Contacts of the helix formed by residues 38 - 53 (chain A) in PDB entry 1WS6
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 3.9 19.9 - - + -
37A SER* 1.3 85.5 - - - +
39A VAL* 1.3 66.1 + - - +
40A ARG* 4.8 5.8 - - + +
41A LEU* 3.2 37.1 - - + +
42A ARG* 3.1 22.0 + - - +
160A GLN* 4.4 6.5 - - - +
175A TYR* 5.5 5.6 - - + +
178A ASN* 3.9 18.8 - - + +
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Residues in contact with VAL 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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16A VAL* 6.4 1.6 - - + -
19A LEU* 4.1 17.9 - - + +
37A SER 4.2 3.1 - - - +
38A PRO* 1.3 68.2 - - - +
40A ARG* 1.3 63.2 + - - +
41A LEU 3.1 1.6 - - - -
42A ARG* 3.4 25.0 + - - +
43A LYS* 2.9 34.2 + - + +
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Residues in contact with ARG 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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38A PRO* 5.3 4.9 - - + -
39A VAL* 1.3 80.5 - - - +
41A LEU* 1.3 58.0 - - - +
43A LYS* 4.0 8.9 - - + +
44A ALA* 2.9 31.0 + - - +
174A VAL 5.0 0.4 + - - -
175A TYR* 3.7 44.6 - - + +
176A GLY* 4.2 6.3 - - - +
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Residues in contact with LEU 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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37A SER* 4.9 0.7 - - - +
38A PRO* 3.2 34.5 + - + +
39A VAL 3.1 0.2 - - - -
40A ARG* 1.3 77.9 - - - +
42A ARG* 1.3 78.9 + - + +
44A ALA* 3.0 4.0 + - - +
45A LEU* 2.8 24.8 + - + +
129A PHE* 4.9 5.8 - - + -
160A GLN* 3.7 23.1 - - - +
175A TYR* 3.3 39.7 - - + -
178A ASN* 4.9 9.2 - - + -
179A ALA 5.2 0.9 - - - -
180A LEU* 3.5 32.2 - - + +
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Residues in contact with ARG 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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16A VAL* 4.6 12.8 - - - +
17A ARG 3.1 36.1 + - - +
18A ILE* 4.7 0.6 - - - +
19A LEU* 3.6 19.5 - - + +
28A LEU* 5.5 1.0 - - - +
37A SER* 3.6 38.3 + - - +
38A PRO 3.1 6.8 + - - +
39A VAL* 3.6 26.9 - - - +
41A LEU* 1.3 88.2 - - + +
43A LYS* 1.3 64.0 + - - +
45A LEU* 3.3 4.2 + - - -
46A PHE* 3.1 42.4 + - + +
68A ALA* 4.3 30.4 + - - +
69A VAL* 4.9 8.1 - - + +
72A GLU* 4.0 16.1 + - + -
129A PHE* 6.5 0.9 - - + -
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Residues in contact with LYS 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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19A LEU* 3.8 21.0 - - + +
39A VAL* 2.9 24.6 + - + +
40A ARG* 4.0 7.9 - - + +
42A ARG* 1.3 76.5 - - - +
44A ALA* 1.3 60.0 + - - +
46A PHE* 4.2 2.4 - - - +
47A ASP* 3.0 52.7 + - - +
50A ARG* 5.2 0.5 + - - -
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Residues in contact with ALA 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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40A ARG 2.9 21.0 + - - +
41A LEU 3.6 3.1 - - - +
43A LYS* 1.3 75.4 - - - +
45A LEU* 1.3 66.1 + - - +
47A ASP* 3.2 10.6 + - - +
48A TYR* 3.1 22.3 + - - +
173A ARG* 5.1 2.3 + - - +
175A TYR* 3.3 33.2 - - + +
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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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41A LEU* 2.8 21.2 + - + +
42A ARG* 3.7 6.7 - - - +
44A ALA* 1.3 75.4 - - - +
46A PHE* 1.3 73.2 + - + +
48A TYR* 3.3 5.9 + - + +
49A LEU* 2.9 52.5 + - + +
59A PHE* 5.2 0.7 - - + -
69A VAL* 4.8 1.1 - - + -
129A PHE* 3.6 38.4 - - + -
158A VAL* 4.3 21.3 - - + -
173A ARG* 5.5 4.5 - - - +
175A TYR* 5.1 0.6 + - - -
