Contacts of the helix formed by residues 31 - 54 (chain F) in PDB entry 1GN2
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 31 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ASN* 3.5 46.9 - - + +
27F LEU* 2.8 34.1 + - + +
29F HIS 3.3 0.2 - - - -
30F SER* 1.3 90.6 + - - +
32F HIS* 1.3 64.6 + - - +
34F ALA* 3.6 1.8 + - - +
35F THR* 2.8 31.3 + - - -
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Residues in contact with HIS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E GLU* 4.1 6.9 + - - -
167E TYR* 2.4 45.6 + + - -
172E ASN* 3.9 16.3 - - + +
27F LEU 3.1 18.4 + - - -
28F HIS* 3.3 25.8 - + + +
31F LYS* 1.3 78.3 - - + +
33F HIS* 1.3 68.2 + - - +
35F THR* 3.1 16.0 + - - -
36F TYR* 3.2 25.3 + - + -
164F HIS* 3.7 34.1 + + + +
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Residues in contact with HIS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 3.8 9.6 - - + +
7F PRO* 3.8 11.3 - - + +
28F HIS 2.9 15.8 + - - +
29F HIS* 3.3 15.2 + - - +
32F HIS* 1.3 73.0 - - - +
34F ALA* 1.3 64.6 + - - +
36F TYR* 3.1 17.9 + - + +
37F VAL* 3.1 19.3 + - + +
73F HIS* 3.1 34.2 + - - -
76F HIS* 3.0 31.1 - + + +
77F THR* 3.4 18.6 + - - -
80F TRP* 2.9 27.1 + + - +
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Residues in contact with ALA 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 3.8 26.4 - - + +
29F HIS 3.3 4.2 + - - -
30F SER 3.5 24.7 - - - +
31F LYS 3.6 2.7 + - - +
32F HIS 3.2 0.6 - - - -
33F HIS* 1.3 78.1 - - - +
35F THR* 1.3 58.0 + - - +
37F VAL* 3.4 6.9 + - - +
38F LYS* 3.0 28.1 + - - +
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Residues in contact with THR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LYS 2.8 17.2 + - - -
32F HIS* 3.1 12.7 + - - +
33F HIS 3.1 0.8 - - - -
34F ALA* 1.3 78.1 - - - +
36F TYR* 1.3 64.8 + - + +
38F LYS* 3.5 6.9 + - - +
39F GLY* 3.0 23.4 + - - -
69F ASN* 4.3 3.7 - - - +
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Residues in contact with TYR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.2 29.7 + - + -
33F HIS* 3.1 14.4 + - - +
35F THR* 1.3 78.9 - - + +
37F VAL* 1.3 56.7 + - - +
39F GLY 3.1 0.7 + - - -
40F ALA* 2.7 36.2 + - - +
68F PHE* 4.0 17.6 - + - -
69F ASN* 3.5 27.4 - - - +
72F GLY* 4.0 11.0 - - - -
73F HIS* 3.8 17.9 - - - +
76F HIS* 3.6 24.5 - + - -
145F HIS* 2.7 38.8 + + - -
162F TRP* 3.8 19.2 - - - -
164F HIS* 4.4 6.2 - + - -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 3.7 23.7 - - - +
5F THR* 4.1 0.4 - - - -
6F LEU* 3.9 25.6 - - + +
33F HIS* 3.1 18.5 + - + +
34F ALA* 3.6 9.4 - - - +
36F TYR* 1.3 80.7 - - - +
38F LYS* 1.3 65.2 + - - +
40F ALA* 3.3 6.9 + - - +
41F ASN* 3.1 26.2 + - - +
73F HIS* 3.5 37.2 - - + +
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Residues in contact with LYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ALA 3.0 17.2 + - - +
35F THR* 3.9 7.4 - - + +
36F TYR 3.2 0.4 - - - -
37F VAL* 1.3 78.3 - - + +
39F GLY* 1.3 60.7 + - - +
41F ASN* 3.2 7.6 + - + +
42F ASP* 2.9 59.9 + - - +
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Residues in contact with GLY 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F THR 3.0 15.5 + - - -
36F TYR 3.5 3.6 - - - -
38F LYS* 1.3 81.0 - - - +
40F ALA* 1.3 54.9 + - - +
42F ASP* 3.8 6.9 - - - +
43F ALA* 3.0 29.8 + - - +
65F ASN* 5.6 0.2 - - - +
69F ASN* 3.6 22.9 + - - -
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 3.8 24.5 - - + -
36F TYR 2.7 20.1 + - - +
37F VAL* 3.8 6.7 - - - +
38F LYS 3.2 0.2 - - - -
39F GLY* 1.3 69.3 - - - +
41F ASN* 1.3 67.0 + - - +
43F ALA* 3.3 5.7 + - - +
44F VAL* 3.1 27.0 + - - +
66F LEU* 4.7 2.1 - - + +
69F ASN* 3.4 18.8 - - - +
70F LEU* 4.1 15.3 - - + +
73F HIS* 5.0 2.0 - - + -
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Residues in contact with ASN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLU* 3.7 26.7 + - + +
4F TYR* 2.8 57.3 + - - +
