Contacts of the helix formed by residues 40 - 58 (chain C) in PDB entry 6PSI
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 SER 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PRO 4.4 1.4 + - - -
38C ASN* 2.8 26.3 + - - +
39C LYS* 1.3 77.2 + - - +
41C PRO* 1.4 62.7 - - - +
42C GLU* 3.1 7.2 - - - -
43C ALA* 2.8 38.2 + - - +
44C GLU* 3.1 14.3 + - - +
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Residues in contact with PRO 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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39C LYS 4.4 3.4 - - - +
40C SER* 1.4 81.6 - - - +
42C GLU* 1.3 62.0 + - - +
44C GLU* 3.0 32.9 + - + +
45C GLU* 3.0 25.5 + - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 4.6 7.9 - - - +
41C PRO* 1.3 79.5 - - - +
43C ALA* 1.3 57.5 + - - +
45C GLU* 3.3 13.4 + - - +
46C LYS* 2.8 71.1 + - + +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.1 34.9 - - + +
38C ASN* 3.3 33.7 - - - +
40C SER* 2.8 18.8 + - - +
42C GLU* 1.3 76.3 - - - +
44C GLU* 1.3 56.4 + - + +
46C LYS* 3.8 8.0 - - - -
47C PHE* 2.8 23.1 + - - +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR 4.4 1.3 - - - -
35C PRO* 3.4 43.6 - - + +
40C SER 3.4 13.0 + - - +
41C PRO* 3.0 32.7 + - + +
43C ALA* 1.3 77.7 - - - +
45C GLU* 1.3 58.4 + - + +
47C PHE* 3.3 9.6 - - - +
48C LYS* 2.9 38.3 + - - +
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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 PRO* 3.0 19.3 + - - +
42C GLU* 3.7 20.5 - - - +
44C GLU* 1.3 75.2 - - + +
46C LYS* 1.3 76.5 - - - +
47C PHE 3.3 0.2 - - - -
48C LYS* 3.2 19.5 + - + +
49C GLU* 3.1 25.3 + - - +
92C ASP* 4.6 15.1 - - - +
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Residues in contact with LYS 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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33C TYR* 4.1 30.3 - - + +
42C GLU* 2.8 53.7 + - + +
43C ALA* 3.8 5.8 - - - +
45C GLU* 1.3 90.3 + - - +
47C PHE* 1.4 55.2 + - - +
49C GLU* 3.1 34.4 + - - +
50C ILE* 3.0 33.3 + - + +
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Residues in contact with PHE 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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312B PRO* 5.3 13.5 - - + -
26C TYR* 4.7 6.7 - - - -
29C LEU 4.1 2.5 - - - -
30C ALA* 3.6 38.6 - - + -
33C TYR* 3.3 24.0 - - + +
34C HIS* 4.6 9.0 - + - -
35C PRO* 3.7 27.8 - - + -
43C ALA 2.8 20.3 + - - +
44C GLU* 3.3 9.4 - - - +
45C GLU 3.3 0.2 - - - -
46C LYS* 1.4 71.9 - - - +
48C LYS* 1.3 61.1 + - + +
50C ILE* 3.3 9.4 + - + +
51C ASN* 2.9 66.9 + - - +
87C GLY 5.1 1.8 - - - -
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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
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44C GLU* 2.9 28.9 + - - +
45C GLU* 3.2 18.4 + - - +
47C PHE* 1.3 79.7 - - + +
49C GLU* 1.3 51.8 + - + +
51C ASN* 3.2 5.5 + - - -
52C GLU* 2.7 29.8 + - - +
89C ASP* 2.9 38.8 + - + +
92C ASP* 3.0 36.3 + - + +
93C PHE* 3.0 26.5 - - + -
109C PHE* 6.2 0.2 - - - -
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Residues in contact with GLU 49 (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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5C LYS* 2.9 32.0 + - - +
10C ILE* 3.2 28.0 - - + +
45C GLU 3.1 10.4 + - - +
46C LYS* 3.1 40.6 + - - +
48C LYS* 1.3 75.3 - - + +
50C ILE* 1.4 56.1 + - + +
52C GLU* 3.3 11.1 - - - +
53C ALA 3.1 23.0 + - - -
93C PHE* 5.3 0.7 - - + -
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Residues in contact with ILE 50 (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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10C ILE* 3.9 13.2 - - + +
11C LEU* 3.6 19.3 - - + +
26C TYR* 3.6 37.5 - - + +
29C LEU* 3.6 36.8 - - + +
30C ALA* 4.3 0.9 - - - +
33C TYR* 3.6 26.2 - - + -
