Contacts of the helix formed by residues 40 - 54 (chain I) in PDB entry 2WWA
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 GLU 40 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39I TRP* 1.4 86.4 + - - +
41I LEU* 1.4 66.5 + - - +
42I THR* 3.3 23.4 - - + +
43I LYS* 3.5 22.5 - - - +
44I ALA* 3.1 22.9 + - - +
110I THR 4.5 9.4 - - - +
111I LYS 4.7 4.5 - - - +
112I LEU* 4.0 26.2 - - + -
114I VAL* 5.2 2.4 - - - +
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Residues in contact with LEU 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I GLU* 1.4 75.1 - - - +
42I THR* 1.4 56.8 + - - +
44I ALA* 3.6 5.3 + - - +
45I GLN* 3.0 32.6 + - - +
95I LEU* 3.9 27.9 - - + +
98I ALA* 3.8 29.2 - - + +
99I ALA* 4.0 22.2 - - + -
102I ALA* 4.3 11.2 - - + -
112I LEU* 3.9 32.0 - - + +
114I VAL* 5.0 4.3 - - + -
148I LEU* 5.4 0.9 - - + -
150I VAL* 4.3 16.8 - - + -
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Residues in contact with THR 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I GLU* 3.9 23.3 - - + +
41I LEU* 1.4 76.0 - - - +
43I LYS* 1.4 63.3 + - + +
45I GLN* 3.4 8.9 + - - -
46I LYS* 3.1 52.8 + - - +
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Residues in contact with LYS 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TRP* 3.5 59.9 - - + +
40I GLU* 3.5 27.4 + - - +
41I LEU 3.4 0.4 - - - -
42I THR* 1.4 82.0 - - + +
44I ALA* 1.4 61.8 + - - +
46I LYS* 4.2 3.1 - - + +
47I TYR* 3.2 25.5 + - - +
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Residues in contact with ALA 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ILE* 3.8 39.9 - - + +
37I ASN 5.2 0.4 - - - +
39I TRP* 4.2 2.8 - - + -
40I GLU 3.1 18.1 + - - +
41I LEU 3.8 4.0 - - - +
43I LYS* 1.4 75.0 - - - +
45I GLN* 1.4 61.7 + - - +
47I TYR* 3.6 3.0 + - - +
48I LEU* 3.3 29.5 + - - +
95I LEU* 3.9 17.3 - - + -
114I VAL* 5.7 4.7 - - + -
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Residues in contact with GLN 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I LEU* 3.0 20.7 + - - +
42I THR* 3.6 8.9 - - - +
43I LYS 3.4 0.2 - - - -
44I ALA* 1.4 77.2 - - - +
46I LYS* 1.4 82.2 + - + +
48I LEU 3.3 2.1 + - - -
49I GLU* 3.0 53.4 + - - +
92I GLN* 3.5 23.3 - - - +
95I LEU* 4.2 8.0 - - + +
99I ALA* 5.7 4.9 - - - +
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Residues in contact with LYS 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I THR* 3.1 35.6 + - - +
43I LYS* 4.4 3.8 - - + +
45I GLN* 1.4 102.8 + - + +
47I TYR* 1.4 63.9 + - - +
49I GLU* 3.6 22.3 + - - +
50I GLN* 3.2 34.9 + - - +
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Residues in contact with TYR 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ILE 5.1 0.4 - - - +
39I TRP* 3.9 28.7 - + + -
43I LYS* 3.2 24.6 + - - +
44I ALA* 3.8 4.9 - - - +
45I GLN 3.3 0.2 - - - -
46I LYS* 1.4 77.3 - - - +
48I LEU* 1.4 57.8 + - + +
50I GLN* 3.3 12.4 + - - +
51I VAL* 3.0 50.4 + - + +
55I GLN* 4.1 20.7 + - + +
56I ARG* 5.4 1.6 - - - +
57I ALA 3.7 10.7 + - - -
58I ILE* 3.6 36.6 - - + -
59I PRO* 4.2 12.0 - - + +
74I LYS* 4.0 32.5 - - + +
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Residues in contact with LEU 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I THR* 4.5 12.3 - - + -
36I ILE* 4.4 7.0 - - + +
44I ALA 3.3 15.0 + - - +
47I TYR* 1.4 75.2 - - + +
49I GLU* 1.4 62.1 + - - +
51I VAL* 3.5 19.1 - - + +
52I LEU* 3.6 5.4 + - - +
58I ILE* 4.3 25.1 - - + -
88I VAL* 3.3 37.8 - - + +
91I VAL* 3.8 31.9 - - + -
92I GLN* 3.5 35.9 - - + +
95I LEU* 3.9 5.6 - - + -
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Residues in contact with GLU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I GLN* 3.0 46.2 + - - +
46I LYS* 3.8 25.1 - - - +
47I TYR 3.3 0.4 - - - -
48I LEU* 1.4 76.8 - - - +
50I GLN* 1.4 62.3 + - + +
51I VAL 3.3 0.7 - - - -
52I LEU* 3.4 17.8 + - - +
53I ASP* 3.1 15.6 - - - +
92I GLN* 3.8 14.5 + - - +
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Residues in contact with GLN 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LYS* 3.2 24.5 + - + +
47I TYR* 3.3 13.5 + - - +
49I GLU* 1.4 74.6 - - + +
51I VAL* 1.4 57.6 + - - +
52I LEU 3.3 0.2 - - - -
53I ASP* 3.3 11.9 + - - +
54I HIS* 3.0 12.8 + - - +
55I GLN* 3.0 40.0 + - + +
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I TYR* 3.0 33.3 + - + +
48I LEU* 3.5 16.2 - - + +
50I GLN* 1.4 74.4 - - - +
52I LEU* 1.4 66.0 + - - +
53I ASP 3.4 0.3 + - - -
54I HIS 3.6 6.1 + - - -
55I GLN* 3.2 23.1 - - + +
56I ARG 2.9 27.1 - - - +
57I ALA* 3.3 20.6 - - - +
84I PRO 5.3 0.4 - - - +
85I ALA* 5.7 2.7 - - + -
88I VAL* 3.5 32.8 - - + -
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LEU 3.6 7.7 + - - +
49I GLU* 3.4 13.2 + - - +
50I GLN 3.3 0.4 - - - -
51I VAL* 1.4 82.3 - - - +
53I ASP* 1.4 69.6 + - - +
85I ALA* 4.0 28.7 - - + +
88I VAL* 5.2 7.2 - - + -
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Residues in contact with ASP 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLU* 3.1 19.1 - - - +
50I GLN* 3.3 14.3 + - - +
51I VAL 3.3 0.4 - - - -
52I LEU* 1.4 87.0 - - - +
54I HIS* 1.4 68.5 + - + +
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Residues in contact with HIS 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I GLN 3.0 3.6 + - - +
51I VAL 3.6 3.7 + - - -
53I ASP* 1.4 82.2 + - + +
55I GLN* 1.4 64.0 + - + +
56I ARG* 3.0 26.6 + - - -
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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