Contacts of the helix formed by residues 32 - 46 (chain A) in PDB entry 1WD5
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 ARG 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 1.3 77.6 + - + -
33A GLY* 1.3 69.7 + - - +
34A GLY 3.1 2.0 - - - +
35A VAL* 2.9 21.8 + - - +
36A VAL 3.9 0.5 + - - -
105A ARG* 4.1 21.9 - - - +
109A TYR* 3.8 14.4 - - - +
193A GLU* 3.0 25.1 + - - -
194A VAL* 2.7 38.2 + - + +
195A THR* 3.7 5.8 - - - -
196A ASP* 3.4 33.6 + - - +
199A VAL* 3.7 10.4 - - + +
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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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6A ARG* 3.3 38.0 - - - -
32A ARG* 1.3 79.2 - - - +
34A GLY* 1.3 61.7 + - - +
36A VAL* 3.0 12.6 + - - +
37A VAL* 3.6 3.1 + - - +
128A ASP* 3.7 12.6 - - - -
194A VAL* 4.0 14.4 - - - +
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Residues in contact with GLY 34 (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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29A GLY* 4.0 5.0 - - - -
30A LEU 3.2 15.7 + - - -
32A ARG 3.1 1.8 - - - +
33A GLY* 1.3 78.6 - - - +
35A VAL* 1.3 56.1 + - - +
37A VAL* 3.3 4.2 + - - +
38A ALA* 2.9 29.3 + - - +
126A VAL* 4.2 2.4 - - - +
127A ASP* 3.5 25.7 + - - -
128A ASP* 3.8 11.4 + - - -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 3.9 20.6 - - - +
30A LEU 3.5 5.3 + - - +
31A PRO* 4.2 7.9 - - + -
32A ARG 2.9 14.3 + - - +
34A GLY* 1.3 77.7 - - - +
36A VAL* 1.3 57.6 + - - +
38A ALA* 3.7 6.5 - - - +
39A ASP* 2.9 27.9 + - - +
49A LEU* 4.5 13.2 - - + -
50A ASP 5.6 0.7 - - - +
51A VAL* 4.3 9.6 - - + -
199A VAL* 4.1 29.8 - - + +
202A ILE* 3.9 28.9 - - + -
203A LEU* 4.9 3.1 - - + -
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Residues in contact with VAL 36 (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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6A ARG* 3.7 22.2 - - + -
7A ARG* 3.9 30.8 + - + +
33A GLY 3.0 11.8 + - - +
35A VAL* 1.3 75.2 - - - +
37A VAL* 1.3 67.0 + - - +
39A ASP* 3.3 4.8 + - - +
40A GLU* 3.2 21.1 + - - +
194A VAL* 3.9 32.3 - - + -
202A ILE* 4.0 22.2 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.8 28.9 - - + +
10A GLY* 3.7 21.7 - - - +
13A LEU* 4.1 12.3 - - + -
33A GLY 3.6 3.8 + - - +
34A GLY 3.3 6.1 + - - +
36A VAL* 1.3 75.9 - - - +
38A ALA* 1.3 61.1 + - - +
40A GLU* 3.3 5.0 + - - +
41A VAL* 3.1 21.3 + - - +
126A VAL* 3.6 21.5 - - + -
127A ASP 4.6 0.2 - - - +
128A ASP* 3.8 32.1 - - + +
156A PRO* 4.2 8.1 - - + -
188A TYR* 4.4 4.0 - - - +
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Residues in contact with ALA 38 (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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27A VAL* 3.6 16.5 - - + +
29A GLY* 3.6 21.5 - - - +
34A GLY 2.9 18.4 + - - +
35A VAL 3.7 2.9 - - - +
36A VAL 3.2 0.2 - - - -
37A VAL* 1.3 75.5 - - - +
39A ASP* 1.3 59.6 + - - +
41A VAL* 3.2 3.9 + - - +
42A ALA* 2.9 30.5 + - - +
49A LEU* 3.6 19.5 - - + -
126A VAL* 4.1 9.6 - - + +
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Residues in contact with ASP 39 (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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7A ARG* 2.8 27.2 + - - +
35A VAL 2.9 19.5 + - - +
36A VAL* 3.7 5.2 - - - +
37A VAL 3.3 0.2 - - - -
38A ALA* 1.3 75.6 - - - +
40A GLU* 1.3 62.8 + - - +