46C LYS* 3.0 17.6 + - + +
47C PHE* 3.4 11.0 - - + +
49C GLU* 1.4 77.2 - - + +
51C ASN* 1.3 57.8 + - - +
54C TYR* 3.0 28.9 + - - +
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.4 22.1 + - - -
47C PHE* 2.9 54.6 + - - +
48C LYS* 3.4 8.3 - - - +
50C ILE* 1.3 72.6 - - - +
52C GLU* 1.3 59.2 + - - +
54C TYR* 4.2 5.4 - - - -
55C ALA* 2.9 29.3 + - - +
87C GLY 3.1 24.9 + - - -
88C PHE* 3.5 25.5 - - + +
89C ASP 5.3 0.2 - - - +
93C PHE* 3.9 7.4 - - + -
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 2.9 27.0 + - - -
7C TYR* 3.4 13.2 - - + -
10C ILE* 3.4 17.3 - - - +
48C LYS 2.7 18.4 + - - +
49C GLU* 3.3 7.5 - - - +
51C ASN* 1.3 71.5 - - - +
53C ALA* 1.3 65.4 + - - +
55C ALA* 3.0 11.4 + - - +
56C VAL* 3.1 20.5 + - - +
93C PHE* 3.4 23.6 - - + +
94C SER* 3.1 39.2 + - - -
97C PHE* 3.5 22.1 - - + +
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Residues in contact with ALA 53 (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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7C TYR* 3.4 46.2 - - + +
10C ILE* 4.1 4.7 - - + -
11C LEU* 3.6 21.5 - - + -
49C GLU 3.1 13.1 + - - +
50C ILE 3.9 0.2 - - - +
52C GLU* 1.3 80.4 - - - +
54C TYR* 1.3 57.1 + - - +
56C VAL* 3.3 2.6 + - - +
57C LEU* 2.9 34.5 + - - +
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Residues in contact with TYR 54 (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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358B CYS* 4.3 9.7 - - - -
11C LEU* 4.2 6.0 - - + +
22C ILE* 5.2 1.1 - - + -
23C LYS* 3.7 42.3 - - + +
26C TYR* 3.7 48.9 - + + -
50C ILE 3.0 19.3 + - - +
51C ASN 4.1 2.9 - - - +
53C ALA* 1.3 75.1 - - - +
55C ALA* 1.3 58.7 + - - +
57C LEU* 4.2 5.4 - - - +
58C SER* 2.7 67.0 + - - +
88C PHE* 3.6 31.9 - + - -
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Residues in contact with ALA 55 (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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51C ASN 2.9 23.1 + - - +
52C GLU* 3.0 10.1 + - - +
54C TYR* 1.3 76.7 - - - +
56C VAL* 1.3 58.2 + - - +
58C SER* 4.5 3.0 + - - -
62C LYS* 3.4 27.5 + - - +
85C PHE* 3.7 26.0 - - + -
88C PHE* 3.7 29.1 - - + -
93C PHE* 4.5 0.2 - - + -
97C PHE* 4.3 5.4 - - + -
101C PHE* 5.2 0.6 - - - -
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Residues in contact with VAL 56 (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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7C TYR* 3.6 37.5 - - + -
52C GLU 3.1 16.4 + - - +
53C ALA 4.0 0.7 - - - +
55C ALA* 1.3 75.5 - - - +
57C LEU* 1.4 63.5 + - - +
62C LYS* 2.8 44.9 - - - +
63C ARG 3.2 0.5 + - - -
65C ILE* 5.1 0.7 - - + -
66C TYR* 3.8 15.5 - - + +
97C PHE* 3.5 24.0 - - + -
100C LEU* 4.4 5.6 - - + -
101C PHE* 3.6 24.5 - - + -
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Residues in contact with LEU 57 (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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7C TYR* 3.7 36.8 - - + +
8C TYR* 4.2 10.5 - - + +
19C GLN* 3.3 23.3 - - - +
22C ILE* 3.5 43.5 - - + +
53C ALA 2.9 16.5 + - - +
54C TYR* 3.1 6.0 + - - -
56C VAL* 1.4 87.8 - - - +
58C SER* 1.3 57.7 + - - +
59C ASP 3.8 1.1 - - - -
63C ARG* 3.4 37.0 - - - +
66C TYR* 3.7 21.8 - - + -
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Residues in contact with SER 58 (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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19C GLN* 3.1 23.2 + - - +
54C TYR* 2.7 59.1 + - - -
55C ALA* 4.5 4.9 - - - -
56C VAL 3.8 1.4 - - - -
57C LEU* 1.3 72.4 - - - +
59C ASP* 1.3 78.1 + - - +
88C PHE* 5.2 4.6 - - - -
146C SER* 4.8 1.6 + - - -
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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
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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