Contacts of the helix formed by residues 14 - 33 (chain A) in PDB entry 3CWR
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 ASP 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL 4.6 3.2 - - - +
13A PRO* 1.3 69.8 - - - +
15A ALA* 1.3 64.1 + - - +
16A VAL 3.1 0.7 + - - -
17A VAL* 3.3 4.7 + - - +
18A ARG* 3.0 42.7 + - - +
55A ARG* 2.9 44.8 + - - -
56A PHE* 3.7 11.3 - - + -
157B PRO* 6.1 0.2 - - - +
160B ARG* 3.8 25.3 + - - -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.1 9.3 - - + +
14A ASP* 1.3 77.8 - - - +
16A VAL* 1.3 63.9 + - + +
18A ARG* 3.7 20.9 - - - +
19A GLU* 3.0 40.3 + - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.2 31.2 - - + -
13A PRO* 3.5 13.0 - - + +
14A ASP 3.1 1.0 + - - -
15A ALA* 1.3 80.5 - - + +
17A VAL* 1.3 68.8 + - + +
19A GLU* 3.3 14.3 + - - +
20A SER* 3.3 18.9 + - - -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO 4.4 0.8 + - - +
14A ASP* 3.3 7.7 + - - +
16A VAL* 1.3 81.1 - - + +
18A ARG* 1.3 67.8 + - - +
20A SER* 3.0 7.4 + - - -
21A ILE* 3.0 32.7 + - + +
48A ILE* 4.2 20.4 - - + -
52A THR* 3.9 19.3 - - + -
56A PHE* 3.7 26.2 - - + -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.0 33.0 + - - +
15A ALA* 3.7 25.3 - - - +
17A VAL* 1.3 76.9 - - - +
19A GLU* 1.3 62.8 + - + +
21A ILE* 3.2 7.7 + - - +
22A VAL* 3.0 30.9 + - + +
56A PHE* 3.9 28.5 - - + -
66A LEU* 4.4 25.3 - - + +
69A GLU* 4.8 8.2 + - - -
159B GLU* 5.9 4.8 - - - +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.0 30.5 + - - +
16A VAL* 3.5 14.4 - - - +
17A VAL 3.2 0.2 - - - -
18A ARG* 1.3 76.8 - - - +
20A SER* 1.3 62.9 + - - +
22A VAL* 3.3 13.0 - - + +
23A GLY* 3.0 21.1 + - - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL 3.3 9.6 + - - -
17A VAL* 3.0 13.1 + - - -
19A GLU* 1.3 79.5 - - - +
21A ILE* 1.3 57.1 + - - +
23A GLY* 3.4 1.3 + - - -
24A ALA* 3.0 30.0 + - - +
27A ARG* 4.9 2.4 + - - -
46A ALA* 2.8 34.0 + - - +
48A ILE* 5.1 4.9 - - - -
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.0 17.8 + - + +
18A ARG* 3.5 6.5 - - - +
20A SER* 1.3 79.7 - - - +
22A VAL* 1.3 59.6 + - + +
24A ALA* 3.3 2.6 + - - +
25A ALA* 2.9 28.3 + - + +
42A VAL* 4.0 3.3 - - + +
46A ALA* 4.1 7.2 - - + -
48A ILE* 3.5 32.3 - - + -
53A LEU* 3.8 13.9 - - + -
56A PHE* 3.6 42.2 - - + -
63A LEU* 3.9 27.4 - - + -
66A LEU* 4.0 15.3 - - + -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.0 26.6 + - + +
19A GLU* 3.3 19.3 - - + +
21A ILE* 1.3 76.7 - - + +
23A GLY* 1.3 64.1 + - - +
25A ALA* 3.4 6.7 + - - +
26A GLN* 3.0 24.9 + - - +
63A LEU 5.5 0.2 - - - +
66A LEU* 3.6 44.0 - - + +
67A LEU* 3.8 11.6 - - + +
70A SER* 4.2 23.8 - - - +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 3.0 17.2 + - - -
20A SER* 3.9 1.6 - - - -
22A VAL* 1.3 77.2 - - - +
24A ALA* 1.3 57.2 + - - +
26A GLN* 3.4 5.3 + - - +
