Contacts of the helix formed by residues 33 - 52 (chain C) in PDB entry 6S1M
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 HIS 33 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 3.9 31.6 + - + +
22B ALA 3.9 13.9 + - - -
23B THR* 4.2 15.6 - - + +
232B GLN* 5.6 0.2 - - - -
27C SER* 4.7 0.2 - - - -
32C VAL* 1.3 81.4 - - - +
34C VAL* 1.3 74.8 + - + +
35C ASN* 3.1 42.7 + - + +
36C GLN* 4.2 6.9 + - + +
37C ALA* 3.1 24.8 + - - +
132C PHE* 4.5 19.5 + - - -
133C SER 5.6 0.4 - - - -
134C ALA* 4.7 13.4 - - + -
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY 5.7 1.1 - - - +
225B GLN* 3.3 44.0 - - - +
232B GLN* 5.8 0.9 - - - +
23C TYR* 3.5 22.6 - - + -
24C LYS* 6.1 1.6 - - + -
27C SER* 4.6 11.4 - - - +
32C VAL 4.7 0.2 - - - -
33C HIS* 1.3 79.1 + - + +
35C ASN* 1.3 67.1 + - - +
37C ALA* 3.1 8.1 + - - +
38C LYS* 3.1 34.1 + - - +
132C PHE* 3.2 29.8 - - + +
133C SER* 5.3 0.2 - - - -
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.5 20.1 - - + +
21B ASN* 4.3 15.4 - - + +
22B ALA 4.5 6.5 + - - +
227B GLY 4.0 1.6 - - - +
228B ASP* 5.9 0.2 - - - -
229B GLU* 4.5 12.3 + - - +
232B GLN* 3.2 31.7 + - - +
33C HIS* 3.1 24.1 + - + +
34C VAL* 1.3 75.2 - - - +
36C GLN* 1.3 57.5 + - - +
38C LYS* 2.9 30.2 + - - +
39C GLN* 3.0 33.4 + - - +
134C ALA* 5.3 0.2 - - - +
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 4.4 15.8 - - + +
18B SER 4.6 11.6 + - - +
19B ALA 5.4 2.4 - - - +
21B ASN* 3.4 24.5 + - - +
32C VAL* 3.6 20.4 - - + +
33C HIS* 3.6 8.3 + - + +
34C VAL 3.3 0.4 - - - -
35C ASN* 1.3 77.6 - - - +
37C ALA* 1.3 57.7 + - - +
39C GLN* 3.4 16.6 + - - +
40C MET* 2.9 54.3 + - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 3.9 25.1 - - + +
26C LEU* 4.4 13.6 - - + +
27C SER* 4.1 9.9 - - - -
32C VAL* 4.1 4.7 - - + +
33C HIS 3.1 15.9 + - - +
34C VAL 3.1 9.4 + - - +
36C GLN* 1.3 74.6 - - - +
38C LYS* 1.3 64.6 + - - +
40C MET* 3.3 11.4 + - - +
41C LEU* 3.0 28.9 + - - +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 30.2 - - + +
225B GLN 3.5 12.1 + - - -
227B GLY 3.9 15.8 + - - +
232B GLN* 4.2 0.6 - - - +
23C TYR* 4.1 15.9 - - + -
34C VAL* 3.1 35.6 + - - +
35C ASN* 2.9 28.9 + - - +
37C ALA* 1.3 77.5 - - - +
39C GLN* 1.3 56.4 + - - +
41C LEU* 3.3 10.2 + - - +
42C TYR* 3.0 28.2 + - - +
99C HIS* 3.7 37.5 - - + +
100C VAL* 4.2 13.2 - - - +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.6 24.2 + - - +
13B LEU* 4.0 19.3 - - + +
15B SER* 3.3 26.2 - - - +
16B PRO 4.0 10.8 + - - -
17B PRO* 3.7 21.3 - - + +
18B SER* 3.8 12.3 + - - -
21B ASN* 3.4 17.2 + - - +
35C ASN* 3.0 14.9 + - - +
36C GLN* 3.4 21.8 - - - +
38C LYS* 1.3 73.9 - - - +
40C MET* 1.3 59.5 + - - +
42C TYR* 3.4 2.5 + - - +
43C ASP* 2.9 29.3 + - - +
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 4.0 16.6 - - + +
6C TYR* 4.0 48.5 - - + -
10C ILE* 4.5 2.9 - - + +
26C LEU* 4.8 13.5 - - + +
30C LEU* 4.6 11.7 - - + -
32C VAL* 3.8 27.8 - - + -
36C GLN* 2.9 42.8 + - - +
37C ALA* 3.4 12.6 - - - +
39C GLN* 1.3 76.6 - - - +
41C LEU* 1.3 57.5 + - - +
43C ASP* 3.2 3.9 + - - +
44C TYR* 3.0 27.7 + - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 5.0 6.3 - - + -
21C VAL* 4.8 8.3 - - + +
22C THR 4.4 3.8 - - - +
23C TYR* 4.0 32.8 - - + +
26C LEU* 3.7 22.0 - - + -
37C ALA 3.0 15.1 + - - +
38C LYS* 3.7 8.5 - - - +
40C MET* 1.3 77.1 - - - +
42C TYR* 1.3 58.5 + - - +
44C TYR* 3.4 5.6 + - + +
45C VAL* 3.0 30.0 + - - +
100C VAL* 4.6 19.4 - - + +
101C TYR 4.7 8.1 - - - +
103C ILE* 3.8 41.8 - - + +
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 4.8 4.9 - - - +
