Contacts of the helix formed by residues 34 - 52 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M THR* 5.6 8.3 + - - +
30M ILE* 3.2 29.8 + - - +
31M GLY* 2.9 8.1 + - - +
32M ILE 3.6 0.4 - - - -
33M ASP* 1.3 73.7 - - - +
35M ALA* 1.3 63.9 + - - +
36M GLU* 3.7 9.5 + - - +
37M ALA* 3.3 30.3 + - + +
38M ALA 3.3 12.0 + - - -
152M VAL* 3.3 15.1 - - - +
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Residues in contact with ALA 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ASP 3.4 7.1 + - - +
34M ASN* 1.3 71.5 - - - +
36M GLU* 1.3 66.7 + - - +
38M ALA* 3.1 4.4 + - - +
39M TYR* 3.0 35.0 + - + -
151M PHE* 4.0 25.8 - - + -
152M VAL* 4.4 7.2 - - - -
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Residues in contact with GLU 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M ASN* 3.3 8.2 + - - +
35M ALA* 1.3 80.0 - - - +
37M ALA* 1.3 57.0 + - - +
39M TYR* 3.5 6.4 + - - +
40M ALA* 3.0 27.6 + - + +
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Residues in contact with ALA 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M THR* 5.7 2.2 - - - +
6M LEU* 4.1 24.5 - - + +
30M ILE* 4.4 10.3 - - + -
34M ASN* 3.3 32.7 + - + +
35M ALA 3.2 0.6 - - - -
36M GLU* 1.3 77.3 - - - +
38M ALA* 1.3 60.8 + - - +
40M ALA* 3.1 8.9 + - - +
41M ILE* 3.0 34.5 + - - +
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Residues in contact with ALA 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ILE* 4.5 6.6 - - + +
34M ASN 3.3 2.4 + - - -
35M ALA* 3.1 10.2 + - - +
37M ALA* 1.3 77.6 - - - +
39M TYR* 1.3 60.6 + - - +
41M ILE* 3.3 2.5 + - - +
42M GLN* 3.1 18.5 + - - +
151M PHE* 5.7 0.2 - - + -
152M VAL* 3.4 41.7 - - + +
155M VAL* 3.7 17.7 - - + -
156M ALA* 3.4 20.3 + - - +
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Residues in contact with TYR 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ALA* 3.0 30.9 + - + +
36M GLU* 3.9 6.1 - - - +
38M ALA* 1.3 77.0 - - - +
40M ALA* 1.3 58.4 + - - +
42M GLN* 3.4 10.0 + - - +
43M HIS* 2.9 29.5 + - - +
77M PRO 4.3 4.7 + - - -
78M ASP* 3.8 10.7 + - - -
79M PHE* 3.2 73.3 + + - -
151M PHE* 4.5 12.5 - + - -
155M VAL* 3.4 28.4 - - + +
210M TRP* 4.4 3.6 - - - -
214M LYS* 4.3 18.9 + - - -
218M LEU* 6.1 2.5 - - + -
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Residues in contact with ALA 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 4.1 19.7 - - + -
36M GLU* 3.0 16.6 + - + +
37M ALA* 3.1 10.1 + - - +
39M TYR* 1.3 74.3 - - - +
41M ILE* 1.3 60.8 + - - +
43M HIS* 3.3 8.7 + - - +
44M ILE* 2.9 38.0 + - + +
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Residues in contact with ILE 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 4.0 23.3 - - + +
9M LEU* 4.0 30.3 - - + -
10M ALA* 3.8 17.9 - - - +
13M LEU* 3.8 27.6 - - + -
26M LEU* 5.1 1.8 - - + -
30M ILE* 4.2 17.9 - - + -
37M ALA 3.0 18.5 + - - +
38M ALA 3.3 6.9 + - - +
40M ALA* 1.3 74.1 - - - +
42M GLN* 1.3 65.7 + - - +
44M ILE* 3.2 10.0 + - - +
45M ASN* 3.2 21.9 + - - +
156M ALA* 3.9 18.2 - - + +
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Residues in contact with GLN 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ALA 3.1 9.4 + - - +
39M TYR* 3.4 13.6 + - - +
41M ILE* 1.3 75.1 - - - +
43M HIS* 1.3 57.4 + - - +
45M ASN* 3.2 6.8 + - - +
46M VAL* 2.9 30.3 + - + +
79M PHE* 3.0 41.3 + - - -
81M THR* 3.1 23.7 + - - -
155M VAL* 3.2 30.9 + - - +
156M ALA 3.9 7.7 + - - +
158M ASN* 3.2 34.8 + - + +
159M ALA 4.0 0.6 - - - +
