Contacts of the helix formed by residues 35 - 56 (chain M) in PDB entry 4GUN
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 LYS 35 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ASP 5.0 0.7 - - - +
31M LEU* 2.8 34.4 + - + +
34M ASN* 1.3 87.0 + - + +
36M HIS* 1.4 58.8 + - - +
37M HIS 3.7 0.2 - - - -
38M VAL* 3.6 2.8 + - - +
39M ALA* 3.0 29.2 + - - +
182P ASN* 3.7 42.8 - - + +
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Residues in contact with HIS 36 (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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31M LEU 3.0 26.1 + - - -
32M HIS* 3.4 20.2 - - + +
35M LYS* 1.4 68.1 - - - +
37M HIS* 1.3 65.3 + - - +
39M ALA* 3.1 17.3 + - - +
40M TYR* 3.1 28.2 + - + -
80M HIS* 4.9 0.2 - - - +
172M TRP* 6.1 0.2 - - - -
174M HIS* 3.4 43.7 + + + +
173P GLU* 4.0 6.2 + - - -
177P TYR* 2.7 36.8 + + - -
182P ASN* 3.6 21.4 - - + +
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Residues in contact with HIS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M LEU* 3.6 10.5 - - + +
11M PRO* 3.4 25.0 - - + +
32M HIS 3.0 15.6 + - - +
33M ILE* 3.5 15.9 + - - +
36M HIS* 1.3 71.3 - - - +
38M VAL* 1.3 62.5 + - - +
40M TYR* 3.1 10.5 + - + +
41M VAL* 3.1 22.9 + - + +
76M GLY 4.6 0.9 - - - -
77M HIS* 3.0 39.2 + - - -
80M HIS* 3.6 9.9 - - + +
81M SER* 3.4 19.5 - - - -
84M TRP* 2.8 31.1 + - + -
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Residues in contact with VAL 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M LEU* 3.8 24.0 - - + -
33M ILE 3.4 12.0 + - - +
34M ASN* 3.2 30.1 - - - +
35M LYS 3.9 2.0 - - - +
36M HIS 3.2 0.6 - - - -
37M HIS* 1.3 76.8 - - - +
39M ALA* 1.4 56.2 + - - +
41M VAL* 3.2 11.0 + - + +
42M ASN* 3.0 46.0 + - - +
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Residues in contact with ALA 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M LYS 3.0 15.8 + - - +
36M HIS* 3.1 13.0 + - - +
38M VAL* 1.4 76.1 - - - +
40M TYR* 1.3 58.9 + - + +
42M ASN* 3.6 7.1 + - - +
43M GLY* 2.9 26.0 + - - -
73M HIS* 3.8 7.9 + - + -
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Residues in contact with TYR 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ILE* 4.8 1.1 - - - -
36M HIS* 3.1 32.8 + - + -
37M HIS* 3.1 9.2 + - - +
39M ALA* 1.3 75.9 - - + +
41M VAL* 1.3 59.7 + - - +
44M TYR* 2.9 30.8 + - - +
72M PHE* 3.6 26.4 - + - -
73M HIS* 3.4 39.3 - + - +
76M GLY* 3.8 11.0 - - - -
77M HIS* 3.9 8.5 - - - +
80M HIS* 3.4 33.9 - + - -
155M GLN* 3.0 26.3 + - + -
172M TRP* 3.7 19.6 - - - -
174M HIS* 4.2 6.5 - + - -
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Residues in contact with VAL 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ILE* 3.6 31.3 - - + +
9M SER* 3.9 9.0 - - - -
10M LEU* 3.9 22.4 - - + +
37M HIS* 3.1 35.2 + - + +
38M VAL* 3.4 12.1 - - + +
40M TYR* 1.3 74.8 - - - +
42M ASN* 1.3 67.6 - - - +
44M TYR* 3.9 1.7 - - - +
45M ASN* 3.1 33.4 + - - +
77M HIS* 4.0 12.6 - - - +
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Residues in contact with ASN 42 (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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38M VAL* 3.0 36.4 + - - +
39M ALA* 4.0 6.3 - - - +
41M VAL* 1.3 79.7 - - - +
43M GLY* 1.3 60.6 + - - +
45M ASN* 3.4 6.4 + - - +
46M ALA* 2.9 32.2 + - - +
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Residues in contact with GLY 43 (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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39M ALA 2.9 14.4 + - - -
40M TYR 3.3 0.2 + - - -
42M ASN* 1.3 74.4 - - - +
44M TYR* 1.3 58.5 + - - +
46M ALA* 3.5 5.0 + - - +
47M ALA* 3.0 29.5 + - - +
73M HIS* 3.5 32.2 - - - -
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Residues in contact with TYR 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLU 3.8 20.5 + - - -
8M ILE* 3.6 39.3 - - + -
40M TYR 2.9 17.6 + - - +
43M GLY* 1.3 74.2 - - - +
45M ASN* 1.3 62.9 - - - +
47M ALA* 3.2 4.3 + - - +
48M ILE* 2.9 58.4 + - + +
70M ILE* 4.0 23.1 - - + -
73M HIS* 3.3 12.0 - - + +
74M GLY* 3.6 21.1 - - - -
55N VAL* 4.1 8.0 + - - +
58N ARG* 5.6 0.2 - - - -
60N LEU* 3.5 28.0 - - + +
63N VAL* 3.8 16.7 - - + +
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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
----------------------------------------------------------
2M ILE* 3.3 22.1 - - + +
7M LYS* 3.3 28.9 - - + +
8M ILE* 2.9 48.2 + - - +
41M VAL* 3.1 23.2 + - - +
42M ASN* 3.4 6.7 + - - +
44M TYR* 1.3 83.6 - - - +
46M ALA* 1.3 59.4 + - - +
48M ILE* 4.7 0.2 - - - -
49M ASP* 3.3 21.0 + - - +
