Contacts of the helix formed by residues 44 - 62 (chain A) in PDB entry 1W3U
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 GLY 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 3.1 21.4 + - - -
43A ARG* 1.3 79.0 - - - +
45A ALA* 1.4 66.5 + - - -
46A VAL 3.2 4.0 + - - -
47A TYR* 3.5 2.9 + - - -
48A GLU* 2.9 25.5 + - - +
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Residues in contact with ALA 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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43A ARG 4.1 0.6 + - - -
44A GLY* 1.4 74.4 - - - -
46A VAL* 1.3 60.9 + - + +
48A GLU* 3.8 6.2 - - - +
49A ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 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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30A TYR* 3.5 32.3 + - + -
31A GLN* 5.4 2.2 - - - +
33A THR* 4.7 14.1 - - + -
35A MET* 6.5 0.7 - - + -
37A ILE* 4.4 1.1 - - + -
40A MET* 3.5 26.9 - - + -
44A GLY* 3.2 1.2 - - - -
45A ALA* 1.3 78.7 - - + +
47A TYR* 1.3 67.7 + - - +
49A ALA* 3.4 10.9 + - - +
50A VAL* 3.5 13.5 + - - +
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Residues in contact with TYR 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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37A ILE* 4.4 21.8 - - + -
40A MET* 4.6 13.4 - - + +
41A SER 3.4 20.4 + - - +
42A HIS* 3.4 28.9 - - + -
44A GLY 3.5 2.2 + - - -
45A ALA 3.4 0.2 - - - -
46A VAL* 1.3 82.1 - - - +
48A GLU* 1.3 63.4 + - - +
50A VAL* 2.9 13.0 + - + +
51A HIS* 2.8 63.7 + + + -
236A LEU* 4.1 1.6 - - + -
240A PRO* 3.8 14.9 - - + +
242A SER* 3.3 39.9 - - - -
245A ILE* 3.2 24.6 - - + +
246A TYR* 5.2 0.2 - - + -
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Residues in contact with GLU 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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42A HIS 3.6 13.0 - - - +
43A ARG* 4.2 16.5 + - - +
44A GLY 2.9 27.1 + - - +
45A ALA* 3.8 7.4 - - - +
46A VAL 3.2 0.2 - - - -
47A TYR* 1.3 77.6 - - - +
49A ALA* 1.3 63.1 + - - +
51A HIS* 4.0 6.7 - - - -
52A ASN* 2.9 56.9 + - - +
234A ASN* 3.9 5.0 + - - -
236A LEU* 3.3 31.3 - - - +
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Residues in contact with ALA 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 ALA 3.0 17.9 + - - +
46A VAL* 3.7 7.0 - - - +
47A TYR 3.1 0.6 - - - -
48A GLU* 1.3 76.1 - - - +
50A VAL* 1.3 60.7 + - + +
52A ASN* 4.2 3.7 - - - +
53A GLU* 2.9 35.6 + - - +
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Residues in contact with VAL 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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30A TYR* 3.4 28.7 - - + +
37A ILE* 4.4 7.6 - - + -
46A VAL 3.5 9.6 + - - +
47A TYR* 2.9 15.7 + - + +
49A ALA* 1.3 80.2 - - + +
51A HIS* 1.3 64.2 + - - +
53A GLU* 3.3 7.9 + - - +
54A ALA* 2.9 24.4 + - - +
245A ILE 4.4 1.8 - - - +
246A TYR* 3.6 42.6 - - + +
249A ASN* 4.0 19.1 - - + +
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Residues in contact with HIS 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 TYR* 2.8 48.7 + + + +
48A GLU* 3.5 7.6 - - - +
50A VAL* 1.3 77.1 - - - +
52A ASN* 1.3 62.1 + - - +
54A ALA* 3.6 0.5 + - - +
55A GLN* 3.4 47.9 + - - +
72A PHE* 3.6 25.3 - + - -
234A ASN* 2.8 36.0 + - - -
235A SER* 3.9 10.3 - - - -
236A LEU* 3.4 25.2 - - + +
240A PRO* 4.3 0.4 - - + -
245A ILE* 3.8 19.8 - - + +
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Residues in contact with ASN 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 GLU* 2.9 41.5 + - - +
49A ALA* 4.2 3.5 - - - +
51A HIS* 1.3 75.2 - - - +
53A GLU* 1.3 64.8 + - - +
55A GLN* 3.2 14.5 + - - +
56A ALA* 3.1 21.7 + - - +
69A LYS* 5.5 0.3 + - - -
234A ASN* 2.9 27.1 + - - +
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Residues in contact with GLU 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 ALA* 2.9 21.8 + - - +
50A VAL* 3.6 7.9 - - - +
52A ASN* 1.3 76.4 - - - +
54A ALA* 1.3 57.0 + - - +
56A ALA* 3.2 6.4 + - - +
57A ARG* 2.5 80.6 + - + +
249A ASN* 3.1 21.7 + - - +
253A LYS* 3.7 7.5 + - - -
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Residues in contact with ALA 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 VAL 2.9 16.8 + - - +
