Contacts of the helix formed by residues 30 - 49 (chain C) in PDB entry 6MZL
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 GLU 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET 3.7 2.3 - - - +
29C CYS* 1.3 75.1 - - - +
31C SER* 1.3 62.0 + - - +
32C TYR 3.2 0.2 - - - -
33C SER* 2.9 27.7 + - - +
34C ARG* 3.4 35.8 + - - +
470F TYR* 3.8 9.3 + - - +
471F GLN* 2.4 35.1 + - - +
489F PHE* 4.4 8.3 - - - -
69H SER* 6.1 1.4 - - - -
137N TYR* 3.7 22.6 + - + +
138N TYR* 3.9 1.3 + - - +
141N ARG* 4.5 17.9 + - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET* 3.1 29.0 + - - +
29C CYS* 4.1 0.6 - - - +
30C GLU* 1.3 76.6 - - - +
32C TYR* 1.3 65.9 + - - +
33C SER 3.4 0.2 - - - -
34C ARG* 3.4 17.0 + - - +
35C SER* 2.9 28.4 + - - -
38C ARG* 5.6 2.7 + - - -
34L ARG* 6.2 1.8 - - - -
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Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET 4.2 13.0 - - - -
29C CYS* 3.6 28.4 + - + +
30C GLU 3.2 1.0 - - - -
31C SER* 1.3 82.7 + - - +
33C SER* 1.3 57.2 + - - +
35C SER* 2.5 26.0 + - - -
36C LEU* 2.9 23.0 + - + +
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C CYS 4.6 1.4 + - - -
30C GLU* 2.9 19.1 + - - +
32C TYR* 1.3 75.2 - - - +
34C ARG* 1.3 59.7 + - - +
36C LEU* 3.3 9.2 + - - +
37C LEU* 3.0 31.9 + - - +
134N VAL* 3.8 17.7 - - - +
137N TYR* 4.8 11.4 - - - -
138N TYR* 2.6 40.1 + - - -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 3.5 35.4 + - - +
31C SER* 3.4 17.0 + - - +
32C TYR 3.2 0.4 - - - -
33C SER* 1.3 77.6 + - - +
35C SER* 1.3 56.2 + - - +
37C LEU* 3.3 4.3 + - - +
38C ARG* 2.9 50.4 + - - +
62C THR* 4.9 2.9 - - - +
63C ASP* 5.7 4.5 + - - -
66C GLN* 3.3 28.5 + - - +
68H THR* 4.6 16.4 + - - +
69H SER* 5.7 4.9 - - - -
34L ARG* 6.2 0.2 - - - +
138N TYR* 3.3 15.7 + - - +
141N ARG* 4.5 14.3 - - - +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER 2.9 12.9 + - - -
32C TYR* 2.5 33.2 + - - +
34C ARG* 1.3 75.5 - - - +
36C LEU* 1.3 59.9 + - - +
38C ARG* 3.2 23.5 + - - +
39C VAL* 2.9 33.4 + - - +
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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
----------------------------------------------------------
32C TYR* 2.9 24.6 + - + +
33C SER* 3.7 9.0 - - - +
34C ARG 3.3 0.4 - - - -
35C SER* 1.3 77.6 + - - +
37C LEU* 1.3 61.1 + - - +
39C VAL* 3.2 16.2 + - + +
40C SER* 2.9 26.2 + - - -
131N PRO* 4.9 22.1 - - + +
134N VAL* 3.8 29.4 - - + -
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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
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33C SER 3.0 13.1 + - - +
34C ARG* 3.6 6.3 - - - +
36C LEU* 1.3 74.3 - - - +
38C ARG* 1.3 61.2 + - - +
40C SER* 2.5 27.7 + - - +
41C VAL* 2.9 17.5 + - - +
62C THR* 4.1 11.0 - - + +
65C LEU* 5.3 11.4 - - + -
66C GLN* 3.5 38.8 - - + +
69C LEU* 5.2 13.9 - - + -
130N ILE* 4.2 25.1 - - + -
131N PRO* 6.2 0.4 - - + -
134N VAL* 4.4 11.2 - - + -
135N THR* 5.4 2.0 - - - +
138N TYR* 3.7 21.5 - - + -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 5.6 1.8 + - - -
34C ARG* 2.9 38.9 + - - +
35C SER* 3.3 19.0 - - - +
37C LEU* 1.3 76.7 - - - +
39C VAL* 1.3 55.8 + - + +
41C VAL* 3.3 4.5 + - - +
42C ALA* 2.9 29.0 + - - +
58C CYS* 5.3 3.6 - - + +
59C HIS* 3.2 42.5 + - - +
62C THR* 3.7 26.1 + - + +
34L ARG* 5.6 5.7 - - - +
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C SER* 2.9 21.0 + - - +
36C LEU* 3.2 20.4 + - + +
38C ARG* 1.3 74.8 - - + +
40C SER* 1.3 57.6 + - - +
42C ALA* 3.3 8.9 + - + +
