Contacts of the helix formed by residues 16 - 32 (chain C) in PDB entry 3P3W
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 THR 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.8 14.0 - - - +
13C MET* 3.1 33.6 + - + +
14C ARG 3.6 10.3 - - - +
15C ASN* 1.3 81.8 - - - +
17C VAL* 1.3 62.7 + - - +
18C GLN 3.6 1.3 - - - -
19C GLU* 3.6 29.4 - - - +
20C HIS* 3.4 22.9 + - - +
76C PHE* 4.4 21.1 - - + -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN* 3.7 8.5 - - - +
16C THR* 1.3 77.6 - - - +
18C GLN* 1.3 66.4 + - - +
19C GLU 3.2 1.8 - - - -
20C HIS* 3.1 19.0 + - + +
21C SER* 3.3 14.2 + - - -
268C PRO* 3.8 27.0 - - + +
269C GLU* 3.8 25.1 - - + -
276C LYS* 6.0 1.0 - - - +
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 1.3 77.7 - - - +
19C GLU* 1.3 72.0 + - - +
22C ALA* 3.3 20.8 + - - +
259C TRP* 3.3 22.6 - - - +
268C PRO 4.9 1.3 - - - -
269C GLU* 2.8 46.2 + - + +
273C ALA* 3.0 24.5 + - + -
274C PRO 3.2 16.8 + - - -
275C LEU* 4.0 4.3 - - - +
276C LYS* 4.2 24.8 - - + +
279C SER* 3.1 21.8 + - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.2 2.0 - - - -
15C ASN 4.4 2.8 - - - +
16C THR* 3.6 32.5 - - - +
17C VAL 3.2 0.6 - - - -
18C GLN* 1.3 90.8 + - - +
20C HIS* 1.3 57.2 + - - +
22C ALA* 3.2 2.4 + - - +
23C PHE* 2.7 36.7 + - - +
76C PHE* 3.6 32.8 - - + -
276C LYS* 4.2 7.2 + - - +
278C THR* 3.1 48.2 + - - +
279C SER* 4.1 6.9 - - - +
282C THR* 3.9 5.4 + - + +
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Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.0 23.5 - + + -
16C THR 3.4 14.5 + - - +
17C VAL* 3.1 15.8 + - + +
19C GLU* 1.3 79.1 - - - +
21C SER* 1.3 61.8 + - - +
23C PHE* 3.5 5.0 + + - +
24C ARG* 3.1 45.9 + - + +
47C VAL* 3.8 30.2 - - + +
49C HIS* 3.9 22.1 - + - -
266C GLU 6.0 0.2 + - - -
268C PRO* 6.0 2.6 - - + +
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL 3.3 5.7 + - - -
20C HIS* 1.3 79.6 + - - +
22C ALA* 1.3 56.0 + - - +
24C ARG* 4.0 7.4 - - - +
25C PHE* 2.8 35.7 + - - +
259C TRP* 3.6 18.8 - - - -
266C GLU 4.4 0.7 + - - -
267C PHE* 3.4 20.1 - - - -
268C PRO* 3.1 44.0 + - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLN 3.3 18.5 + - - +
19C GLU 3.2 1.9 + - - +
21C SER* 1.3 76.5 - - - +
23C PHE* 1.3 63.0 + - - +
25C PHE* 4.4 1.5 - - - +
26C ALA* 3.3 24.1 + - - +
255C PHE* 4.7 9.4 - - + -
259C TRP* 3.6 17.0 - - + -
275C LEU* 5.2 0.7 - - + -
279C SER* 3.4 17.0 - - - +
282C THR* 3.3 21.6 + - - +
283C HIS* 4.6 5.6 - - - +
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Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.1 33.0 - - + -
10C GLY* 4.8 6.5 - - - -
12C PHE* 3.6 29.4 - + + -
19C GLU 2.7 17.5 + - - +
20C HIS* 3.6 6.1 - + - +
22C ALA* 1.3 76.7 - - - +
24C ARG* 1.3 61.8 + - + +
26C ALA* 3.9 2.4 + - - +
27C VAL* 3.5 25.0 + - + +
45C TYR* 3.6 34.8 - + + -
47C VAL* 5.2 0.9 - - + -
74C PHE* 3.5 39.9 - + + -
282C THR* 4.1 9.4 + - - -
286C ILE* 3.6 28.4 - - + +
289C ILE* 5.7 1.3 - - + -
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C HIS* 3.1 37.3 + - + +
21C SER* 3.3 9.6 + - - +
23C PHE* 1.3 76.5 - - + +
25C PHE* 1.3 63.7 + - - +
27C VAL* 3.2 15.6 + - - +
28C GLN* 3.3 23.3 + - - +
45C TYR* 3.1 38.3 + - + +
266C GLU* 3.5 32.2 + - - +
267C PHE* 3.6 30.4 - - + -