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Residues in contact with HIS 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR 2.9 19.2 + - - +
40M ALA* 3.5 9.2 - - - +
42M GLN* 1.3 75.5 - - - +
44M ILE* 1.3 70.3 + - + +
46M VAL* 3.2 8.7 + - + +
47M GLN* 2.8 58.6 + - + +
220M GLU* 4.2 27.4 + - - -
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Residues in contact with ILE 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M LYS* 4.8 10.3 - - - -
6M LEU* 4.9 11.0 - - + +
7M GLU* 3.6 43.1 - - + +
10M ALA* 3.9 20.6 - - + -
14M ARG* 4.5 7.9 - - - +
40M ALA* 2.9 37.0 + - + +
41M ILE* 3.2 9.8 + - - +
43M HIS* 1.3 75.6 - - + +
45M ASN* 1.3 58.2 + - - +
47M GLN* 3.3 6.6 + - - +
48M HIS* 2.9 28.0 + - + +
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Residues in contact with ASN 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ALA* 3.2 27.2 + - - +
13M LEU* 3.8 16.8 - - - +
14M ARG* 2.8 43.0 + - + +
41M ILE* 3.2 13.1 + - - +
42M GLN* 3.7 8.7 - - - +
43M HIS 3.2 0.6 - - - -
44M ILE* 1.3 77.1 - - - +
46M VAL* 1.3 64.0 + - + +
48M HIS* 3.7 3.5 - - - +
49M ASP* 3.2 30.9 + - - +
156M ALA 4.8 3.6 + - - -
158M ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M GLN* 2.9 29.7 + - + +
43M HIS* 3.2 9.6 + - - +
45M ASN* 1.3 74.5 - - + +
47M GLN* 1.3 65.5 + - - +
49M ASP* 3.2 3.6 + - - +
50M VAL* 2.9 39.1 + - + +
56M VAL* 4.4 4.7 - - + -
59M ARG* 5.3 3.4 - - - +
81M THR* 3.6 38.4 - - + +
83M PHE* 4.1 23.7 - - + -
158M ASN* 4.7 3.8 - - - +
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Residues in contact with GLN 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M HIS* 2.8 49.7 + - + +
44M ILE* 3.5 6.7 - - - +
46M VAL* 1.3 83.4 - - - +
48M HIS* 1.3 61.3 + - - +
50M VAL* 3.5 20.0 + - - +
51M ALA* 3.1 23.0 + - - +
220M GLU* 5.4 0.7 - - - +
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Residues in contact with HIS 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ARG* 3.7 43.3 + - - +
44M ILE* 2.9 18.4 + - + +
45M ASN* 3.7 8.7 - - - +
47M GLN* 1.3 76.3 - - - +
49M ASP* 1.3 75.2 + - - +
51M ALA* 3.3 15.7 + - - +
52M GLN* 3.3 37.9 + - + +
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Residues in contact with ASP 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ARG* 4.8 2.8 - - - -
45M ASN 3.2 16.9 + - - +
46M VAL 3.2 3.6 + - - +
48M HIS* 1.3 88.6 - - - +
50M VAL* 1.3 63.9 + - - +
52M GLN* 3.0 27.3 + - - +
53M GLY 3.4 0.3 + - - -
54M ARG* 3.0 62.4 + - + +
83M PHE* 4.1 9.1 - - + -
1307M NA 3.3 19.5 - - - -
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Residues in contact with VAL 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M VAL* 2.9 26.6 + - + +
47M GLN* 3.8 21.5 - - - +
48M HIS 3.4 0.2 - - - -
49M ASP* 1.3 75.2 - - - +
51M ALA* 1.3 57.8 + - - +
53M GLY* 2.8 21.5 + - - -
54M ARG 3.6 19.9 - - - +
56M VAL* 4.0 24.5 - - + +
83M PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M GLN 3.1 13.6 + - - +
48M HIS* 3.4 13.5 - - - +
49M ASP 3.2 0.2 - - - -
50M VAL* 1.3 76.0 - - - +
52M GLN* 1.3 58.9 + - + +
53M GLY 3.3 1.4 + - - -
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Residues in contact with GLN 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M HIS* 3.3 33.1 + - + +
49M ASP* 3.0 27.1 + - - +
51M ALA* 1.3 76.3 - - + +
53M GLY* 1.3 59.2 + - - +
54M ARG* 3.4 3.9 + - + +
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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