Contacts of the helix formed by residues 37 - 55 (chain A) in PDB entry 3W8I
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 ASN 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU 3.2 2.6 + - - +
34A GLU 3.6 3.6 - - - -
36A VAL* 1.3 83.5 + - - +
38A LEU* 1.3 65.4 + - - +
39A SER* 3.2 14.3 + - - -
40A ALA* 3.0 30.8 + - + +
41A ALA* 3.1 23.6 + - - +
391B ALA* 4.7 9.6 + - - +
392B CYS* 3.7 25.3 - - + -
395B ILE* 4.5 1.1 - - + +
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Residues in contact with LEU 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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34A GLU* 3.3 44.4 + - + +
37A ASN* 1.3 73.8 - - - +
39A SER* 1.3 58.4 + - - +
41A ALA* 3.3 1.0 + - - +
42A GLN* 2.9 65.9 + - + +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.2 11.7 + - - -
38A LEU* 1.3 78.5 - - - +
40A ALA* 1.3 58.2 + - - +
42A GLN* 3.3 13.8 + - - +
43A THR* 2.9 32.8 + - - -
391B ALA* 5.5 5.8 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.0 15.9 + - - +
39A SER* 1.3 76.8 - - - +
41A ALA* 1.3 57.8 + - - +
43A THR* 3.2 10.5 + - - -
44A LEU* 2.9 33.7 + - - +
388B ALA* 3.6 25.9 - - - +
391B ALA* 4.2 8.7 - - + +
392B CYS* 4.0 9.0 - - + -
395B ILE* 3.6 20.4 - - + -
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Residues in contact with ALA 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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30A PHE* 3.9 15.9 - - - +
33A LEU* 3.7 28.9 - - + +
34A GLU* 3.8 11.9 - - + +
37A ASN 3.1 18.2 + - - +
38A LEU 3.6 3.6 - - - +
40A ALA* 1.3 74.4 - - - +
42A GLN* 1.3 60.5 + - - +
44A LEU* 3.1 12.4 + - - +
45A ARG* 2.9 30.1 + - - +
395B ILE* 4.1 2.6 - - - +
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Residues in contact with GLN 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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34A GLU* 5.0 6.2 + - - +
38A LEU* 2.9 52.1 + - + +
39A SER* 3.6 12.1 - - - +
41A ALA* 1.3 75.6 - - - +
43A THR* 1.3 57.4 + - - +
45A ARG* 3.8 11.1 - - - +
46A ALA* 2.9 32.9 + - - +
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Residues in contact with THR 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 SER* 2.9 18.7 + - - -
40A ALA* 3.2 12.6 - - - -
42A GLN* 1.3 76.9 - - - +
44A LEU* 1.3 63.1 + - - +
46A ALA* 3.9 3.9 - - - +
47A ALA* 2.9 26.5 + - - +
384B SER* 3.4 33.9 - - - +
387B VAL* 4.6 12.6 - - + +
388B ALA* 3.9 11.4 - - + +
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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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30A PHE* 3.9 16.8 - - + -
33A LEU* 4.9 5.2 - - + -
40A ALA 2.9 24.0 + - - +
41A ALA* 3.1 8.5 + - - +
43A THR* 1.3 77.5 - - - +
45A ARG* 1.3 62.9 + - - +
47A ALA* 3.2 4.5 + - + +
48A PHE* 2.9 31.6 + - + -
384B SER 4.9 0.4 - - - -
385B ILE* 3.9 35.2 - - + +
388B ALA* 3.7 24.5 - - + -
395B ILE* 3.9 28.5 - - + +
396B THR* 6.0 0.9 - - - +
399B MET* 4.0 22.7 - - + -
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Residues in contact with ARG 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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27A TYR* 3.8 37.8 + - + +
30A PHE* 3.5 41.3 + - + +
31A ASN* 2.5 32.9 + - - +
34A GLU* 3.5 20.6 + - - +
41A ALA* 2.9 16.5 + - - +
42A GLN* 3.8 11.0 - - - +
43A THR 3.4 0.2 - - - -
44A LEU* 1.3 77.4 - - - +
46A ALA* 1.3 63.5 + - - +
48A PHE* 3.3 1.7 + - - +
49A ILE* 2.9 44.8 + - + +
90A GLU* 4.5 8.1 + - - -
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Residues in contact with ALA 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 GLN 2.9 18.6 + - - +
43A THR* 3.9 4.7 - - - +
45A ARG* 1.3 76.1 - - - +
47A ALA* 1.3 56.6 + - - +
49A ILE* 3.3 11.5 + - - +