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Residues in contact with PHE 25 (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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21C SER 2.8 20.9 + - - +
22C ALA* 4.4 2.5 - - - +
23C PHE 3.5 0.2 - - - -
24C ARG* 1.3 73.6 - - - +
26C ALA* 1.3 57.4 + - - +
28C GLN* 3.1 16.9 + - + -
29C LEU* 3.0 57.0 + - + +
255C PHE* 3.7 26.5 - + - -
258C ARG* 3.8 30.3 - - + -
259C TRP* 3.9 35.4 - + + -
262C LEU* 3.8 26.2 - - + -
267C PHE* 3.5 16.8 - + + -
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Residues in contact with ALA 26 (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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22C ALA 3.3 17.1 + - - +
23C PHE 4.1 0.7 - - - +
24C ARG 3.3 0.2 - - - -
25C PHE* 1.3 78.6 - - - +
27C VAL* 1.3 60.1 + - - +
29C LEU* 3.8 7.8 - - - +
30C TYR* 3.4 20.1 + - - +
255C PHE* 5.2 0.6 - - - -
283C HIS* 3.6 31.7 + - + +
286C ILE* 3.9 37.0 - - + +
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 6.2 0.4 - - + -
23C PHE* 3.5 19.5 - - + +
24C ARG 3.2 8.2 + - - +
25C PHE 3.2 0.6 - - - -
26C ALA* 1.3 76.7 - - - +
28C GLN* 1.3 53.4 + - - +
30C TYR* 3.1 6.5 + - - +
31C ASN* 2.7 57.8 + - - +
43C LEU* 3.9 31.0 - - + +
45C TYR* 4.1 35.2 - - + -
286C ILE* 4.3 9.9 - - + -
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Residues in contact with GLN 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 3.3 20.9 + - - +
25C PHE* 3.1 25.3 + - + +
27C VAL* 1.3 77.7 - - - +
29C LEU* 1.3 59.5 + - - +
31C ASN* 3.7 7.5 + - + +
32C THR* 3.1 32.1 + - + +
262C LEU* 5.0 3.5 - - - +
267C PHE* 3.5 30.5 - - - -
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Residues in contact with LEU 29 (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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25C PHE* 3.0 64.8 + - + +
26C ALA* 3.8 11.4 - - - +
28C GLN* 1.3 77.3 - - - +
30C TYR* 1.3 56.9 + - - +
32C THR* 2.7 29.9 + - - +
33C ASN* 4.1 3.1 + - - +
255C PHE* 4.9 8.5 - - + -
258C ARG* 5.8 8.1 - - - -
283C HIS* 4.4 18.4 - - + -
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Residues in contact with TYR 30 (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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26C ALA 3.4 11.5 + - - +
27C VAL* 3.1 9.2 + - - +
29C LEU* 1.3 79.5 - - - +
31C ASN* 1.3 66.4 + - - +
32C THR 3.4 0.9 + - - -
33C ASN* 3.5 27.1 + - - +
40C PRO* 4.4 10.0 - - + +
41C PHE* 3.1 60.5 + + - -
43C LEU* 3.7 40.6 - - + -
286C ILE* 4.9 9.2 - - + -
290C ALA* 4.3 15.0 - - + -
294C ARG* 3.3 26.7 + - - -
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Residues in contact with ASN 31 (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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27C VAL* 2.7 39.5 + - - +
28C GLN* 4.2 7.5 - - + +
29C LEU 3.4 0.4 - - - -
30C TYR* 1.3 75.2 - - - +
32C THR* 1.3 60.2 + - + +
33C ASN 3.5 5.4 + - - +
42C HIS* 3.6 36.8 + - + +
43C LEU* 3.6 31.1 + - - +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLN* 3.1 18.7 + - + +
29C LEU* 2.7 27.5 + - - +
31C ASN* 1.3 75.9 - - + +
33C ASN* 1.3 82.4 - - - +
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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
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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