Contacts of the helix formed by residues 48 - 62 (chain C) in PDB entry 4U1D
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 VAL 48 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO* 6.0 0.7 - - + -
34C PHE* 4.5 12.6 - - + -
35C ILE* 4.4 14.8 - - + -
39C ARG* 5.2 4.5 - - - +
40C ILE* 4.1 33.2 - - + -
43C ALA* 3.7 29.4 - - + -
44C THR 3.8 7.4 - - - +
45C PRO* 3.3 4.8 + - + +
47C THR* 1.3 84.7 - - - +
49C GLU* 1.3 61.7 + - - +
50C PRO* 3.2 3.4 - - - -
51C VAL* 2.8 30.1 + - - +
52C VAL* 3.3 3.7 + - - +
75C TYR* 4.4 12.8 - - + -
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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
----------------------------------------------------------
45C PRO 3.0 16.0 + - - +
46C SER* 4.0 9.6 - - - +
48C VAL* 1.3 77.0 - - - +
50C PRO* 1.4 62.2 - - + +
52C VAL* 3.0 11.5 + - - +
53C PHE* 2.8 54.6 + - + -
75C TYR* 4.4 2.8 + - - -
88C SER* 3.2 25.5 + - - +
91C ALA* 3.2 29.1 - - - +
92C VAL* 3.8 8.5 - - + -
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Residues in contact with PRO 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 6.1 2.7 - - + -
12C ILE* 4.7 15.2 - - + +
46C SER 3.4 19.1 - - - +
47C THR* 4.0 4.7 - - - +
48C VAL 3.4 6.5 - - - +
49C GLU* 1.4 91.8 - - + +
51C VAL* 1.3 56.9 + - + +
53C PHE* 3.3 14.6 + - + +
54C LYS* 3.0 26.2 + - - +
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 3.6 42.6 - - + +
11C ALA* 4.4 2.2 - - + -
12C ILE* 4.5 7.2 - - + -
31C LEU* 3.7 26.1 - - + +
34C PHE* 3.7 22.4 - - + -
35C ILE* 3.6 21.5 - - + -
48C VAL 2.8 13.4 + - - +
50C PRO* 1.3 77.4 - - + +
52C VAL* 1.3 58.1 + - - +
54C LYS* 3.2 6.7 + - - +
55C PHE* 2.8 27.4 + - - +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.6 33.0 - - + -
48C VAL 3.8 9.6 - - - +
49C GLU* 3.0 8.2 + - - +
51C VAL* 1.3 73.6 - - - +
53C PHE* 1.3 61.7 + - - +
55C PHE* 3.3 5.6 + - - +
56C LEU* 2.9 34.5 + - + +
72C LEU* 4.5 4.5 - - + -
75C TYR* 3.8 34.5 - - + -
92C VAL* 3.5 37.0 - - + -
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Residues in contact with PHE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 2.8 42.1 + - + +
50C PRO* 3.3 16.4 - - + +
52C VAL* 1.3 75.9 - - - +
54C LYS* 1.3 56.4 + - - +
56C LEU* 3.1 8.2 + - + +
57C GLU* 2.9 36.4 + - - +
91C ALA* 4.1 5.8 - - + -
92C VAL* 3.6 20.9 - - + -
95C LYS* 3.5 53.9 - - + -
99C LEU* 4.7 0.5 - - - +
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Residues in contact with LYS 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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12C ILE* 4.5 25.8 - - + +
15C ALA* 4.9 4.0 - - + -
16C ASP* 3.4 31.2 + - - -
31C LEU* 3.6 18.6 - - + -
50C PRO 3.0 13.8 + - - +
51C VAL* 3.2 11.2 + - - +
53C PHE* 1.3 75.6 - - - +
55C PHE* 1.3 62.6 + - - +
57C GLU* 3.2 26.8 + - - +
58C ILE* 3.1 41.1 + - - +
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Residues in contact with PHE 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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28C LEU* 3.4 33.7 - - + +