50A LYS* 2.9 30.3 + - - +
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Residues in contact with ALA 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 THR 2.9 19.5 + - - +
44A LEU* 3.5 7.4 - - + +
46A ALA* 1.3 75.8 - - - +
48A PHE* 1.3 56.8 + - - +
50A LYS* 3.3 6.6 + - - +
51A ALA* 2.9 29.8 + - - +
381B LEU* 3.6 18.6 - - + +
384B SER* 3.5 31.9 - - - +
385B ILE 5.3 0.2 - - - +
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Residues in contact with PHE 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 LEU* 4.1 10.7 - - + +
26A MET* 4.0 22.2 - - + -
30A PHE* 3.6 20.9 - + + -
44A LEU* 2.9 29.2 + - + +
45A ARG 3.8 3.1 - - - +
47A ALA* 1.3 73.1 - - - +
49A ILE* 1.3 60.6 + - - +
51A ALA* 3.3 3.4 + - + +
52A GLU* 2.9 33.3 + - - +
59A THR* 4.5 22.8 + - + -
62A ILE* 4.1 35.7 - - + -
66A ILE* 6.0 1.6 - - + -
357B ILE* 6.6 0.2 - - + -
361B PHE* 5.4 0.4 - + - -
381B LEU* 4.0 25.4 - - + -
385B ILE* 4.5 11.2 - - + -
399B MET* 4.1 29.2 - - + -
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Residues in contact with ILE 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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18A VAL* 4.5 12.5 - - + +
22A LEU* 3.9 13.9 - - + -
27A TYR* 3.3 30.5 - - + +
45A ARG* 2.9 40.3 + - + +
46A ALA* 3.5 8.7 - - - +
48A PHE* 1.3 75.1 - - - +
50A LYS* 1.3 58.6 + - + +
52A GLU* 3.6 1.4 + - - +
53A LYS* 2.9 33.0 + - + +
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Residues in contact with LYS 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 ALA 2.9 17.0 + - - +
47A ALA* 3.7 5.8 - - - +
49A ILE* 1.3 75.9 - - - +
51A ALA* 1.3 60.4 + - - +
53A LYS* 3.3 8.5 + - + +
54A GLU* 2.9 53.1 + - - +
380B GLU* 2.3 43.1 + - - +
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Residues in contact with ALA 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 ALA 2.9 16.6 + - - +
48A PHE* 3.8 3.8 - - + +
50A LYS* 1.3 76.6 - - - +
52A GLU* 1.3 58.7 + - - +
54A GLU* 3.4 3.0 + - - +
55A ASN* 3.0 22.3 + - - +
58A LEU* 3.7 23.8 - - + +
62A ILE* 5.5 0.9 - - + -
377B ALA* 4.2 14.0 - - - +
381B LEU* 3.9 33.7 - - + -
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Residues in contact with GLU 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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18A VAL* 5.5 1.1 - - + -
19A SER* 2.5 44.9 + - - +
22A LEU* 4.3 10.1 - - + -
48A PHE 2.9 17.5 + - - +
49A ILE 4.0 2.5 - - - +
51A ALA* 1.3 73.4 - - - +
53A LYS* 1.3 67.1 + - - +
55A ASN 4.0 2.0 - - - -
56A PRO* 3.3 25.5 - - - +
57A GLY* 2.7 26.0 + - - -
58A LEU* 3.2 5.1 + - - -
59A THR* 2.8 44.7 + - - +
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Residues in contact with LYS 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 ILE* 2.9 23.7 + - + +
50A LYS* 3.4 9.9 - - + +
52A GLU* 1.3 78.5 - - - +
54A GLU* 1.3 72.3 + - - +
56A PRO* 4.5 4.5 - - - +
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Residues in contact with GLU 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 LYS* 2.9 53.1 + - - +
51A ALA* 3.8 4.4 - - - +
53A LYS* 1.3 88.7 + - - +
55A ASN* 1.3 60.0 + - - +
56A PRO* 3.9 5.0 - - - +
373B SER* 5.3 12.9 + - - +
377B ALA* 4.2 21.4 - - + +
380B GLU* 4.9 4.7 - - - +
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Residues in contact with ASN 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 ALA 3.0 10.4 + - - +
52A GLU* 3.3 6.1 - - - +
54A GLU* 1.3 79.8 - - - +
56A PRO* 1.3 74.9 + - - +
57A GLY 5.2 0.2 - - - -
58A LEU* 3.0 33.1 - - + +
371B ASN* 4.1 7.1 + - - -
373B SER* 4.5 5.7 + - - +
374B ARG* 3.3 55.8 + - + +
377B ALA* 4.7 2.7 - - + -
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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