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Residues in contact with ALA 46 (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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42M ASN 2.9 18.3 + - - +
43M GLY* 4.0 5.2 - - - +
45M ASN* 1.3 73.8 - - - +
47M ALA* 1.4 61.6 + - - +
49M ASP* 3.6 7.8 + - - +
50M ALA* 3.1 26.9 + - - +
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Residues in contact with ALA 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M GLY 3.0 18.2 + - - +
44M TYR* 3.2 4.7 + - - +
46M ALA* 1.4 75.4 - - - +
48M ILE* 1.3 58.5 + - - +
50M ALA* 3.4 2.9 + - - +
51M LEU* 2.9 29.7 + - - +
66M ILE* 3.3 11.1 - - + +
69M ASN* 4.0 24.0 - - + +
70M ILE* 3.7 25.6 - - + +
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Residues in contact with ILE 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ILE* 3.8 18.8 - - + -
6M GLU* 4.3 7.4 - - + +
44M TYR* 2.9 53.3 + - + +
45M ASN 4.1 2.5 - - - +
47M ALA* 1.3 70.8 - - - +
49M ASP* 1.3 65.5 + - - +
51M LEU* 3.3 8.7 + - + +
52M GLU* 3.2 47.9 + - - +
70M ILE* 4.1 22.4 - - + -
51N LEU* 5.8 0.7 - - + -
55N VAL* 3.7 38.8 - - + -
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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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2M ILE* 3.9 36.4 + - + +
45M ASN 3.3 19.5 + - - +
46M ALA* 3.6 8.9 - - - +
47M ALA 3.3 0.2 - - - -
48M ILE* 1.3 77.2 - - - +
50M ALA* 1.3 60.7 + - - +
52M GLU* 3.9 8.9 + - - +
53M LYS* 3.6 20.8 + - - +
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Residues in contact with ALA 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ALA 3.1 17.4 + - - +
47M ALA* 3.7 6.1 - - - +
48M ILE 3.4 0.2 - - - -
49M ASP* 1.3 72.9 - - - +
51M LEU* 1.3 60.1 + - - +
53M LYS* 3.4 11.5 - - - +
54M ALA* 3.1 23.6 + - - +
66M ILE* 3.6 27.4 - - + +
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Residues in contact with LEU 51 (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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47M ALA 2.9 18.2 + - - +
48M ILE* 3.3 14.1 + - + +
50M ALA* 1.3 72.6 - - - +
52M GLU* 1.4 70.6 + - + +
54M ALA* 3.2 3.9 + - - +
55M VAL* 2.9 52.8 + - + +
63M VAL* 3.9 13.0 - - + +
66M ILE* 4.1 9.2 - - + +
67M GLN* 3.2 29.2 - - - +
70M ILE* 3.6 19.5 - - + -
51N LEU* 3.6 22.9 - - + -
52N GLU* 6.3 2.9 - - + -
55N VAL* 5.8 1.6 - - + -
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Residues in contact with GLU 52 (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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3G THR* 4.5 23.4 + - + +
4G GLU* 5.2 5.4 + - + +
5G ASN* 3.1 22.0 + - - +
2M ILE* 4.5 10.3 + - - +
6M GLU* 3.0 26.8 - - - +
48M ILE* 3.3 33.9 - - - +
49M ASP* 4.0 9.6 - - - +
51M LEU* 1.4 88.7 - - + +
53M LYS* 1.3 56.6 + - - +
55M VAL* 3.9 6.6 - - - +
56M GLY* 3.1 26.2 + - - -
6N GLU* 4.8 3.2 - - - +
52N GLU* 5.4 7.6 - - - +
55N VAL* 4.5 5.2 - - - +
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Residues in contact with LYS 53 (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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3G THR* 4.8 11.3 - - + +
49M ASP* 3.6 15.6 + - - +
50M ALA* 3.4 14.6 - - - +
52M GLU* 1.3 78.8 - - - +
54M ALA* 1.4 60.2 + - - +
56M GLY* 3.7 1.4 + - - -
57M LYS* 3.6 41.9 + - - +
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Residues in contact with ALA 54 (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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50M ALA 3.1 17.2 + - - +
51M LEU 3.8 2.0 - - - +
53M LYS* 1.4 74.2 - - - +
55M VAL* 1.4 64.2 + - - +
56M GLY 3.3 0.2 - - - -
57M LYS* 3.3 4.6 + - - +
58M ARG 3.3 2.8 + - - -
59M ASP* 3.2 33.6 + - + +
62M SER* 3.7 29.8 - - - -
63M VAL* 3.6 16.8 - - + +
66M ILE* 4.2 4.3 - - + -
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Residues in contact with VAL 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 2.9 47.6 + - + +
52M GLU* 3.9 7.0 - - - +
53M LYS 3.4 0.2 - - - -
54M ALA* 1.4 73.5 - - - +
56M GLY* 1.3 61.0 + - - +
58M ARG* 3.4 11.8 + - - +
63M VAL* 3.8 19.7 - - + -
6N GLU* 3.3 45.5 - - + +
44N TYR* 4.2 5.4 + - - +
48N ILE* 3.8 28.3 - - + -
52N GLU* 4.6 3.8 - - + +
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Residues in contact with GLY 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G GLU* 3.5 35.7 - - - +
52M GLU 3.1 15.7 + - - -
53M LYS 4.1 2.5 - - - -
54M ALA 3.3 0.2 - - - -
55M VAL* 1.3 78.2 - - - +
57M LYS* 1.4 58.7 + - - +
58M ARG 3.4 0.2 - - - -
5N ASN* 3.9 13.8 - - - +
6N GLU* 4.3 2.2 - - - -
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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