Contacts of the helix formed by residues 13 - 37 (chain B) 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 PRO 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 1.3 91.3 - - + +
14B ASP* 1.3 67.2 - - - +
15B ALA* 4.2 8.7 - - + +
16B VAL* 3.0 31.8 + - + +
17B VAL* 3.1 11.1 + - - +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 6.5 0.7 - - + -
160A ARG* 3.7 24.9 + - + -
12B VAL 3.6 3.1 + - - +
13B PRO* 1.3 73.1 - - - +
15B ALA* 1.3 56.8 + - - +
17B VAL* 3.2 3.5 + - - +
18B ARG* 2.8 39.5 + - - +
55B ARG* 3.0 42.4 + - - -
56B PHE* 3.5 20.9 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.1 5.8 - - + +
14B ASP* 1.3 79.3 - - - +
16B VAL* 1.3 61.1 + - + +
18B ARG* 3.7 14.2 - - - +
19B GLU* 3.0 35.6 + - + +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.7 21.1 - - + -
13B PRO* 3.0 28.8 + - + +
15B ALA* 1.3 78.8 - - + +
17B VAL* 1.3 65.9 + - - +
19B GLU* 3.3 9.8 + - + +
20B SER* 3.0 23.3 + - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.7 30.3 - - + +
13B PRO 3.1 14.4 + - - +
14B ASP* 3.2 8.9 + - - +
16B VAL* 1.3 78.1 - - - +
18B ARG* 1.3 62.0 + - - +
20B SER* 3.1 7.6 + - - -
21B ILE* 2.9 32.3 + - + +
48B ILE* 4.1 29.8 - - + -
52B THR* 4.2 7.4 - - + -
55B ARG* 6.3 0.4 - - - +
56B PHE* 3.6 27.4 - - + -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 6.2 1.4 - - - +
14B ASP* 2.8 25.9 + - - +
15B ALA* 3.7 11.6 - - - +
17B VAL* 1.3 77.2 - - - +
19B GLU* 1.3 63.5 + - - +
21B ILE* 3.1 11.5 + - - +
22B VAL* 2.9 31.4 + - + +
56B PHE* 3.7 32.6 - - + +
66B LEU* 4.1 31.3 - - + +
69B GLU* 4.7 9.0 + - - -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.0 24.5 + - + +
16B VAL* 3.6 10.2 - - + +
17B VAL 3.2 0.2 - - - -
18B ARG* 1.3 78.9 - - + +
20B SER* 1.3 56.6 + - - +
22B VAL* 3.4 7.1 + - - +
23B GLY* 2.9 26.0 + - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 3.0 15.1 + - - -
17B VAL* 3.1 11.9 + - - -
19B GLU* 1.3 76.7 - - - +
21B ILE* 1.3 58.0 - - - +
23B GLY* 3.5 1.0 + - - -
24B ALA* 3.0 30.0 + - - +
27B ARG* 4.7 3.5 + - - +
45B GLU 4.6 0.7 + - - -
46B ALA* 2.8 36.3 + - - -
48B ILE* 6.0 0.7 - - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.9 19.8 + - + +
18B ARG* 3.5 8.1 - - - +
20B SER* 1.3 76.8 - - - +
22B VAL* 1.3 59.2 + - - +
24B ALA* 3.3 3.3 + - - +
25B ALA* 2.9 28.7 + - + +
42B VAL* 4.0 7.4 - - + +
46B ALA* 4.1 9.0 - - + -
48B ILE* 3.8 23.3 - - + -
53B LEU* 3.8 14.4 - - + -
56B PHE* 3.7 40.8 - - + -
63B LEU* 3.8 26.9 - - + -
66B LEU* 4.0 15.3 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.9 28.3 + - + +
19B GLU* 3.9 6.1 - - - +
21B ILE* 1.3 75.0 - - - +
23B GLY* 1.3 64.2 + - - +
25B ALA* 3.3 7.1 + - - +
26B GLN* 3.0 23.7 + - + +
66B LEU* 3.7 37.9 - - + +
67B LEU* 3.7 15.7 - - + +
70B SER* 3.2 31.9 - - - +
71B TRP* 5.7 0.2 - - - +
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU 2.9 16.6 + - - -
20B SER* 3.9 1.3 - - - -
22B VAL* 1.3 78.2 - - - +
24B ALA* 1.3 57.2 + - - +
26B GLN* 3.3 5.0 + - - +
27B ARG* 2.9 48.2 + - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER 3.0 18.0 + - - +
21B ILE 3.3 4.2 + - - +
23B GLY* 1.3 74.3 - - - +
25B ALA* 1.3 64.9 + - - +
27B ARG* 3.3 6.2 + - - +
28B LEU* 3.1 30.0 + - - +
42B VAL* 3.8 17.5 - - + +
45B GLU* 3.3 37.7 - - + -
46B ALA* 3.8 4.9 - - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 2.9 17.6 + - + +
22B VAL* 3.7 7.2 - - - +
24B ALA* 1.3 76.6 - - - +
26B GLN* 1.3 63.0 + - - +
29B LEU* 3.0 27.4 + - - +