51A HIS 3.7 6.5 - - - +
52A ASN 3.2 0.2 - - - -
53A GLU* 1.3 78.0 - - - +
55A GLN* 1.3 62.9 + - - +
58A LEU* 3.0 21.5 + - - +
72A PHE* 3.8 19.3 - - + -
245A ILE* 4.3 9.2 - - + +
248A VAL* 4.8 1.1 - - + -
249A ASN* 3.2 28.2 + - + +
252A LEU* 3.3 17.5 - - + +
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Residues in contact with GLN 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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51A HIS* 3.4 31.3 + - - +
52A ASN* 3.2 19.7 + - - +
54A ALA* 1.3 76.8 - - - +
56A ALA* 1.3 63.7 + - - +
58A LEU* 3.2 3.1 + - - +
59A LEU* 3.0 29.9 + - + +
69A LYS* 2.9 26.2 + - - +
70A VAL* 3.3 37.3 + - + +
72A PHE* 3.6 15.6 - - + -
234A ASN* 2.8 21.3 + - - -
235A SER* 5.7 0.8 - - - -
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Residues in contact with ALA 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 ASN 3.1 12.4 + - - +
53A GLU* 3.8 6.7 - - - +
55A GLN* 1.3 78.5 - - - +
57A ARG* 1.3 60.5 + - + +
59A LEU* 3.3 9.2 + - - +
60A ALA* 2.8 31.2 + - - +
64A ASN* 5.0 2.1 + - - +
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Residues in contact with ARG 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 GLU* 2.5 54.3 + - + +
54A ALA 3.9 2.7 - - - +
56A ALA* 1.3 74.5 - - + +
58A LEU* 1.3 65.3 + - - +
60A ALA* 3.2 7.0 + - - +
61A LEU* 3.0 29.6 + - + +
249A ASN* 3.2 17.9 - - - -
252A LEU* 4.0 22.9 + - + -
253A LYS* 3.3 36.6 - - - +
256A GLU* 3.2 26.5 + - - +
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Residues in contact with LEU 58 (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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54A ALA 3.0 16.1 + - - +
55A GLN 3.6 4.0 - - - +
56A ALA 3.2 0.2 - - - -
57A ARG* 1.3 77.5 - - - +
59A LEU* 1.3 64.8 + - - +
61A LEU* 3.1 17.4 + - - +
62A LEU* 3.4 19.8 + - + +
70A VAL* 4.2 14.1 - - + -
72A PHE* 5.0 3.6 - - + -
178A ILE* 5.6 1.1 - - + -
179A LEU* 3.9 28.3 - - + -
199A LEU* 5.0 2.9 - - + -
206A VAL* 3.7 34.5 - - + -
208A ILE* 3.5 28.0 - - + -
248A VAL* 5.1 1.8 - - + -
252A LEU* 3.9 15.5 - - + +
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Residues in contact with LEU 59 (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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55A GLN* 3.0 22.0 + - + +
56A ALA* 3.8 6.3 - - - +
58A LEU* 1.3 76.7 - - - +
60A ALA* 1.3 56.0 + - - +
62A LEU* 3.0 15.3 + - + +
63A GLY 3.2 0.2 + - - -
64A ASN* 2.7 50.1 + - - +
65A PRO* 4.6 11.2 - - + +
68A TYR* 3.9 29.4 - - + +
70A VAL* 3.7 21.3 - - + +
185A LEU* 4.2 25.4 - - + -
208A ILE* 4.4 2.0 - - + -
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Residues in contact with ALA 60 (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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56A ALA 2.8 17.7 + - - +
57A ARG* 3.6 8.1 - - - +
58A LEU 3.1 0.2 - - - -
59A LEU* 1.3 75.2 - - - +
61A LEU* 1.3 68.1 + - - +
63A GLY* 3.1 13.0 + - - -
64A ASN* 4.2 14.1 - - + +
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Residues in contact with LEU 61 (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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57A ARG* 3.0 21.8 + - + +
58A LEU* 3.1 7.8 + - - +
60A ALA* 1.3 78.0 - - + +
62A LEU* 1.3 55.7 + - - +
63A GLY 3.6 0.5 + - - -
179A LEU* 4.2 10.1 - - + -
252A LEU* 3.7 35.4 - - + +
255A ILE* 3.7 25.4 - - + -
256A GLU* 4.4 16.4 - - + +
260A GLY* 3.7 29.4 - - - -
261A LEU* 3.3 33.8 + - + +
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Residues in contact with LEU 62 (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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58A LEU* 3.4 29.8 + - + +
59A LEU* 3.0 11.4 + - + +
61A LEU* 1.3 78.5 - - - +
63A GLY* 1.3 56.1 + - - +
64A ASN 3.2 4.5 + - - -
65A PRO* 3.5 14.5 - - + +
178A ILE* 6.0 0.2 - - + -
179A LEU* 4.2 6.5 - - + -
182A PRO* 5.3 0.2 - - + -
183A PHE* 3.6 60.0 - - + +
185A LEU* 4.3 17.9 + - + +
208A ILE* 4.0 15.3 - - + -
261A LEU* 3.6 21.3 - - + -
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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
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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