42A ALA* 3.3 2.1 + - - +
43A ARG* 2.7 56.6 + - - +
49A LEU* 3.8 9.8 - - + +
202A ILE* 3.6 20.5 - - + +
206A TRP* 2.8 32.4 + - - -
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Residues in contact with GLU 40 (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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7A ARG* 2.9 64.4 + - - +
10A GLY* 4.1 6.1 - - - -
11A ALA 3.7 11.7 - - - +
36A VAL 3.2 8.5 + - - +
37A VAL 3.6 8.1 - - - +
39A ASP* 1.3 77.8 - - - +
41A VAL* 1.3 62.9 + - - +
43A ARG* 3.3 10.7 + - - +
44A ARG* 2.7 66.4 + - - +
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Residues in contact with VAL 41 (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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10A GLY* 3.5 17.3 - - - +
13A LEU* 4.2 26.9 - - + -
14A ALA* 4.1 10.3 - - + +
17A LEU* 3.9 13.0 - - + -
27A VAL* 4.0 18.4 - - + -
37A VAL 3.1 20.3 + - - +
38A ALA* 3.2 8.3 + - - +
40A GLU* 1.3 77.0 - - - +
42A ALA* 1.3 64.8 + - - +
44A ARG* 3.1 1.9 + - - +
45A LEU* 2.9 48.0 + - + +
124A VAL* 5.1 0.2 - - + -
126A VAL* 4.8 4.0 - - + -
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Residues in contact with ALA 42 (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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27A VAL* 3.9 20.4 - - + +
38A ALA 2.9 16.5 + - - +
39A ASP 3.7 4.7 - - - +
40A GLU 3.3 0.2 - - - -
41A VAL* 1.3 77.0 - - - +
43A ARG* 1.3 57.1 + - - +
45A LEU* 4.7 0.4 - - - +
46A GLY* 3.1 8.1 + - - -
47A GLY 2.8 31.2 + - - +
48A GLU 4.1 2.0 - - - -
49A LEU* 3.8 32.5 - - + +
206A TRP* 4.0 7.7 - - + -
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Residues in contact with ARG 43 (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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7A ARG* 4.4 7.3 - - - +
39A ASP* 2.7 50.3 + - - +
40A GLU* 3.8 9.4 - - - +
42A ALA* 1.3 78.9 - - - +
44A ARG* 1.3 62.5 + - + +
46A GLY* 3.7 7.2 + - - -
202A ILE* 5.3 0.4 + - - +
205A GLU* 3.9 26.9 + - - +
206A TRP* 3.8 28.2 - - + +
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Residues in contact with ARG 44 (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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11A ALA* 3.7 30.2 - - - +
14A ALA* 3.5 22.7 - - + -
15A GLU* 4.5 6.2 + - - -
40A GLU* 2.7 42.6 + - + +
41A VAL 3.1 0.2 + - - -
43A ARG* 1.3 80.6 - - + +
45A LEU* 1.3 63.3 + - - +
46A GLY 3.6 0.5 + - - -
2955A MES 3.8 23.2 - - - -
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Residues in contact with LEU 45 (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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14A ALA* 3.7 24.0 - - + +
17A LEU* 4.1 19.5 - - + -
18A ALA* 4.1 20.2 - - + +
22A LEU* 4.7 9.4 - - + -
24A ALA* 5.4 1.0 + - - -
25A PRO* 4.3 28.4 - - + +
27A VAL* 5.1 1.1 - - + -
41A VAL* 2.9 36.9 + - + +
42A ALA* 5.0 0.4 - - - -
44A ARG* 1.3 78.8 - - - +
46A GLY* 1.3 65.0 + - - +
47A GLY* 3.4 5.1 + - - +
124A VAL* 5.3 1.3 - - + -
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Residues in contact with GLY 46 (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* 4.3 13.2 - - - +
42A ALA 3.1 6.2 + - - -
43A ARG* 3.7 6.1 + - - -
44A ARG 3.3 4.2 + - - -
45A LEU* 1.3 79.7 - - - +
47A GLY* 1.3 62.9 + - - +
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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