Contacts of the helix formed by residues 50 - 60 (chain C) in PDB entry 1WOI
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 PHE 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C GLY* 2.9 25.3 + - - +
49C ARG* 1.3 94.3 - - + +
51C ALA* 1.3 63.1 + - - +
52C PRO* 3.5 1.3 - - - -
53C ARG* 3.5 16.1 + - + +
54C ALA* 3.1 21.3 + - - +
277C PRO* 4.0 11.0 - - + -
278C ASN* 4.9 13.2 - - + -
44D PHE* 4.1 13.7 - + - -
45D ARG* 4.1 19.3 - - + -
46D PRO* 4.0 23.8 - - + -
9F TYR* 3.7 30.1 - - + -
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Residues in contact with ALA 51 (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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47C GLY 3.9 1.2 + - - -
48C ALA 3.0 10.2 + - - +
50C PHE* 1.3 75.9 - - - +
52C PRO* 1.3 60.8 - - - +
54C ALA* 3.1 1.3 + - - -
55C LEU* 2.7 37.7 + - + +
118C GLY 3.1 23.8 - - - +
275C LEU* 3.4 37.2 - - + +
277C PRO* 4.0 9.8 - - - +
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Residues in contact with PRO 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY* 4.2 0.9 - - - -
36C VAL 4.0 0.7 - - - +
37C PRO* 3.9 21.1 - - + -
48C ALA 3.6 3.6 - - - +
49C ARG 3.5 14.6 - - - +
50C PHE 3.6 0.4 - - - -
51C ALA* 1.3 90.0 - - + +
53C ARG* 1.3 56.9 + - - +
55C LEU* 3.3 1.9 + - - +
56C ARG* 2.9 51.8 + - - +
85C ASP* 4.1 9.9 - - - +
117C LEU* 3.3 42.2 - - + +
118C GLY 3.3 8.3 - - - +
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Residues in contact with ARG 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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13C PRO* 5.6 0.4 - - + -
49C ARG 5.9 0.2 - - - +
50C PHE* 3.5 17.6 + - + +
51C ALA 3.2 0.6 - - - -
52C PRO* 1.3 79.8 - - - +
54C ALA* 1.3 63.8 + - - +
56C ARG* 3.3 13.6 + - + +
57C GLU* 3.0 42.9 + - + +
85C ASP* 5.2 0.2 + - - -
44D PHE* 6.2 1.0 - - - -
8F PRO 3.2 22.4 + - - -
9F TYR* 3.4 23.1 + - - +
10F GLY 3.3 16.2 + - - -
11F GLY 2.9 28.6 + - - +
13F PRO* 3.9 19.3 - - + +
57F GLU* 4.0 30.4 + - - +
60F LEU* 3.4 16.5 - - - +
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Residues in contact with ALA 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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50C PHE 3.1 8.5 + - - +
51C ALA* 3.1 3.1 + - - +
53C ARG* 1.3 76.8 - - - +
55C LEU* 1.3 59.0 + - - +
57C GLU* 3.4 13.1 + - - +
58C ALA* 2.9 29.8 + - - +
275C LEU* 4.7 0.4 - - + -
277C PRO* 3.5 38.6 - - + -
286C GLU* 4.1 19.7 - - + +
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Residues in contact with LEU 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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15C PHE* 4.3 6.3 - - + -
51C ALA* 2.7 34.0 + - + +
52C PRO 3.6 4.0 - - - +
54C ALA* 1.3 71.6 - - - +
56C ARG* 1.3 59.2 - - - +
58C ALA* 3.4 3.9 + - - +
59C SER* 2.8 29.6 + - - -
117C LEU* 3.9 38.4 - - + -
118C GLY 4.5 2.0 - - - +
272C LEU* 4.0 20.2 - - + -
275C LEU* 3.8 22.4 - - + -
286C GLU 4.1 3.8 - - - +
289C MET* 4.0 13.5 - - + +
290C ALA* 3.8 29.4 - - - +
293C VAL* 5.6 1.1 - - + -
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Residues in contact with ARG 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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13C PRO* 3.5 30.1 - - + +
14C THR 4.0 0.9 - - - +
15C PHE* 3.8 16.3 - - + +
33C ALA* 5.0 0.8 + - - +
34C LEU* 4.6 1.6 - - - +
35C GLY* 3.7 7.4 - - - +
52C PRO* 2.9 38.4 + - - +
53C ARG* 3.6 10.6 - - + +
55C LEU* 1.3 76.1 - - - +
57C GLU* 1.3 64.3 + - - +
59C SER* 2.6 25.2 + - - -
60C LEU* 3.5 11.3 + - - +
82C ASP* 2.8 32.6 + - - -
84C GLY 2.9 31.3 + - - -
85C ASP* 2.8 26.4 + - - -
117C LEU* 4.5 9.7 - - + +
11F GLY 5.0 2.8 + - - -
12F ILE* 3.3 17.0 - - - +
13F PRO* 5.8 2.0 - - - -
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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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44A PHE* 6.0 1.0 - - - -
8C PRO* 4.8 1.0 - - - +
13C PRO* 3.8 25.6 - - + +
53C ARG* 3.0 27.8 + - - +
54C ALA* 3.6 10.9 - - - +
56C ARG* 1.3 77.7 - - - +
58C ALA* 1.3 61.7 + - - +
60C LEU* 3.2 23.5 + - - +
61C ARG* 4.5 2.6 + - - +
53F ARG* 4.0 21.8 + - - +
57F GLU* 2.5 30.6 - - - +
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Residues in contact with ALA 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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44A PHE* 6.2 0.7 - - - -
54C ALA 2.9 18.5 + - - +
55C LEU 3.8 0.7 - - - +
57C GLU* 1.3 77.5 - - - +
59C SER* 1.3 61.3 + - - +
60C LEU 3.1 0.2 - - - -
61C ARG* 3.1 23.2 + - - +
62C SER* 4.2 1.9 + - - -
286C GLU* 3.2 37.9 - - + +
287C LEU* 3.8 21.0 - - + +
290C ALA* 3.5 10.9 - - + +
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C THR 3.8 0.9 + - - -
15C PHE* 3.6 21.3 - - - -
16C ALA* 2.9 30.1 + - - -
55C LEU 2.8 15.6 + - - -
56C ARG 2.6 20.1 + - - -
58C ALA* 1.3 72.1 - - - +
60C LEU* 1.3 56.4 + - - +
61C ARG 3.0 6.3 - - - -
62C SER* 2.8 33.7 + - - +
63C VAL* 3.5 4.0 + - - +
290C ALA* 3.7 9.4 - - - +
294C MET* 5.3 2.5 - - - -
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Residues in contact with LEU 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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8C PRO* 3.3 28.6 - - + +
10C GLY 4.0 8.7 - - - +
13C PRO* 4.1 16.4 - - + -
14C THR 3.8 18.8 - - - +
17C ARG* 3.3 43.6 + - + +
56C ARG 3.6 5.8 - - - +
57C GLU 3.4 13.5 - - - +
58C ALA 3.1 1.4 - - - -
59C SER* 1.3 77.4 + - - +
61C ARG* 1.3 57.9 + - - +
62C SER 3.2 1.3 - - - -
63C VAL* 3.5 16.4 - - - +
53F ARG* 3.3 35.7 - - - +
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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