Contacts of the helix formed by residues 34 - 52 (chain H) in PDB entry 2WQT
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 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H THR* 5.6 8.3 + - - +
30H ILE* 3.2 29.1 + - + +
31H GLY* 2.9 9.6 + - - +
32H ILE 3.6 0.4 - - - -
33H ASP* 1.3 73.5 - - - +
35H ALA* 1.3 64.1 + - - +
36H GLU* 3.7 9.5 + - - +
37H ALA* 3.2 30.1 + - + +
38H ALA 3.3 12.6 + - - -
152H VAL* 3.3 15.9 - - + +
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASP 3.4 7.5 + - - +
34H ASN* 1.3 73.6 + - - +
36H GLU* 1.3 64.1 + - - +
38H ALA* 3.2 4.0 + - - +
39H TYR* 3.0 36.2 + - + -
151H PHE* 4.0 25.6 - - + -
152H VAL* 4.2 6.9 - - - +
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ASN* 3.3 8.6 + - - +
35H ALA* 1.3 78.8 - - - +
37H ALA* 1.3 56.8 + - - +
39H TYR* 3.5 6.1 + - - +
40H ALA* 3.0 27.6 + - + +
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Residues in contact with ALA 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H THR* 5.7 2.5 - - - +
6H LEU* 4.1 25.0 - - + +
30H ILE* 4.4 10.5 - - + -
34H ASN* 3.2 33.5 + - + +
35H ALA 3.2 0.2 - - - -
36H GLU* 1.3 77.6 - - - +
38H ALA* 1.3 60.3 + - - +
40H ALA* 3.0 9.1 + - - +
41H ILE* 2.9 34.4 + - - +
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Residues in contact with ALA 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ILE* 4.5 6.1 - - + +
34H ASN 3.3 2.6 + - - -
35H ALA* 3.2 10.2 + - - +
37H ALA* 1.3 76.6 - - - +
39H TYR* 1.3 63.2 + - - +
41H ILE* 3.3 2.7 + - - +
42H GLN* 3.1 17.8 + - - +
152H VAL* 3.4 42.8 - - + +
155H VAL* 3.7 17.7 - - + -
156H ALA* 3.4 19.5 + - - +
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Residues in contact with TYR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ALA* 3.0 31.5 + - + +
36H GLU* 3.9 5.8 - - - +
38H ALA* 1.3 75.0 - - - +
40H ALA* 1.3 56.8 + - - +
42H GLN* 3.4 10.0 + - - +
43H HIS* 2.9 29.9 + - - +
77H PRO 4.3 4.5 + - - -
78H ASP* 3.8 10.9 + - - -
79H PHE* 3.3 71.5 + + - -
151H PHE* 4.4 15.0 - + - -
155H VAL* 3.4 26.1 - - + +
210H TRP* 4.4 3.8 - - - -
214H LYS* 4.3 19.0 + - - -
218H LEU* 5.9 3.1 - - + -
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 4.1 19.1 - - + -
36H GLU* 3.0 15.7 + - + +
37H ALA* 3.0 11.5 + - - +
39H TYR* 1.3 73.8 - - - +
41H ILE* 1.3 58.8 + - - +
43H HIS* 3.3 8.1 + - - +
44H ILE* 2.9 38.0 + - + +
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Residues in contact with ILE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 4.0 24.2 - - + +
9H LEU* 4.0 29.8 - - + -
10H ALA* 3.8 23.6 - - - +
13H LEU* 3.8 21.8 - - + -
26H LEU* 5.1 1.6 - - + -
30H ILE* 4.2 17.9 - - + -
37H ALA 2.9 19.3 + - - +
38H ALA 3.3 6.7 + - - +
40H ALA* 1.3 72.7 - - - +
42H GLN* 1.3 65.4 + - - +
44H ILE* 3.3 9.6 + - - +
45H ASN* 3.2 22.7 + - - +
156H ALA* 3.9 17.7 - - + +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ALA 3.1 9.6 + - - +
39H TYR* 3.6 17.4 - - - +
41H ILE* 1.3 75.6 - - - +
43H HIS* 1.3 58.1 + - - +
45H ASN* 3.2 5.9 + - - +
46H VAL* 2.9 31.4 + - + +
79H PHE* 3.0 40.0 + - - -
81H THR* 3.1 23.4 + - - -
155H VAL 3.2 26.0 + - - +
156H ALA 3.9 7.8 + - - -
158H ASN* 3.2 35.5 + - + +
159H ALA 4.0 0.2 - - - +
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Residues in contact with HIS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H TYR 2.9 18.4 + - - +