37B MSE 3.8 23.3 - - + +
42B VAL* 3.9 17.7 - - + +
63B LEU* 4.7 17.5 - - + +
67B LEU* 5.0 7.2 - - + -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.0 17.0 + - + +
23B GLY* 3.7 6.1 - - - +
25B ALA* 1.3 75.1 - - - +
27B ARG* 1.3 66.9 + - + +
29B LEU* 3.2 17.1 + - - +
30B SER* 3.0 49.6 + - - +
67B LEU* 3.6 16.0 - - + +
71B TRP* 3.5 21.0 + - - -
105B GLU* 3.3 39.5 + - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 4.7 4.0 + - - +
23B GLY* 2.9 38.1 + - - +
24B ALA* 3.3 11.6 + - - +
26B GLN* 1.3 77.9 - - + +
28B LEU* 1.3 59.8 + - + +
30B SER* 3.4 5.5 + - - -
31B SER* 3.0 30.4 + - - -
45B GLU* 2.5 65.2 + - - +
46B ALA* 5.0 0.2 - - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 3.1 18.3 + - - +
25B ALA 3.8 3.4 - - - +
27B ARG* 1.3 75.0 - - + +
29B LEU* 1.3 64.7 + - - +
31B SER* 3.3 9.3 + - - +
32B GLY 2.9 21.0 + - - -
33B GLY 3.5 1.2 + - - -
36B ALA* 3.5 39.2 - - + +
37B MSE 4.0 5.8 - - + -
41B GLY* 3.5 37.0 - - - +
42B VAL* 3.6 14.8 - - + +
45B GLU* 4.5 16.4 - - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 3.0 17.3 + - - +
26B GLN* 3.2 12.8 + - - +
28B LEU* 1.3 76.8 - - - +
30B SER* 1.3 60.2 + - - +
33B GLY* 2.9 47.8 + - - +
34B ALA* 3.9 9.0 - - + +
37B MSE 3.8 23.3 - - + +
64B ILE* 4.2 11.4 - - + -
67B LEU* 3.6 31.0 - - + -
109B LEU* 4.5 13.0 - - + -
112B MSE 3.9 25.3 - - + +
123B PHE* 6.0 0.4 - - + -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.0 33.6 + - - +
27B ARG* 3.7 6.3 - - - -
29B LEU* 1.3 77.4 - - - +
31B SER* 1.3 62.0 + - - +
105B GLU* 4.6 7.8 + - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG 3.0 17.4 + - - -
28B LEU* 3.3 16.1 + - - +
30B SER* 1.3 80.4 - - - +
32B GLY* 1.3 59.6 + - - +
36B ALA* 4.7 1.7 - - - +
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 2.9 6.3 + - - -
31B SER* 1.3 82.4 + - - +
33B GLY* 1.3 66.0 + - - +
35B ALA* 3.9 8.1 + - - +
36B ALA* 3.5 22.9 + - - +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 3.7 3.3 - - - +
29B LEU* 2.9 30.0 + - - +
30B SER 4.7 0.2 - - - -
32B GLY* 1.3 75.9 - - - +
34B ALA* 1.3 66.7 + - - -
35B ALA 3.1 0.2 - - - -
36B ALA* 3.0 11.6 + - - +
37B MSE 3.4 7.1 + - - -
112B MSE 4.6 8.1 - - - -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.9 12.4 - - + +
33B GLY* 1.3 71.6 - - - -
35B ALA* 1.3 62.5 + - - +
37B MSE 3.1 17.7 + - - +
60B ARG* 3.1 24.1 + - - +
112B MSE 3.9 10.9 - - - -
119B LEU* 3.7 40.6 - - + -
123B PHE* 4.3 9.0 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY 4.1 7.9 - - - +
33B GLY 3.1 0.8 - - - -
34B ALA* 1.3 80.8 - - - +
36B ALA* 1.3 59.8 + - - +
38B THR* 3.5 18.5 - - - +
60B ARG* 4.6 5.8 + - - +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.5 49.1 - - + +
31B SER* 4.7 1.8 - - - +
32B GLY* 3.5 21.2 + - - +
33B GLY 3.0 2.4 + - - +
35B ALA* 1.3 77.9 - - - +
37B MSE 1.3 56.9 + - - +
38B THR* 3.0 16.9 + - - +
41B GLY* 4.8 1.2 - - - -
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Residues in contact with MSE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.8 28.9 - - - +
28B LEU* 4.0 9.6 - - + -
29B LEU* 3.8 28.3 - - + -
33B GLY 3.4 8.0 + - - +
34B ALA* 3.1 12.4 + - - +
36B ALA* 1.3 75.2 - - - +
38B THR* 1.3 61.1 + - - +
42B VAL* 4.0 16.6 - - + -
60B ARG* 3.0 63.0 - - + +
63B LEU* 4.0 9.9 - - + +
64B ILE* 3.8 23.6 - - + -
67B LEU* 5.4 0.7 - - - -
123B PHE* 4.4 6.3 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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