43C GLN* 2.8 50.4 + - + +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 2.9 12.5 + - - -
37C LEU* 2.5 33.4 + - - +
39C VAL* 1.3 77.9 - - - +
41C VAL* 1.3 57.4 + - - +
43C GLN* 3.2 15.4 + - - +
44C ILE* 3.0 38.7 + - - +
65C LEU* 5.0 3.6 - - - +
129N THR* 6.2 0.4 - - - -
130N ILE* 3.9 33.5 - - - +
131N PRO* 5.7 1.8 - - - -
160N GLN* 5.9 0.4 - - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU 2.9 18.7 + - - +
38C ARG* 3.6 10.1 - - - +
40C SER* 1.3 77.1 + - - +
42C ALA* 1.3 57.2 + - - +
44C ILE* 3.2 9.8 + - + +
45C CYS* 2.9 35.0 + - - -
58C CYS* 4.1 31.2 - - + +
61C LEU* 5.5 7.0 - - + -
62C THR* 3.8 15.3 - - + +
65C LEU* 3.7 27.4 - - + -
163N ILE* 4.7 17.3 - - + -
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG 2.9 17.2 + - - +
39C VAL* 3.3 9.4 + - - +
41C VAL* 1.3 76.1 - - - +
43C GLN* 1.3 57.6 + - + +
45C CYS* 3.4 8.7 + - - +
46C GLN* 2.9 37.6 + - + +
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Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 2.8 38.5 + - + +
40C SER* 3.2 13.6 + - - +
42C ALA* 1.3 75.0 - - + +
44C ILE* 1.3 61.3 + - + +
46C GLN* 3.2 18.8 + - - +
47C ALA* 2.9 26.3 + - - +
118C THR* 4.5 12.4 - - - +
119C PHE 3.9 17.6 + - - -
120C PRO 5.0 5.5 - - - -
129N THR* 3.3 29.1 + - + +
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Residues in contact with ILE 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 SER* 3.0 20.8 + - - +
41C VAL* 3.2 7.8 + - + +
43C GLN* 1.3 75.7 - - + +
45C CYS* 1.3 58.7 + - - +
47C ALA* 3.2 8.2 + - + +
48C LEU* 2.9 40.0 + - + +
65C LEU* 6.2 0.7 - - + -
110C TYR* 4.6 2.2 - - - +
114C ILE* 5.9 6.3 - - + -
118C THR* 5.7 1.8 - - + -
130N ILE* 5.8 0.7 - - + -
160N GLN* 3.8 41.3 - - + -
163N ILE* 3.8 33.9 - - + -
164N SER* 3.5 22.4 - - - +
167N ALA* 5.6 0.2 - - + -
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Residues in contact with CYS 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 VAL* 2.9 33.3 + - - +
42C ALA* 3.7 8.1 - - - +
44C ILE* 1.3 74.9 - - - +
46C GLN* 1.3 54.9 + - - +
48C LEU* 3.5 1.3 - - - -
49C GLY 2.5 30.8 + - - -
50C TRP* 3.0 47.1 + - + +
53C VAL* 5.1 11.0 - - + -
58C CYS* 5.1 5.8 - - - -
163N ILE* 5.8 2.2 - - - -
167N ALA* 5.3 7.4 - - - -
195N LEU* 6.1 2.2 - - - -
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Residues in contact with GLN 46 (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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42C ALA* 2.9 23.4 + - + +
43C GLN* 3.2 22.5 + - - +
45C CYS* 1.3 73.4 - - - +
47C ALA* 1.3 66.8 + - - +
49C GLY* 3.6 10.4 + - - +
50C TRP 5.1 2.2 - - - +
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Residues in contact with ALA 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 GLN 2.9 12.5 + - - +
44C ILE* 3.2 11.2 + - + +
46C GLN* 1.3 77.4 - - - +
48C LEU* 1.3 66.1 + - + +
114C ILE* 4.7 13.2 - - + -
117C VAL* 5.2 10.6 - - + +
118C THR* 3.7 24.0 - - + +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 2.9 32.1 + - + +
45C CYS 3.9 2.7 - - - +
47C ALA* 1.3 83.0 - - + +
49C GLY* 1.3 59.7 + - - +
50C TRP* 4.1 13.9 - - - +
164N SER* 4.2 16.6 - - - +
167N ALA* 3.7 30.3 - - + -
168N ASN* 3.5 25.4 - - - +
171N LEU* 4.6 20.9 - - + +
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C CYS 2.5 15.3 + - - -
46C GLN* 4.0 8.7 - - - -
47C ALA 3.5 1.2 - - - -
48C LEU* 1.3 76.5 - - - +
50C TRP* 1.3 62.3 + - - +
51C ASP* 3.6 2.9 + - - +
171N LEU* 6.3 1.8 - - - -
192N LYS* 6.0 0.5 - - - +
193N TYR* 4.5 15.3 - - - -
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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