Contacts of the helix formed by residues 39 - 57 (chain A) in PDB entry 3R2W
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 HIS 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.3 38.9 - - + -
37A PHE 4.1 0.2 - - - +
38A GLU* 1.3 77.5 - - - +
40A THR* 1.3 77.7 + - - +
42A LYS* 3.8 20.7 - - + +
43A ASP* 3.1 32.1 + - - +
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Residues in contact with THR 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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29A LEU* 4.2 10.8 - - + -
32A ALA* 5.6 2.1 - - - +
36A GLU 3.5 21.5 + - - -
37A PHE* 3.6 6.7 + - - -
38A GLU 3.4 0.2 - - - -
39A HIS* 1.3 88.1 - - + +
41A LYS* 1.3 53.9 + - - +
42A LYS 3.2 1.3 - - - -
43A ASP* 3.1 9.0 + - + +
44A LEU* 2.8 53.2 + - + +
181A ARG 6.1 0.4 - - - +
207A TRP* 6.0 5.6 - - + -
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 31.7 - - + +
37A PHE* 3.6 15.5 + - + +
38A GLU* 5.1 2.0 - - - +
40A THR* 1.3 75.6 - - - +
42A LYS* 1.3 65.0 + - - +
44A LEU* 3.9 8.1 - - - +
45A ASP* 3.2 27.8 + - - +
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Residues in contact with LYS 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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38A GLU 3.6 19.6 + - - +
39A HIS* 3.8 20.8 + - + +
41A LYS* 1.3 78.4 - - - +
43A ASP* 1.3 87.3 + - - +
45A ASP* 4.3 0.5 - - - +
46A GLY* 3.5 12.5 + - - -
178A ASN 4.8 6.3 + - - -
179A GLN 5.4 0.2 - - - -
180A SER* 4.3 7.7 + - - +
217A ALA* 5.6 1.1 - - - -
218A SER* 4.5 15.9 - - - +
221A ASN* 3.1 41.5 - - + +
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Residues in contact with ASP 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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39A HIS* 3.1 22.9 - - - +
40A THR* 3.1 10.3 + - + +
42A LYS* 1.3 98.2 + - - +
44A LEU* 1.3 57.8 + - + +
46A GLY* 2.6 25.1 + - - -
47A PHE 2.8 10.0 + - - -
180A SER* 2.9 30.9 + - - -
181A ARG* 3.8 20.2 + - - +
182A TYR* 3.4 23.4 - - + -
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Residues in contact with LEU 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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25A LEU* 4.3 38.0 - - + +
28A ILE* 5.5 7.2 - - + -
29A LEU* 3.7 37.9 - - + +
40A THR* 2.8 29.3 + - + +
41A LYS* 4.2 4.9 - - - -
43A ASP* 1.3 71.9 - - + +
45A ASP* 1.3 58.2 + - - +
47A PHE* 3.3 12.8 - - + +
48A ARG* 2.9 25.6 + - - +
181A ARG 5.2 3.8 - - - +
182A TYR* 5.9 0.2 - - + -
183A PRO* 4.3 27.6 - - + -
207A TRP* 4.6 15.7 - - + -
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Residues in contact with ASP 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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22A LYS* 3.5 22.5 + - - -
25A LEU* 5.2 9.2 - - - +
26A GLU* 5.5 1.0 - - - +
41A LYS* 3.2 18.2 + - - +
42A LYS 4.3 1.6 - - - +
43A ASP 3.1 0.6 - - - -
44A LEU* 1.3 76.9 - - - +
46A GLY* 1.3 60.1 + - - +
47A PHE 3.3 0.2 - - - -
48A ARG* 3.3 21.4 - - - +
49A LYS* 3.3 22.3 + - - +
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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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42A LYS 3.5 11.0 + - - -
43A ASP 2.6 14.7 + - - -
45A ASP* 1.3 74.0 - - - +
47A PHE* 1.3 54.5 + - - -
49A LYS* 3.8 5.8 + - - +
50A LEU* 3.2 31.2 + - - +
182A TYR* 3.8 12.5 + - - -
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Residues in contact with PHE 47 (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 LEU* 5.6 7.2 - - + -
43A ASP 2.8 9.4 + - - +
44A LEU* 3.3 16.2 - - + +
46A GLY* 1.3 77.3 - - - +
48A ARG* 1.3 57.2 + - - +
50A LEU* 3.1 6.8 + - + +
51A PHE* 2.7 54.0 + + + +
182A TYR* 3.7 36.7 + + + -
183A PRO* 3.5 42.6 - - + -
185A ILE* 4.8 13.7 - - + -
192A PRO* 5.3 6.7 - - + -
208A TYR* 3.6 17.9 - + - -
357A LEU* 4.2 18.2 - - + -
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Residues in contact with ARG 48 (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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22A LYS* 4.3 16.6 - - + +