31C LEU* 3.5 16.5 - - + +
32C HIS* 3.5 49.8 - + + -
35C ILE* 3.6 15.9 - - + -
51C VAL 2.8 13.2 + - - +
52C VAL* 3.4 10.5 - - - +
54C LYS* 1.3 77.0 - - - +
56C LEU* 1.3 70.9 + - + +
59C GLY* 3.0 23.2 + - - -
67C LEU* 3.4 26.5 - - + -
68C LEU* 3.9 20.5 - - + +
71C GLY* 4.0 17.3 - - - -
72C LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 2.9 19.7 + - + +
53C PHE* 3.1 8.9 + - + +
55C PHE* 1.3 94.4 - - + +
57C GLU* 1.3 65.1 + - - +
59C GLY* 3.9 0.2 - - - -
60C VAL* 3.0 30.0 + - - +
68C LEU* 4.0 10.9 - - + +
72C LEU* 3.9 20.2 - - + -
92C VAL* 3.3 35.9 - - + +
95C LYS* 4.1 9.9 - - + -
96C PHE* 3.5 32.8 - - + +
99C LEU* 3.4 11.7 - - + -
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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
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53C PHE* 2.9 22.8 + - - +
54C LYS* 3.2 36.3 + - - +
56C LEU* 1.3 78.4 - - - +
58C ILE* 1.3 64.9 + - + +
60C VAL* 3.5 2.9 + - - +
61C GLU* 3.4 25.8 + - - +
95C LYS* 4.3 18.1 + - - +
99C LEU* 3.5 19.7 - - + -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 4.4 11.0 - - + -
19C ILE* 4.8 12.1 - - + -
24C LYS* 4.3 4.3 - - + +
27C ALA* 4.7 10.3 - - + -
28C LEU* 3.7 32.5 - - + +
31C LEU* 3.6 28.7 - - + -
54C LYS* 3.1 27.4 + - + +
57C GLU* 1.3 78.8 - - + +
59C GLY* 1.3 61.3 + - - +
61C GLU* 3.2 7.7 + - - +
62C LEU* 3.1 35.7 + - + +
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.5 25.9 - - - +
55C PHE 3.0 15.2 + - - -
58C ILE* 1.3 76.4 - - - +
60C VAL* 1.3 57.5 + - - +
62C LEU 3.7 0.3 + - - -
63C LYS* 3.2 5.4 + - - -
64C LYS 3.0 27.2 + - - -
68C LEU* 3.7 20.8 - - - +
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Residues in contact with VAL 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 LEU 3.0 20.4 + - - +
57C GLU 3.8 3.6 - - - +
58C ILE 3.2 0.2 - - - -
59C GLY* 1.3 75.0 - - - +
61C GLU* 1.3 72.2 + - - +
63C LYS* 3.0 13.9 + - - +
68C LEU* 4.2 1.1 - - + -
96C PHE* 3.8 32.1 - - + -
99C LEU* 4.0 24.2 - - + +
100C VAL* 4.5 4.0 - - - +
103C LYS* 3.6 31.2 - - + -
154C TRP* 3.8 11.2 - - + -
157C PHE* 4.3 16.7 - - + -
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Residues in contact with GLU 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 3.4 15.2 - - - +
58C ILE* 3.2 9.3 + - - +
60C VAL* 1.3 80.8 - - - +
62C LEU* 1.3 66.7 + - + +
63C LYS* 3.3 1.9 + - - +
103C LYS* 3.3 39.8 + - - +
154C TRP* 4.3 12.8 - - - -
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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
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24C LYS* 3.6 60.6 - - + +
25C GLN* 3.9 11.0 - - + +
28C LEU* 4.2 8.7 - - + -
58C ILE* 3.1 28.3 + - + +
59C GLY 4.4 1.1 - - - +
61C GLU* 1.3 79.9 - - + +
63C LYS* 1.3 70.4 + - - +
64C LYS* 3.2 24.8 + - + +
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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