40H ALA* 3.5 9.2 - - - +
41H ILE 3.2 0.2 - - - -
42H GLN* 1.3 74.6 - - - +
44H ILE* 1.3 70.8 + - + +
46H VAL* 3.3 8.4 + - + +
47H GLN* 2.9 58.0 + - + +
220H GLU* 4.2 27.4 + - - -
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Residues in contact with ILE 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H LYS* 4.8 10.1 - - - -
6H LEU* 4.9 11.2 - - + +
7H GLU* 3.7 42.0 - - + +
10H ALA* 3.8 20.2 - - + -
14H ARG* 4.5 8.5 - - - +
40H ALA* 2.9 37.7 + - + +
41H ILE* 3.5 8.7 - - - +
43H HIS* 1.3 77.5 - - + +
45H ASN* 1.3 58.9 - - - +
47H GLN* 3.5 6.4 - - - +
48H HIS* 2.9 28.3 + - + +
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Residues in contact with ASN 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ALA* 3.3 27.6 + - - +
13H LEU* 3.8 20.6 - - - +
14H ARG* 2.8 44.7 + - + +
41H ILE* 3.2 10.8 + - - +
42H GLN* 3.7 7.9 - - - +
43H HIS 3.2 0.6 - - - -
44H ILE* 1.3 78.1 - - - +
46H VAL* 1.3 64.5 + - - +
48H HIS* 3.6 3.4 - - - +
49H ASP* 3.2 32.0 + - - +
156H ALA 4.8 3.4 + - - -
158H ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H GLN* 2.9 29.4 + - + +
43H HIS* 3.8 9.4 - - - +
45H ASN* 1.3 75.5 - - + +
47H GLN* 1.3 64.1 + - - +
49H ASP* 3.2 4.2 + - - +
50H VAL* 2.9 38.8 + - + +
56H VAL* 4.4 4.5 - - + -
59H ARG* 5.3 3.1 - - - +
81H THR* 3.6 39.7 - - + +
83H PHE* 4.1 23.5 - - + -
158H ASN* 4.6 3.8 - - - +
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Residues in contact with GLN 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H HIS* 2.9 50.1 + - + +
44H ILE* 3.5 6.7 - - - +
46H VAL* 1.3 84.5 - - - +
48H HIS* 1.3 60.6 + - - +
50H VAL* 3.4 19.3 + - - +
51H ALA* 3.1 22.7 + - - +
220H GLU* 5.4 1.0 - - - +
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Residues in contact with HIS 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 3.7 42.8 + - - +
18H GLU* 6.0 0.2 + - - -
44H ILE* 2.9 18.1 + - + +
45H ASN* 3.6 9.4 - - - +
46H VAL 3.3 0.2 - - - -
47H GLN* 1.3 77.4 - - - +
49H ASP* 1.3 74.9 + - - +
51H ALA* 3.3 16.3 + - - +
52H GLN* 3.3 37.6 + - + +
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Residues in contact with ASP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ARG* 4.8 5.4 - - - -
45H ASN* 3.2 19.5 + - - +
46H VAL 3.2 4.2 + - - +
48H HIS* 1.3 87.2 - - - +
50H VAL* 1.3 65.8 + - - +
52H GLN* 3.0 27.1 + - - +
53H GLY 3.4 0.3 + - - -
54H ARG* 3.0 62.6 + - + +
83H PHE* 4.1 8.7 - - + -
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 2.9 25.0 + - + +
47H GLN* 3.8 20.2 - - - +
48H HIS 3.3 0.2 - - - -
49H ASP* 1.3 75.9 - - - +
51H ALA* 1.3 57.8 + - - +
53H GLY* 2.8 21.7 + - - -
54H ARG 3.7 18.6 - - - +
56H VAL* 3.9 25.1 - - + +
83H PHE* 4.3 3.4 - - + -
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Residues in contact with ALA 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN 3.1 13.4 + - - +
48H HIS* 3.4 13.2 - - - +
50H VAL* 1.3 77.2 - - - +
52H GLN* 1.3 58.8 + - + +
53H GLY 3.2 1.2 + - - -
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Residues in contact with GLN 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H HIS* 3.3 34.2 + - + +
49H ASP* 3.0 27.8 + - - +
51H ALA* 1.3 78.2 - - + +
53H GLY* 1.3 60.3 + - - +
54H ARG* 3.4 3.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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