Contacts of the helix formed by residues 41 - 62 (chain G) in PDB entry 5Y3A
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 ASP 41 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ASP 3.4 5.3 + - - +
40G THR* 1.3 73.7 + - - +
42G ALA* 1.3 68.6 + - - +
43G ARG* 3.4 26.6 + - - +
44G VAL* 3.4 29.0 + - + +
45G THR* 2.9 25.2 + - - -
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Residues in contact with ALA 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.7 24.6 - - + +
31G LEU* 4.2 12.9 - - + +
34G TYR* 4.6 11.4 - - + -
40G THR 3.6 3.7 + - - +
41G ASP* 1.3 74.5 + - - +
43G ARG* 1.3 60.3 + - - +
44G VAL 3.2 0.4 - - - -
45G THR* 3.3 8.5 + - - -
46G ALA* 3.0 31.8 + - - +
94G TYR* 6.0 0.7 - - - -
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLY 4.4 3.4 - - - +
31G LEU* 4.9 16.8 - - + +
41G ASP* 3.6 19.3 + - - +
42G ALA* 1.3 78.9 - - - +
44G VAL* 1.3 56.4 + - + +
46G ALA* 3.7 5.0 + - - +
47G ALA* 3.0 29.7 + - - +
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Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ASP* 3.4 33.6 + - + +
42G ALA 3.2 0.6 - - - -
43G ARG* 1.3 73.9 - - + +
45G THR* 1.3 59.8 + - - +
47G ALA* 3.3 5.3 + - + +
48G ILE* 3.0 51.0 + - + +
62H LYS* 4.4 10.8 - - + +
63H LEU* 4.3 2.5 - - + -
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Residues in contact with THR 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.8 17.5 - - + -
40G THR* 4.3 6.8 + - - -
41G ASP 2.9 16.5 + - - -
42G ALA* 3.3 8.6 + - - -
44G VAL* 1.3 78.4 - - - +
46G ALA* 1.3 56.5 + - - +
48G ILE* 3.5 1.4 + - - +
49G ALA* 2.9 31.2 + - - +
81G VAL* 5.7 1.3 - - + -
92G CYS* 3.9 10.5 - - - -
94G TYR* 3.7 34.8 + - + -
63H LEU* 3.5 29.5 + - + +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 5.0 1.7 - - + +
25G LEU* 3.5 29.8 - - + +
29G GLY* 3.9 14.3 - - - +
31G LEU* 3.8 26.0 - - + -
42G ALA 3.0 16.4 + - - +
43G ARG 4.0 2.5 - - - +
45G THR* 1.3 74.0 - - - +
47G ALA* 1.3 60.8 + - - +
49G ALA* 4.3 1.6 - - - -
50G SER* 3.0 31.0 + - - -
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLY* 3.8 12.2 + - - +
43G ARG 3.0 20.3 + - - +
44G VAL* 3.3 7.8 + - + +
46G ALA* 1.3 74.6 - - - +
48G ILE* 1.3 61.8 + - + +
50G SER* 3.0 18.5 + - - -
51G ASN* 2.8 25.0 + - - +
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Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G VAL* 3.0 32.7 + - + +
47G ALA* 1.3 77.1 - - + +
49G ALA* 1.3 60.3 + - - +
51G ASN* 3.1 8.2 + - - +
52G ILE* 3.0 49.1 + - + +
59H GLN* 3.4 48.5 - - + +
62H LYS* 4.0 15.5 - - + +
63H LEU* 3.7 32.5 - - + -
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.8 3.8 - - + -
45G THR* 2.9 19.0 + - + +
46G ALA* 3.9 5.8 - - - +
48G ILE* 1.3 79.5 - - - +
50G SER* 1.3 59.4 + - - +
52G ILE* 4.8 1.1 - - - +
53G TRP* 3.3 24.6 + - - +
81G VAL* 5.7 0.4 - - + -
83G ILE* 3.8 31.5 - - + +
90G LEU* 4.4 2.0 - - - +
92G CYS* 4.0 27.6 - - + -
63H LEU* 5.4 2.9 - - + +
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Residues in contact with SER 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.1 3.1 - - - +
27G ASN 4.8 2.0 - - - -
28G GLU 3.9 8.1 + - - -
29G GLY* 3.3 31.2 + - - -
46G ALA 3.0 12.7 + - - -
47G ALA* 3.0 17.3 + - - -
49G ALA* 1.3 74.9 - - - +
51G ASN* 1.3 63.2 + - - +
53G TRP* 3.9 1.4 - - - +
54G ALA* 2.9 30.0 + - - +
90G LEU* 3.8 22.8 - - - +
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Residues in contact with ASN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ALA* 2.8 26.5 + - - +
48G ILE* 3.1 7.0 + - - +
50G SER* 1.3 83.5 + - - +
52G ILE* 1.3 59.8 + - - +
54G ALA* 3.2 6.0 + - - +
55G ALA* 2.9 31.3 + - - +
55H LEU* 5.3 2.2 - - + +
59H GLN* 3.4 38.7 + - - +
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 3.0 37.9 + - + +
49G ALA* 4.3 4.7 - - - +
51G ASN* 1.3 73.3 - - + +
53G TRP* 1.3 66.2 + - - +