14B LEU* 3.2 42.0 + - + -
15B SER* 3.3 32.5 - - - +
16B PRO* 4.0 5.4 - - + -
38C LYS 3.0 15.9 + - - +
39C GLN* 3.8 3.6 - - - +
40C MET 3.3 0.2 - - - -
41C LEU* 1.3 73.6 - - - +
43C ASP* 1.3 61.8 + - - +
45C VAL* 3.3 13.6 - - + +
46C GLU* 2.9 64.9 + - + +
100C VAL* 4.4 15.4 - - + +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 4.3 15.3 - - + +
17B PRO* 3.6 13.3 - - + +
3C ASP* 3.9 9.0 - - - +
6C TYR* 2.3 33.5 + - + +
7C LEU* 6.3 0.9 - - - -
39C GLN 2.9 14.3 + - - +
40C MET 3.2 8.3 + - - +
42C TYR* 1.3 80.3 - - - +
44C TYR* 1.3 62.1 + - - +
46C GLU* 3.3 6.4 + - - +
47C ARG* 3.0 48.5 + - - +
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Residues in contact with TYR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 5.1 4.6 - - + -
7C LEU* 4.4 22.0 - - + -
10C ILE* 3.6 42.8 - - + -
11C ASP* 3.5 26.0 + - - -
14C VAL* 4.7 4.1 - - + +
15C THR* 4.1 14.4 - - - +
40C MET 3.0 15.2 + - - +
41C LEU* 3.8 4.3 - - - +
43C ASP* 1.3 75.8 - - - +
45C VAL* 1.3 69.1 + - + +
47C ARG* 3.9 4.5 - - - +
48C LYS* 3.0 56.8 + - + +
57C LEU* 4.3 19.3 - - + +
103C ILE* 4.1 21.3 - - + -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 3.0 17.1 + - - +
42C TYR* 3.3 25.4 - - + +
44C TYR* 1.3 81.7 - - + +
46C GLU* 1.3 61.6 + - - +
49C ARG* 2.9 49.5 + - + +
57C LEU* 3.8 22.0 - - + -
59C VAL* 3.8 29.6 - - + -
61C TYR* 6.6 0.2 - - + -
100C VAL* 5.4 7.9 - - + -
103C ILE* 5.0 5.6 - - + -
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Residues in contact with GLU 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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16B PRO* 4.6 10.0 - - - +
42C TYR* 2.9 58.5 + - + +
43C ASP* 3.8 6.0 - - - +
45C VAL* 1.3 79.0 - - - +
47C ARG* 1.3 57.5 + - + +
49C ARG* 4.2 2.6 - - - +
50C LYS* 2.9 36.3 + - + +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASP* 2.7 39.1 + - - -
4C GLN* 4.7 5.1 + - - -
7C LEU* 3.8 22.0 - - + +
43C ASP* 3.0 37.2 + - - +
44C TYR* 3.9 4.5 - - - +
46C GLU* 1.3 78.1 - - + +
48C LYS* 1.3 61.9 + - + +
50C LYS* 3.8 3.7 - - - +
51C GLU* 3.0 31.7 + - - +
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.6 20.1 - - - +
8C GLU* 5.8 0.4 + - - -
11C ASP* 3.8 19.2 + - - +
44C TYR* 3.0 51.7 + - + +
45C VAL 3.8 1.1 - - - +
47C ARG* 1.3 80.4 - - + +
49C ARG* 1.3 60.4 + - - +
51C GLU* 3.4 27.3 + - - +
52C ASN* 3.9 19.2 + - - +
53C SER 4.4 1.0 + - - -
55C ALA* 4.6 13.1 - - + +
57C LEU* 4.8 11.0 - - + -
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 2.9 38.4 + - + +
46C GLU* 4.2 3.4 - - - +
48C LYS* 1.3 77.7 - - - +
50C LYS* 1.3 61.8 + - - +
51C GLU 3.5 0.2 - - - -
53C SER* 3.7 31.7 + - - +
55C ALA* 6.1 2.6 - - + +
57C LEU* 3.4 39.4 + - + +
58C HIS* 4.4 0.6 - - - +
59C VAL* 3.7 35.7 - - - +
61C TYR* 4.7 5.9 + - - -
82C GLU* 5.7 3.2 - - - +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 2.9 21.0 + - + +
47C ARG* 3.9 3.8 - - - +
49C ARG* 1.3 76.6 - - - +
51C GLU* 1.3 64.1 + - - +
52C ASN 5.3 0.2 - - - -
53C SER* 5.1 0.6 + - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ARG 3.0 16.2 + - - +
48C LYS* 3.4 37.4 + - - +
49C ARG 3.5 0.4 - - - -
50C LYS* 1.3 79.6 - - - +
52C ASN* 1.3 75.4 + - + +
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Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LYS 3.9 10.3 + - - +
50C LYS 3.5 0.4 - - - -
51C GLU* 1.3 96.5 + - + +
53C SER* 1.3 69.5 + - - +
54C GLY* 3.2 25.7 + - - +
55C ALA* 4.5 7.4 - - + +
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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