180A LEU* 4.2 15.6 - - + +
182A LEU* 4.9 9.9 - - + -
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Residues in contact with PHE 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 ARG* 3.1 32.1 + - + +
43A LYS* 4.5 2.5 - - - +
45A LEU* 1.3 81.0 - - + +
47A ASP* 1.3 66.6 + - - +
48A TYR 3.0 1.6 - - - -
49A LEU* 4.0 24.0 - - + -
50A ARG* 3.0 33.8 + - - +
59A PHE* 4.2 7.9 - + - -
69A VAL* 3.7 38.1 - - + -
72A GLU* 3.4 23.1 - - + +
73A ALA* 3.8 26.7 - - + -
76A GLU* 3.6 31.4 - - - +
78A TRP* 4.6 7.6 - - - -
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Residues in contact with ASP 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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43A LYS* 3.0 53.7 + - - +
44A ALA* 3.2 10.1 + - - +
46A PHE* 1.3 76.9 - - - +
48A TYR* 1.3 62.3 + - - +
50A ARG* 2.9 29.3 + - - +
51A LEU* 3.3 20.8 + - - +
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Residues in contact with TYR 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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44A ALA 3.1 8.6 + - - +
45A LEU* 3.4 9.4 - - + +
46A PHE 3.0 0.4 - - - -
47A ASP* 1.3 78.7 - - - +
49A LEU* 1.3 67.5 + - + +
51A LEU* 3.1 14.1 + - + +
52A ARG* 2.7 80.3 + - + +
156A LEU* 3.8 22.7 - - + -
173A ARG* 3.3 29.4 - - - +
182A LEU* 4.0 18.5 - - + +
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Residues in contact with LEU 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 LEU* 2.9 49.9 + - + +
46A PHE* 3.3 28.7 + - + +
48A TYR* 1.3 100.3 - - + +
50A ARG* 1.3 58.1 + - - +
52A ARG* 4.4 0.4 - - - +
53A TYR* 2.8 44.8 + - + +
59A PHE* 4.2 14.8 - - + -
78A TRP* 4.2 18.6 - - + +
127A VAL* 4.6 9.9 - - + -
156A LEU* 4.3 13.5 - - + -
158A VAL* 5.3 0.7 - - + -
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Residues in contact with ARG 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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20A GLY* 5.6 4.0 - - - -
43A LYS 5.2 0.2 + - - -
46A PHE* 3.0 23.1 + - - +
47A ASP* 2.9 41.6 + - - +
49A LEU* 1.3 77.9 - - - +
51A LEU* 1.3 63.6 - - - +
54A PRO* 3.5 23.4 - - - +
56A ARG* 3.6 35.1 + - - +
76A GLU* 3.1 34.2 + - - +
78A TRP* 5.6 1.1 - - - +
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Residues in contact with LEU 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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47A ASP 3.3 16.6 + - - +
48A TYR* 3.1 15.0 + - + +
50A ARG* 1.3 84.8 - - + +
52A ARG* 1.3 63.3 + - + +
54A PRO* 3.9 8.0 - - - +
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Residues in contact with ARG 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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48A TYR* 2.7 69.6 + - + +
51A LEU* 1.3 79.6 - - + +
53A TYR* 1.3 100.6 + - + +
54A PRO* 3.4 6.8 - - - +
154A GLY* 3.9 11.3 + - - -
155A GLY 4.5 0.4 + - - -
156A LEU* 4.2 8.7 - - - +
184A GLU* 2.8 52.6 + - - +
185A VAL 5.5 0.4 + - - -
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Residues in contact with TYR 53 (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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49A LEU* 2.8 26.3 + - + +
50A ARG 3.7 3.4 - - - -
52A ARG* 1.3 112.6 + - + +
54A PRO* 1.3 58.4 - - - +
55A ARG* 3.0 6.1 - - - +
56A ARG* 2.8 33.7 + - - +
78A TRP* 3.6 27.6 - + + -
126A THR* 3.7 22.0 - - + -
127A VAL* 3.9 15.5 - - + -
154A GLY 2.7 29.9 + - - -
155A GLY* 3.3 15.6 - - - -
156A LEU* 3.5 12.7 - - + +
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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