Contacts of the helix formed by residues 34 - 52 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR* 5.6 7.5 + - - +
30R ILE* 3.2 29.7 + - + +
31R GLY* 2.9 13.3 + - - +
32R ILE 3.6 0.6 - - - -
33R ASP* 1.3 70.5 - - - +
35R ALA* 1.3 63.0 + - - +
36R GLU* 3.7 10.2 + - - +
37R ALA* 3.3 29.5 + - + +
38R ALA 3.3 16.5 + - - -
152R VAL* 3.3 11.4 - - + +
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Residues in contact with ALA 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ASP 3.4 7.8 + - - +
34R ASN* 1.3 73.2 - - - +
36R GLU* 1.3 64.5 + - - +
38R ALA* 3.2 3.0 + - - +
39R TYR* 3.0 36.8 + - + -
151R PHE* 3.9 30.5 - - + -
152R VAL* 4.2 3.8 - - - +
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Residues in contact with GLU 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R ASN* 3.3 8.9 + - - +
35R ALA* 1.3 79.2 - - - +
37R ALA* 1.3 58.1 + - - +
39R TYR* 3.5 6.8 + - - +
40R ALA* 3.0 26.6 + - + +
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Residues in contact with ALA 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR* 5.7 2.2 - - - +
6R LEU* 4.1 24.4 - - + +
30R ILE* 4.4 10.8 - - + -
34R ASN* 3.3 32.4 + - + +
35R ALA 3.2 0.8 - - - -
36R GLU* 1.3 76.6 - - - +
38R ALA* 1.3 60.9 + - - +
40R ALA* 3.0 8.8 + - - +
41R ILE* 2.9 34.7 + - - +
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Residues in contact with ALA 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ILE* 4.5 6.1 - - + +
34R ASN 3.3 2.6 + - - -
35R ALA* 3.2 9.8 + - - +
37R ALA* 1.3 78.7 - - - +
39R TYR* 1.3 62.2 + - - +
41R ILE* 3.3 2.5 + - - +
42R GLN* 3.1 17.8 + - - +
151R PHE* 5.7 0.2 - - + -
152R VAL* 3.4 42.8 - - + +
155R VAL* 3.7 18.2 - - + -
156R ALA* 3.4 19.3 + - - -
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Residues in contact with TYR 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R ALA* 3.0 31.8 + - + +
36R GLU* 3.9 5.8 - - - +
38R ALA* 1.3 76.5 - - - +
40R ALA* 1.3 58.2 + - - +
42R GLN* 3.4 9.7 + - - +
43R HIS* 2.9 29.5 + - - +
77R PRO 4.3 4.3 + - - -
78R ASP* 3.8 10.4 + - - -
79R PHE* 3.2 72.3 + + - -
151R PHE* 4.4 14.8 - + - -
155R VAL* 3.4 25.7 - - + +
210R TRP* 4.4 4.0 - - - -
214R LYS* 4.3 18.4 + - - -
218R LEU* 6.1 2.7 - - + -
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Residues in contact with ALA 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R LEU* 4.1 20.2 - - + -
36R GLU* 3.0 18.0 + - + +
37R ALA* 3.0 10.3 + - - +
39R TYR* 1.3 74.1 - - - +
41R ILE* 1.3 59.7 + - - +
43R HIS* 3.3 8.1 + - - +
44R ILE* 2.9 38.0 + - + +
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Residues in contact with ILE 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R LEU* 4.0 23.8 - - + +
9R LEU* 3.9 31.4 - - + -
10R ALA* 3.8 23.8 - - - +
13R LEU* 3.8 21.1 - - + -
26R LEU* 5.1 1.6 - - + -
30R ILE* 4.2 17.9 - - + -
37R ALA 2.9 17.6 + - - +
38R ALA 3.6 6.3 - - - +
40R ALA* 1.3 74.1 - - - +
42R GLN* 1.3 66.0 + - - +
44R ILE* 3.3 8.8 + - - +
45R ASN* 3.2 22.4 + - - +
156R ALA* 3.9 18.4 - - + +
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Residues in contact with GLN 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ALA 3.1 9.0 + - - +
39R TYR* 3.6 17.9 - - - +
40R ALA 3.4 0.2 - - - -
41R ILE* 1.3 75.5 - - - +
43R HIS* 1.3 59.3 + - - +
45R ASN* 3.2 7.9 + - - +
46R VAL* 2.9 30.2 + - + +
79R PHE* 3.0 40.7 + - - -
81R THR* 3.1 24.1 + - - -
155R VAL* 3.2 26.4 + - - +
156R ALA 3.8 7.8 + - - -
158R ASN* 3.2 34.6 + - + +
159R ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R TYR 2.9 18.2 + - - +
