Contacts of the helix formed by residues 35 - 57 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ASN* 3.5 44.4 - - + +
30H ASP 5.1 0.4 - - - +
31H LEU* 3.0 29.0 + - + +
34H ASN* 1.3 86.3 + - + +
36H HIS* 1.4 58.6 + - - +
37H HIS 3.6 0.2 - - - -
38H VAL* 3.5 4.1 + - - +
39H ALA* 3.1 29.7 + - - +
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Residues in contact with HIS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLU* 4.1 5.6 - - - -
176E TYR* 6.1 0.2 - - - -
177E TYR* 2.8 34.0 + + - -
182E ASN* 3.8 23.7 - - + +
31H LEU 2.9 32.0 + - - -
32H HIS* 3.3 22.9 - - + +
35H LYS* 1.4 68.4 - - - +
37H HIS* 1.3 63.5 + - - +
39H ALA* 3.4 15.0 + - - +
40H TYR* 3.2 27.9 + - + -
80H HIS* 5.1 0.2 - - - +
174H HIS* 3.5 43.8 + + + +
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Residues in contact with HIS 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 3.5 12.9 - - + +
11H PRO* 3.5 22.5 - - + +
32H HIS 3.0 15.3 + - - +
33H ILE* 3.3 16.1 + - - +
36H HIS* 1.3 70.1 - - - +
38H VAL* 1.4 59.7 + - - +
40H TYR* 3.1 12.5 + - + +
41H VAL* 3.0 30.2 + - + +
76H GLY 4.7 0.2 - - - -
77H HIS* 3.1 39.8 + - - -
80H HIS* 3.5 16.4 - - + +
81H SER* 3.5 13.5 - - - -
84H TRP* 2.8 33.2 + - + -
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 3.9 20.6 - - + -
33H ILE 3.4 11.1 + - - +
34H ASN* 3.3 31.2 - - - +
35H LYS* 3.7 4.5 - - - +
36H HIS 3.3 0.2 - - - -
37H HIS* 1.4 77.3 - - - +
39H ALA* 1.3 55.6 + - - +
41H VAL* 3.2 9.8 + - + +
42H ASN* 3.0 45.1 + - - +
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LYS 3.1 13.6 + - - +
36H HIS* 3.5 12.8 - - - +
37H HIS 3.3 0.2 - - - -
38H VAL* 1.3 76.6 - - - +
40H TYR* 1.3 59.7 + - + +
42H ASN* 3.9 6.3 - - - +
43H GLY* 2.9 26.7 + - - -
73H HIS* 3.6 8.6 + - + -
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Residues in contact with TYR 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.3 1.3 - - - +
36H HIS* 3.2 28.4 + - + -
37H HIS* 3.1 11.0 + - - +
39H ALA* 1.3 75.7 - - + +
41H VAL* 1.3 60.6 + - - +
44H TYR* 3.0 31.2 + - - +
72H PHE* 3.6 26.1 - + - -
73H HIS* 3.4 38.5 - + - +
76H GLY* 3.8 17.0 - - - -
77H HIS* 3.8 9.6 - - - +
80H HIS* 3.4 29.6 - + - -
155H GLN* 2.8 26.1 + - + -
172H TRP* 3.7 18.2 - - - -
174H HIS* 4.2 6.2 - - - -
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 3.6 31.2 - - + +
9H SER* 4.0 8.3 - - - -
10H LEU* 3.8 25.1 - - + +
37H HIS* 3.0 24.3 + - + +
38H VAL* 3.5 9.9 - - + +
40H TYR* 1.3 76.0 - - - +
42H ASN* 1.3 69.6 + - - +
44H TYR* 3.4 1.9 + - - +
45H ASN* 3.2 33.0 + - - +
77H HIS* 3.8 23.8 - - - +
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Residues in contact with ASN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 3.0 35.8 + - - +
39H ALA* 4.1 5.4 - - - +
41H VAL* 1.3 78.7 - - - +
43H GLY* 1.3 60.1 + - - +
45H ASN* 3.4 8.9 + - - +
46H ALA* 3.0 30.9 + - - +
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Residues in contact with GLY 43 (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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39H ALA 2.9 19.3 + - - -
42H ASN* 1.3 75.7 - - - +
44H TYR* 1.4 55.8 + - - +
46H ALA* 3.9 5.3 - - - +
47H ALA* 3.0 28.6 + - - +
69H ASN* 5.2 0.2 - - - +
73H HIS* 3.5 27.9 - - - -
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Residues in contact with TYR 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G VAL* 3.9 8.4 + - + +
60G LEU* 3.4 37.5 - - + +
63G VAL* 3.6 16.0 - - + +
6H GLU 4.1 17.7 + - - -
8H ILE* 3.7 32.3 - - + -
40H TYR 3.0 18.9 + - - +
42H ASN 3.3 0.2 - - - -
43H GLY* 1.4 73.8 - - - +
45H ASN* 1.3 62.4 + - - +
47H ALA* 3.1 4.7 + - - +
48H ILE* 3.0 65.0 + - + +
70H ILE* 3.9 19.5 - - + -
73H HIS* 3.3 10.9 - - + +
74H GLY* 3.6 21.1 - - - -
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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
----------------------------------------------------------
2H ILE* 3.5 21.5 - - + +
7H LYS* 3.3 26.8 - - + +
8H ILE* 2.9 46.8 + - - +
41H VAL* 3.2 23.6 + - - +
42H ASN* 3.4 9.1 + - - +
44H TYR* 1.3 78.3 - - - +
46H ALA* 1.3 59.2 + - - +
49H ASP* 3.4 20.6 + - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ASN 3.0 17.4 + - - +