37F VAL* 3.1 19.3 + - - +
38F LYS* 3.7 9.2 - - + +
40F ALA* 1.3 77.5 - - - +
42F ASP* 1.3 64.3 + - - +
44F VAL* 3.1 9.5 + - - +
45F ALA* 3.0 21.4 + - - +
136H LYS* 4.7 1.7 + - - -
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LYS* 2.9 61.9 + - - +
39F GLY* 3.8 6.6 - - - +
41F ASN* 1.3 71.9 - - - +
43F ALA* 1.3 58.3 + - - +
45F ALA* 3.1 8.3 + - - +
46F LYS* 2.9 34.7 + - + +
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLY 3.0 19.2 + - - +
40F ALA* 3.6 5.2 - - - +
41F ASN 3.2 0.2 - - - -
42F ASP* 1.3 75.3 - - - +
44F VAL* 1.3 63.8 + - - +
46F LYS* 3.3 7.8 + - - +
47F LEU* 3.3 28.9 + - - +
62F ASN* 4.5 3.7 + - - +
65F ASN* 4.0 12.1 - - + +
66F LEU* 3.6 39.3 - - + +
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 4.0 20.4 - - + -
40F ALA 3.1 13.6 + - - +
41F ASN* 3.4 9.4 - - - +
43F ALA* 1.3 77.9 - - - +
45F ALA* 1.3 64.3 + - + +
47F LEU* 3.3 17.3 + - - +
48F GLU* 3.3 28.0 + - - +
51F ARG* 4.9 1.0 + - - -
66F LEU* 4.0 18.2 - - + -
136H LYS* 4.4 17.5 - - + +
138H LEU* 4.6 12.6 - - + -
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ASN 3.0 12.6 + - - +
42F ASP* 3.5 10.1 - - - +
44F VAL* 1.3 79.5 - - + +
46F LYS* 1.3 64.3 + - + +
48F GLU* 2.9 27.6 + - - +
49F GLU* 2.9 15.5 + - - +
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASP* 2.9 20.2 + - + +
43F ALA* 3.3 5.3 + - - +
45F ALA* 1.3 75.8 - - - +
47F LEU* 1.3 52.6 + - - +
49F GLU* 3.5 34.1 + - - +
50F ALA* 2.8 34.4 + - - +
62F ASN* 3.6 28.8 - - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ALA 3.3 18.6 + - - +
44F VAL* 3.6 10.5 - - - +
45F ALA 3.0 0.6 - - - -
46F LYS* 1.3 75.3 - - - +
48F GLU* 1.3 56.6 + - - +
50F ALA* 3.1 8.0 + - + +
51F ARG* 2.7 53.7 + - - +
56F HIS* 4.9 1.1 - - + +
59F ILE* 4.3 11.9 - - + -
62F ASN* 3.8 39.7 - - + +
63F GLU* 4.7 3.6 - - - +
66F LEU* 4.1 22.4 - - + -
112H GLN* 3.8 28.5 - - + +
138H LEU* 6.1 2.2 - - + -
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Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F VAL* 3.3 24.4 + - - +
45F ALA* 2.9 18.2 + - - +
47F LEU* 1.3 77.6 - - - +
49F GLU* 1.3 60.5 + - - +
51F ARG* 3.0 26.6 + - - +
52F ALA* 2.8 30.6 + - - +
102H ALA 5.5 0.7 - - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F ALA 2.9 11.0 + - - +
46F LYS* 3.8 34.7 + - - +
48F GLU* 1.3 83.1 - - - +
50F ALA* 1.3 59.9 + - - +
52F ALA* 3.8 5.3 - - - +
53F LYS* 3.1 58.7 + - + +
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Residues in contact with ALA 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LYS 2.8 19.6 + - - +
47F LEU* 3.5 9.4 - - + +
49F GLU* 1.3 77.7 - - - +
51F ARG* 1.3 61.5 + - - +
53F LYS* 5.2 2.0 - - - +
54F GLU* 3.1 3.3 + - - -
55F ASP* 3.1 44.3 + - - +
56F HIS* 3.9 18.3 - - + +
62F ASN* 4.3 11.7 - - - +
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Residues in contact with ARG 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F VAL 4.9 1.2 + - - -
47F LEU* 2.7 26.9 + - - +
48F GLU* 3.0 40.1 + - - +
50F ALA* 1.3 77.0 - - - +
52F ALA* 1.3 64.0 + - - +
54F GLU* 3.4 11.2 + - - +
56F HIS* 4.0 15.9 - - + +
102H ALA 3.5 13.8 + - - -
103H PHE* 3.4 50.7 + - - +
108H LYS* 3.7 38.8 - - + +
112H GLN* 2.8 41.2 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F GLU 2.8 15.2 + - - +
49F GLU* 3.8 6.7 - - - +
51F ARG* 1.3 77.7 - - - +
53F LYS* 1.3 65.7 + - + +
54F GLU* 3.1 8.7 + - - +
108H LYS* 4.0 17.3 + - - +
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLU* 3.1 42.9 + - + +
50F ALA* 5.2 0.7 - - - +
52F ALA* 1.3 76.7 - - + +
54F GLU* 1.3 76.9 + - - +
55F ASP* 4.1 22.9 - - + +
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ALA 3.1 6.6 + - - -
51F ARG* 3.4 8.7 + - - +
52F ALA 3.1 12.6 - - - +
53F LYS* 1.3 83.3 - - - +
55F ASP* 1.3 57.7 - - - +
56F HIS* 4.1 6.7 - - - -
108H LYS* 5.2 9.6 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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