40R ALA* 3.5 8.5 - - - +
42R GLN* 1.3 74.7 - - - +
44R ILE* 1.3 70.4 + - + +
46R VAL* 3.3 8.9 + - - +
47R GLN* 2.9 58.6 + - + +
220R GLU* 4.1 27.6 + - - -
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Residues in contact with ILE 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R LYS* 4.8 10.1 - - + -
6R LEU* 4.9 10.3 - - + +
7R GLU* 3.7 42.6 - - + +
10R ALA* 3.8 20.2 - - + -
14R ARG* 4.5 8.3 - - - +
40R ALA* 2.9 37.2 + - + +
41R ILE* 3.3 10.3 + - - +
43R HIS* 1.3 76.9 - - + +
45R ASN* 1.3 57.7 + - - +
47R GLN* 3.5 5.8 - - - +
48R HIS* 2.9 28.1 + - + +
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Residues in contact with ASN 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R ALA* 3.3 26.8 + - - +
13R LEU* 3.8 20.4 - - - +
14R ARG* 2.8 41.1 + - + +
41R ILE* 3.2 9.7 + - - +
42R GLN* 3.7 8.3 - - - +
43R HIS 3.2 0.6 - - - -
44R ILE* 1.3 76.8 - - - +
46R VAL* 1.3 64.4 + - + +
48R HIS* 3.5 4.4 + - - +
49R ASP* 3.1 31.4 + - - +
156R ALA 4.8 3.4 + - - -
158R ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R GLN* 2.9 29.4 + - + +
43R HIS* 3.8 9.2 - - - +
45R ASN* 1.3 75.3 - - + +
47R GLN* 1.3 65.2 + - - +
49R ASP* 3.2 3.5 + - - +
50R VAL* 2.9 39.3 + - + +
56R VAL* 4.3 4.7 - - + -
59R ARG* 5.3 3.1 - - - +
81R THR* 3.6 39.0 - - + +
83R PHE* 4.1 23.5 - - + -
158R ASN* 4.6 4.0 - - - +
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Residues in contact with GLN 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R HIS* 2.9 50.4 + - + +
44R ILE* 3.5 6.5 - - - +
46R VAL* 1.3 83.1 - - - +
48R HIS* 1.3 60.9 + - - +
50R VAL* 3.4 20.0 + - - +
51R ALA* 3.1 22.7 + - - +
220R GLU* 5.4 1.2 - - - +
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Residues in contact with HIS 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ARG* 3.7 42.1 + - - +
44R ILE* 2.9 17.8 + - + +
45R ASN* 3.7 8.7 - - - +
47R GLN* 1.3 76.5 - - - +
49R ASP* 1.3 74.3 + - - +
51R ALA* 3.3 16.4 + - - +
52R GLN* 3.4 34.9 + - + +
1263R K 3.9 8.5 - - - -
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Residues in contact with ASP 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K HIS* 3.4 18.4 - - - +
14R ARG* 4.7 2.1 - - - -
45R ASN 3.1 17.2 + - - +
46R VAL 3.7 3.6 - - - +
48R HIS* 1.3 87.2 - - - +
50R VAL* 1.3 65.9 + - - +
52R GLN* 3.0 21.4 + - - +
53R GLY 3.4 0.3 + - - -
54R ARG* 3.0 57.5 + - + +
83R PHE* 4.2 8.8 - - + -
1263R K 3.9 2.6 - - - -
1318R NA 3.3 17.3 - - - -
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Residues in contact with VAL 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R VAL* 2.9 26.1 + - + +
47R GLN* 3.8 21.1 - - - +
49R ASP* 1.3 75.0 - - - +
51R ALA* 1.3 55.6 + - - +
53R GLY* 2.8 25.1 + - - -
54R ARG 3.6 19.3 - - - +
56R VAL* 4.0 23.8 - - + +
83R PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R GLN 3.1 13.9 + - - +
48R HIS* 3.5 13.0 - - - +
49R ASP 3.2 0.2 - - - -
50R VAL* 1.3 76.6 - - - +
52R GLN* 1.3 59.2 + - + +
53R GLY 3.2 1.4 + - - -
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Residues in contact with GLN 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LYS* 2.9 33.5 + - - +
4K HIS* 4.2 9.3 + - - +
7K GLU* 3.3 48.2 - - + +
48R HIS* 3.4 32.6 + - + +
49R ASP* 3.0 20.4 + - - +
51R ALA* 1.3 77.2 - - + +
53R GLY* 1.3 59.9 + - - +
54R ARG* 3.5 3.0 + - + +
1263R K 3.4 19.3 - - - -
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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
------------------------------------------------------------
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