25A LEU* 4.8 10.5 - - + -
44A LEU 2.9 13.3 + - - +
45A ASP* 3.3 26.0 - - - +
47A PHE* 1.3 74.5 - - - +
49A LYS* 1.3 57.9 + - - +
50A LEU 2.9 4.0 + - - -
51A PHE* 2.9 24.3 + - - +
52A HIS* 3.0 16.7 + - - +
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Residues in contact with LYS 49 (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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45A ASP 3.3 19.7 + - - +
46A GLY* 3.8 8.1 - - - +
47A PHE 3.4 0.2 - - - -
48A ARG* 1.3 76.8 - - - +
50A LEU* 1.3 62.1 + - - +
52A HIS* 4.4 8.9 - - - +
53A ARG* 3.9 14.7 + - - +
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Residues in contact with LEU 50 (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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46A GLY 3.2 19.3 + - - +
47A PHE* 3.1 9.5 + - + +
48A ARG 2.9 0.8 - - - -
49A LYS* 1.3 82.0 - - - +
51A PHE* 1.3 58.4 + - - +
52A HIS 3.3 1.3 - - - -
53A ARG* 3.1 24.2 + - - +
54A PHE* 2.9 23.9 + - - +
182A TYR* 4.1 24.7 - - + +
210A PRO* 5.9 1.6 - - + -
339A MET* 5.8 4.0 - - + +
341A ILE* 3.4 17.9 - - + +
357A LEU* 4.1 24.0 - - + +
358A GLU* 6.1 0.2 - - - -
359A THR* 4.7 21.1 - - + -
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Residues in contact with PHE 51 (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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17A LEU 5.3 0.4 - - - -
18A GLU* 4.3 24.5 - - + -
21A VAL* 4.7 20.0 - - + -
47A PHE* 2.7 33.6 + + + +
48A ARG* 3.5 10.1 - - - +
50A LEU* 1.3 70.3 - - - +
52A HIS* 1.3 65.4 + - - +
54A PHE* 3.1 43.7 + + - +
55A LEU* 3.4 26.1 - - + +
185A ILE* 4.0 29.6 - - + -
190A LEU* 4.0 30.7 - - + -
357A LEU* 4.0 12.0 - - + +
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Residues in contact with HIS 52 (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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15A GLN* 5.6 6.7 - - + -
18A GLU* 3.2 34.7 + - - +
48A ARG 3.0 14.7 + - - +
49A LYS* 4.4 9.4 - - - +
51A PHE* 1.3 77.0 - - - +
53A ARG* 1.3 63.0 + - + +
54A PHE 3.2 1.2 + - - -
55A LEU* 3.6 9.9 + - - +
56A GLN* 3.9 34.8 + - + +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LYS 3.9 11.4 - - - +
50A LEU* 3.1 24.3 + - - +
52A HIS* 1.3 80.2 - - + +
54A PHE* 1.3 59.9 + - - +
55A LEU 3.6 0.2 - - - -
56A GLN* 4.3 6.8 - - - +
57A GLU* 3.9 16.5 + - - +
338A ASP* 4.7 14.3 + - - +
339A MET 3.7 24.8 + - - +
341A ILE* 3.5 21.5 - - + +
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Residues in contact with PHE 54 (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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50A LEU 2.9 11.3 + - - +
51A PHE* 3.1 39.0 + + - +
53A ARG* 1.3 77.7 - - - +
55A LEU* 1.3 76.0 + - + +
56A GLN 3.5 0.9 + - - -
57A GLU* 4.4 9.4 + - - +
185A ILE* 5.6 0.9 - - + -
190A LEU* 4.7 12.8 - - + -
341A ILE* 3.8 12.6 - - + -
343A VAL* 3.4 31.4 - - + -
355A ILE* 4.3 20.0 - - + -
357A LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 55 (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 ARG 3.9 21.3 - - - +
18A GLU* 3.8 31.0 - - + +
51A PHE* 3.4 30.3 - - + +
52A HIS 3.6 4.6 + - - +
54A PHE* 1.3 97.1 - - + +
56A GLN* 1.3 64.6 + - + +
57A GLU* 5.6 0.4 - - - +
190A LEU* 5.0 9.9 - - + -
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Residues in contact with GLN 56 (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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52A HIS* 3.9 35.9 + - + +
53A ARG* 4.4 6.1 - - - +
54A PHE 3.3 0.4 - - - -
55A LEU* 1.3 82.6 - - + +
57A GLU* 1.3 79.8 + - - +
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Residues in contact with GLU 57 (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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53A ARG 3.9 10.9 + - - +
54A PHE 4.4 7.7 + - - +
55A LEU 5.6 0.2 - - - +
56A GLN* 1.3 88.0 - - - +
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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