27A ARG* 2.9 49.1 + - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 3.0 17.3 + - - +
21A ILE 3.6 4.5 - - - +
23A GLY* 1.3 77.2 - - - +
25A ALA* 1.3 62.1 + - - +
27A ARG* 3.2 14.1 + - - +
28A LEU* 3.0 29.6 + - - +
42A VAL* 3.8 10.3 - - + +
45A GLU* 3.6 12.3 - - + +
46A ALA* 3.5 31.4 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.9 17.2 + - + +
22A VAL* 3.7 7.6 - - - +
24A ALA* 1.3 75.3 - - - +
26A GLN* 1.3 64.0 + - - +
28A LEU* 3.4 2.9 + - - +
29A LEU* 3.0 27.7 + - - +
37A MSE 3.9 22.4 - - + +
42A VAL* 4.1 16.5 - - + +
63A LEU* 4.7 16.6 - - + +
67A LEU* 4.9 8.3 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL 3.0 16.8 + - - +
23A GLY* 3.7 5.6 - - - +
25A ALA* 1.3 75.8 - - - +
27A ARG* 1.3 67.5 + - + +
29A LEU* 3.1 15.9 + - - +
30A SER* 2.9 50.9 + - - +
67A LEU* 3.8 17.7 - - + +
71A TRP* 3.4 20.4 + - - -
105A GLU* 3.3 41.4 + - + +
108A SER* 6.3 0.6 - - - -
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.9 1.8 + - - -
23A GLY* 2.9 37.1 + - - +
24A ALA* 3.2 12.3 + - - +
26A GLN* 1.3 77.4 - - + +
28A LEU* 1.3 58.3 + - + +
30A SER* 3.4 6.3 + - - -
31A SER* 3.0 31.8 + - - -
45A GLU* 2.5 59.5 + - + +
46A ALA* 4.9 1.0 - - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 3.0 15.6 + - - +
25A ALA 3.9 3.1 - - - +
27A ARG* 1.3 76.7 - - + +
29A LEU* 1.3 65.9 + - - +
31A SER* 3.3 11.0 + - - +
32A GLY 2.9 21.8 + - - -
33A GLY 3.5 0.8 + - - -
36A ALA* 3.4 42.3 - - + +
37A MSE 4.0 3.8 - - - -
41A GLY* 3.5 33.7 - - - +
42A VAL* 3.6 19.5 - - + +
45A GLU* 4.4 16.2 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.0 17.6 + - - +
26A GLN* 3.1 14.1 + - - +
28A LEU* 1.3 76.0 - - - +
30A SER* 1.3 60.4 + - - +
33A GLY* 2.9 26.8 + - - +
34A ALA* 3.8 28.9 - - + +
37A MSE 3.8 16.5 - - + +
64A ILE* 4.1 17.0 - - + -
67A LEU* 3.7 30.1 - - + -
109A LEU* 4.6 13.0 - - + -
112A MSE 3.8 27.9 - - + +
123A PHE* 6.0 0.2 - - + -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 2.9 36.6 + - - +
27A ARG* 3.9 5.8 - - - -
29A LEU* 1.3 78.0 - - - +
31A SER* 1.3 59.1 + - - +
105A GLU* 4.6 6.4 + - - +
108A SER* 6.2 0.4 - - - -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG 3.0 16.0 + - - -
28A LEU* 3.2 20.1 + - - +
30A SER* 1.3 80.0 - - - +
32A GLY* 1.3 59.9 + - - +
33A GLY 4.0 0.2 - - - -
36A ALA* 4.5 1.7 - - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 2.9 6.5 + - - -
31A SER* 1.3 81.4 + - - +
33A GLY* 1.3 65.1 + - - +
35A ALA* 4.0 6.8 + - - +
36A ALA* 3.6 21.5 + - - +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU 3.6 3.5 - - - +
29A LEU* 2.9 28.1 + - - +
31A SER 4.0 0.2 - - - -
32A GLY* 1.3 74.6 - - - +
34A ALA* 1.3 66.1 + - - -
35A ALA 3.0 3.8 - - - -
36A ALA* 3.0 12.8 + - - +
37A MSE 3.5 6.6 + - - -
112A MSE 4.5 9.2 - - - -
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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