43H GLY* 3.9 6.5 - - - +
45H ASN* 1.3 76.3 - - - +
47H ALA* 1.4 58.6 + - - +
49H ASP* 3.6 6.4 + - - +
50H ALA* 3.1 27.9 + - - +
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLY 3.0 19.2 + - - +
44H TYR 3.1 5.8 + - - +
46H ALA* 1.4 73.8 - - - +
48H ILE* 1.4 58.2 + - - +
50H ALA* 3.4 2.9 + - - -
51H LEU* 2.9 31.3 + - - +
66H ILE* 3.3 10.7 - - + +
69H ASN* 4.0 24.9 - - + +
70H ILE* 3.7 24.9 - - + +
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 5.4 1.3 - - + -
55G VAL* 3.8 28.5 - - + -
63G VAL* 4.5 0.2 - - + -
2H ILE* 3.8 24.2 - - + -
6H GLU* 4.7 1.3 - - + -
44H TYR* 3.0 62.1 + - + +
47H ALA* 1.4 72.0 - - - +
49H ASP* 1.3 60.8 + - - +
51H LEU* 3.3 5.7 + - + +
52H GLU* 2.9 52.1 + - - +
70H ILE* 3.8 24.7 - - + -
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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
----------------------------------------------------------
2H ILE* 3.2 39.4 + - + +
45H ASN 3.4 17.6 + - - +
46H ALA* 3.8 7.6 - - - +
47H ALA 3.4 0.2 - - - -
48H ILE* 1.3 79.2 - - - +
50H ALA* 1.4 59.3 + - - +
52H GLU* 3.7 5.0 + - - +
53H LYS* 3.0 50.6 + - - +
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ALA 3.1 17.4 + - - +
47H ALA* 3.9 4.5 - - - +
48H ILE 3.4 0.2 - - - -
49H ASP* 1.4 73.1 - - - +
51H LEU* 1.4 64.5 + - - +
53H LYS* 3.4 12.0 + - - +
54H ALA* 3.1 18.7 + - - +
66H ILE* 3.6 26.5 - - + +
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Residues in contact with LEU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 5.2 2.2 - - + -
51G LEU* 3.7 27.8 - - + -
52G GLU* 6.5 0.4 - - + -
67G GLN* 5.0 3.6 - - - +
70G ILE* 5.5 4.0 - - + -
47H ALA 2.9 18.8 + - - +
48H ILE* 3.3 8.9 + - + +
50H ALA* 1.4 74.8 - - - +
52H GLU* 1.4 59.3 + - + +
54H ALA* 3.2 2.9 + - - +
55H VAL* 2.9 59.5 + - + +
63H VAL* 4.1 27.4 - - + +
66H ILE* 3.8 21.4 - - + +
67H GLN* 4.8 1.6 - - + +
70H ILE* 3.5 20.0 - - + -
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Residues in contact with GLU 52 (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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6G GLU* 5.2 1.9 - - - +
52G GLU* 5.8 7.3 - - + +
55G VAL* 3.8 6.1 - - - +
2H ILE* 3.6 20.0 + - - +
6H GLU* 3.0 37.4 - - - +
48H ILE* 2.9 30.0 + - + +
49H ASP* 3.8 6.1 - - - +
51H LEU* 1.4 79.7 - - + +
53H LYS* 1.3 61.1 + - + +
55H VAL* 4.1 4.9 - - - +
56H GLY* 3.2 19.8 + - - -
3M THR* 6.2 0.2 - - - -
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Residues in contact with LYS 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ASP* 3.0 44.6 + - - +
50H ALA* 3.4 11.7 + - - +
51H LEU 3.3 0.2 - - - -
52H GLU* 1.3 77.3 - - + +
54H ALA* 1.4 59.7 + - - +
56H GLY* 3.4 3.3 + - - -
57H LYS* 3.2 38.8 + - - +
3M THR* 5.7 2.3 - - - +
4M GLU* 3.9 40.2 - - + +
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ALA 3.1 17.0 + - - +
51H LEU 3.2 2.0 + - - +
53H LYS* 1.4 72.8 - - - +
55H VAL* 1.4 63.8 + - - +
57H LYS* 3.5 12.6 + - - +
58H ARG 3.1 3.1 + - - -
59H ASP* 2.8 31.6 + - + +
62H SER* 3.8 26.0 - - - +
63H VAL* 3.7 17.9 - - + +
66H ILE* 4.0 7.2 - - + -
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLU* 3.8 41.8 - - + +
44G TYR* 4.2 5.7 + - - +
48G ILE* 3.7 39.0 - - + -
52G GLU* 4.4 4.3 - - - +
51H LEU* 2.9 45.5 + - + +
52H GLU* 4.1 5.8 - - - +
54H ALA* 1.4 70.8 - - - +
56H GLY* 1.3 61.9 + - - +
58H ARG* 3.2 13.7 + - - +
63H VAL* 3.7 16.6 - - + -
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Residues in contact with GLY 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ASN* 3.8 15.1 + - - +
6G GLU* 4.3 13.0 - - - -
52H GLU 3.2 15.9 + - - -
53H LYS* 3.7 5.2 - - - -
54H ALA 3.3 0.4 - - - -
55H VAL* 1.3 77.1 - - - +
57H LYS* 1.3 56.9 + - - +
58H ARG 3.4 0.8 + - - -
3M THR* 3.3 36.7 - - - +
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Residues in contact with LYS 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H LYS* 3.2 28.5 + - + +
54H ALA* 3.9 14.6 - - - +
55H VAL 3.3 0.4 - - - -
56H GLY* 1.3 73.6 - - - +
58H ARG* 1.4 68.2 + - - +
59H ASP* 3.2 25.0 + - + +
3M THR* 5.7 0.2 - - - -
5M ASN* 4.2 22.7 - - - +
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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