P VAL* 4.4 19.4 + - + +
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 3.5 21.5 - - - +
48C LEU* 3.2 18.1 + - - +
49C LEU 3.4 0.2 - - - -
50C HIS* 1.3 79.2 - - - +
52C SER* 1.3 57.3 + - - +
54C TRP* 3.3 9.6 + - - +
55C SER* 2.9 30.7 + - - -
173C TYR* 6.1 0.2 - - - -
202C HIS* 3.8 11.2 - - - -
203C TRP* 4.5 8.8 + - - +
204C GLY* 3.8 27.1 - - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 3.1 22.8 + - - +
43C THR* 3.3 17.3 - - - -
44C ARG* 3.7 20.9 + - - +
48C LEU 3.2 9.2 + - - -
49C LEU* 3.2 13.9 + - - -
51C SER* 1.3 81.8 + - - +
53C LYS* 1.3 56.6 + - - +
55C SER* 3.3 4.4 + - - -
56C ALA* 2.9 31.2 + - - +
92P ALA* 4.3 11.6 - - - +
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 5.4 4.6 - - - +
49C LEU 2.9 14.1 + - - +
50C HIS* 3.7 33.2 + - - +
51C SER 3.3 0.2 - - - -
52C SER* 1.3 75.7 - - - +
54C TRP* 1.3 64.7 + - - +
56C ALA* 3.4 2.6 + - - +
57C GLU* 2.9 23.6 + - + +
298C GLU* 5.3 13.9 + - - +
89P LEU* 5.8 0.5 - - - +
92P ALA* 3.7 21.0 - - + +
93P TYR* 3.7 38.5 + - + +
96P VAL* 3.5 31.1 - - + +
98P GLU* 4.4 6.6 + - - +
101P ARG* 5.7 0.8 - - - +
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Residues in contact with TRP 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 6.3 0.2 - - + -
50C HIS 3.1 15.2 + - - +
51C SER* 3.4 11.2 - - - +
53C LYS* 1.3 80.5 - - - +
55C SER* 1.3 64.6 + - - +
57C GLU* 3.3 12.7 + - - +
58C LEU* 3.4 18.7 + - + +
203C TRP* 3.1 71.3 - + + +
204C GLY 5.2 0.2 - - - -
207C LEU* 3.1 52.0 - - + -
236C HIS* 5.0 1.3 - + - -
264C TYR* 3.4 53.6 - + + -
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.1 27.4 + - - +
39C ILE* 2.9 31.4 - - - +
40C ALA* 4.1 15.9 - - - -
43C THR* 5.5 0.7 - - - -
51C SER 2.9 14.3 + - - -
52C SER 3.8 3.6 - - - -
54C TRP* 1.3 83.0 - - - +
56C ALA* 1.3 61.2 + - - +
58C LEU* 3.4 2.5 + - - -
59C ALA* 3.2 17.3 + - - +
201C LEU 3.9 5.8 + - - -
203C TRP* 5.0 7.8 - - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 6.2 0.7 - - - -
40C ALA* 4.3 11.8 - - + +
44C ARG* 6.3 0.4 - - - +
52C SER* 2.9 19.2 + - - +
53C LYS* 3.8 5.8 - - - +
55C SER* 1.3 75.1 - - - +
57C GLU* 1.3 63.1 + - - +
59C ALA* 3.3 8.3 + - - +
60C PHE* 3.0 23.4 + - - +
85P ASP* 5.0 0.9 - - - +
88P THR* 4.2 10.5 - - - +
89P LEU* 3.6 35.3 - - + +
92P ALA* 4.7 1.6 - - + -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 2.9 14.9 + - + +
54C TRP* 3.5 12.6 - - - +
55C SER 3.3 0.2 - - - -
56C ALA* 1.3 76.4 - - - +
58C LEU* 1.3 63.9 + - + +
60C PHE* 3.2 13.1 + - - +
61C SER* 3.1 15.2 + - - -
262C SER* 2.9 16.3 + - - +
263C SER* 2.8 40.5 + - - -
264C TYR* 4.2 18.8 - - + +
89P LEU* 4.2 19.7 - - + +
93P TYR* 4.5 17.4 + - + +
105P PHE* 4.5 8.8 - - - -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.5 18.8 - - + -
54C TRP* 3.4 14.1 + - + +
55C SER 3.4 3.7 + - - +
56C ALA 3.3 0.2 - - - -
57C GLU* 1.3 79.0 - - - +
59C ALA* 1.3 63.6 + - - +
61C SER* 3.0 21.3 + - - -
62C LEU* 3.3 10.6 + - - +
203C TRP* 4.2 20.0 - - + +
228C TRP* 4.3 12.3 - - + -
232C PHE* 3.7 29.4 - - + -
259C PHE* 3.5 35.3 - - + -
262C SER* 3.8 15.9 - - - +
264C TYR* 4.3 15.3 - - + -
265C ILE* 4.4 0.4 - - + -
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Residues in contact with ALA 59 (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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33C LYS* 3.5 14.9 + - + +
36C LEU* 3.5 16.5 - - + +
37C LEU* 4.1 28.0 - - + +
40C ALA* 6.1 0.2 - - + -
55C SER 3.2 14.9 + - - +
56C ALA* 3.6 12.3 - - - +
58C LEU* 1.3 74.6 - - - +
60C PHE* 1.4 63.4 + - - +
62C LEU* 3.1 22.0 + - - +
85P ASP* 3.3 12.1 - - - +
88P THR* 5.9 0.9 - - - +
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Residues in contact with PHE 60 (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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56C ALA 3.0 8.9 + - - +
57C GLU* 3.5 16.6 - - - +
59C ALA* 1.4 73.8 - - - +
61C SER* 1.3 68.8 + - - +
62C LEU 3.3 7.8 - - - +
261C LYS* 5.2 8.3 - - + +
262C SER* 6.2 0.2 - - - -
85P ASP* 3.2 38.5 + - + +
86P ALA* 4.4 15.3 - - + -
89P LEU* 3.3 33.7 - - + -
105P PHE* 4.2 23.8 - + - -
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Residues in contact with SER 61 (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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57C GLU 3.1 5.7 + - - -
58C LEU* 3.0 13.4 + - - -
60C PHE* 1.3 80.7 - - - +
62C LEU* 1.3 60.3 + - - +
63C PRO* 4.0 1.0 - - - +
258C GLY 3.6 4.3 + - - +
259C PHE* 3.2 27.9 + - - -
261C LYS* 3.5 22.4 + - - +
262C SER* 3.0 45.7 + - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.9 31.0 - - + +
32C ILE* 4.1 7.0 - - + -
33C LYS* 3.3 46.5 + - + +
36C LEU* 4.1 5.4 - - + -
58C LEU 3.7 10.8 - - - +
59C ALA 3.1 17.7 + - - +
60C PHE 3.3 6.4 - - - +
61C SER* 1.3 81.8 - - - +
63C PRO* 1.4 72.4 - - + +
64C ALA 3.5 1.0 + - - -
258C GLY 4.0 9.4 - - - +
259C PHE* 3.7 43.5 - - + -
85P ASP* 4.1 0.9 - - - +
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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
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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