55G ALA* 3.4 5.7 + - - +
56G TYR* 3.2 39.4 + - + -
72G ILE* 3.8 23.6 - - + -
74G MET* 3.7 32.8 - - + -
83G ILE* 4.3 10.1 - - + -
56H ALA* 3.8 30.5 - - + +
59H GLN* 4.7 4.9 - - + +
60H GLY 4.5 0.9 - - - +
63H LEU* 5.1 1.1 - - + -
71H ILE* 5.2 0.9 - - + -
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Residues in contact with TRP 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ASN* 5.5 3.4 - - + -
49G ALA 3.3 18.4 + - - +
50G SER 3.9 2.9 - - - +
52G ILE* 1.3 78.8 - - - +
54G ALA* 1.3 55.7 + - - +
56G TYR 3.5 0.3 + - - -
57G ASP* 2.8 50.8 + - + +
69G LEU* 3.6 39.5 - - + +
70G LYS* 3.4 31.6 - - - -
71G PHE* 3.9 4.9 - - - -
72G ILE* 3.7 18.6 - - + -
83G ILE* 3.7 34.1 - - + -
84G THR* 3.8 3.4 - - - -
85G ARG* 3.3 45.6 - - + +
90G LEU* 3.7 27.1 - - + +
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Residues in contact with ALA 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G SER 2.9 20.9 + - - +
51G ASN* 3.2 8.5 + - - +
53G TRP* 1.3 79.3 - - + +
55G ALA* 1.3 55.4 + - - +
57G ASP* 4.0 5.5 - - - +
58G ARG* 2.9 35.7 + - + +
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ASN 2.9 17.0 + - - +
52G ILE* 3.8 7.0 - - - +
53G TRP 3.3 0.2 - - - -
54G ALA* 1.3 76.2 - - - +
56G TYR* 1.3 58.7 + - + +
58G ARG* 3.8 3.0 - - - +
59G ASN* 3.3 32.7 + - - +
52H THR* 3.6 18.8 - - + +
55H LEU* 3.8 27.6 - - + -
56H ALA* 5.9 2.5 - - + -
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ILE* 3.2 27.8 + - + +
55G ALA* 1.3 75.1 - - + +
57G ASP* 1.3 61.3 + - - +
58G ARG 3.3 0.4 - - - -
59G ASN* 5.0 0.9 - - + -
60G GLY* 3.0 17.4 + - - +
69G LEU* 3.9 15.3 - - + -
72G ILE* 4.1 7.4 - - + -
49H PHE* 5.3 9.4 - + - -
52H THR* 3.9 25.4 - - + -
53H PHE* 3.5 25.8 - - - -
56H ALA* 3.9 19.2 - - + +
71H ILE* 3.9 13.7 - - + +
73H CYS* 3.5 30.5 - - + -
75H TYR* 3.0 36.7 + + - +
80H VAL* 5.6 1.6 - - + -
82H GLN* 2.8 29.1 + - - -
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G TRP* 2.8 37.5 + - + +
54G ALA* 4.0 4.7 - - - +
56G TYR* 1.3 74.2 - - - +
58G ARG* 1.3 66.0 + - - +
61G ASN* 3.3 37.8 + - - +
68G ASN 4.5 1.4 + - - -
69G LEU* 3.6 28.5 + - + +
85G ARG* 4.6 7.9 + - - -
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Residues in contact with ARG 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ALA* 2.9 21.9 + - + +
55G ALA* 3.8 6.7 - - - +
57G ASP* 1.3 80.2 - - - +
59G ASN* 1.3 65.6 + - - +
61G ASN* 3.5 4.4 - - - +
62G GLN* 3.0 58.0 + - - +
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Residues in contact with ASN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ALA* 3.3 21.7 + - - +
56G TYR* 4.8 1.1 - - + +
58G ARG* 1.3 83.3 + - - +
60G GLY* 1.3 65.6 + - - +
62G GLN* 3.3 31.3 - - - +
43H HIS* 4.2 1.0 - - - -
48H GLY* 3.8 22.0 + - - -
49H PHE* 3.5 26.1 - - + +
52H THR* 3.5 25.0 + - + +
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Residues in contact with GLY 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR 3.0 21.7 + - - -
57G ASP 4.3 0.4 - - - -
58G ARG 3.2 0.8 - - - -
59G ASN* 1.3 79.7 - - - +
61G ASN* 1.3 60.6 + - - +
68G ASN* 4.0 7.5 - - - +
43H HIS* 3.4 6.4 - - - -
49H PHE* 4.2 3.8 - - - -
75H TYR* 3.4 23.0 + - - -
78H TYR* 3.2 19.5 + - - -
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Residues in contact with ASN 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ASP* 3.3 29.6 + - - +
58G ARG* 3.5 6.8 - - - +
60G GLY* 1.3 71.2 - - - +
62G GLN* 1.3 60.5 + - - +
68G ASN* 3.5 42.8 + - - +
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Residues in contact with GLN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ARG* 3.0 44.9 + - - +
59G ASN* 3.3 29.4 - - - +
60G GLY 3.2 1.2 - - - -
61G ASN* 1.3 82.0 + - - +
43H HIS* 3.2 31.1 + - - +
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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