Contacts of the helix formed by residues 49 - 67 (chain X) in PDB entry 5G04
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 LEU 49 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X MET* 3.3 56.9 + - + +
45X ALA* 5.3 0.2 - - - +
47X ALA* 3.9 17.3 - - + +
48X GLY* 1.3 74.0 - - - +
50X HIS* 1.3 64.7 + - - +
51X SER 3.5 1.3 - - - -
52X ASN* 3.8 18.4 - - + +
53X VAL* 3.2 23.9 + - - +
169Y PRO* 4.6 16.4 - - + +
170Y LYS* 4.7 2.7 - - - -
173Y MET* 3.5 42.8 - - + -
195Y VAL* 5.3 4.9 - - + -
199Y CYS* 5.4 6.1 - - - -
202Y ALA* 5.2 3.1 - - + -
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Residues in contact with HIS 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X ALA* 5.6 4.5 - - + -
48X GLY* 3.2 33.8 + - - -
49X LEU* 1.3 70.2 - - - +
51X SER* 1.3 67.2 + - - +
53X VAL* 3.1 11.0 - - + +
54X ARG* 2.9 27.1 + - - +
85X ASP* 4.4 16.5 - - + +
86X SER* 3.6 18.4 + - - -
89X HIS* 3.2 60.3 + + + +
90X ASP* 4.1 7.4 - - - +
141X LYS* 6.3 0.4 - - - -
173Y MET* 5.2 1.6 - - - +
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Residues in contact with SER 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X HIS* 1.3 79.3 - - - +
52X ASN* 1.3 67.7 + - - -
54X ARG* 3.3 11.4 + - - +
55X LEU* 3.3 17.9 + - - +
89X HIS* 5.5 0.2 - - - -
90X ASP* 4.5 10.1 + - - -
173Y MET* 5.0 10.5 - - - +
177Y ASN* 6.0 2.2 - - - -
204Y ASP* 2.6 33.7 + - - +
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Residues in contact with ASN 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X MET* 3.4 20.5 - - + +
49X LEU* 3.6 21.8 + - + +
50X HIS 3.2 0.4 - - - -
51X SER* 1.3 74.2 - - - +
53X VAL* 1.3 66.7 + - - +
55X LEU* 3.5 0.9 + - - +
56X LEU* 3.3 23.2 + - - +
173Y MET* 3.3 28.0 - - - +
195Y VAL* 5.6 0.6 - - - +
202Y ALA* 3.1 29.7 - - + +
203Y LEU* 4.7 3.1 - - - +
204Y ASP* 2.9 31.1 - - + +
205Y ALA* 3.9 10.5 - - - +
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Residues in contact with VAL 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41X VAL* 4.1 16.4 - - + +
44X MET* 3.5 35.7 - - + -
45X ALA* 3.8 20.4 - - + +
49X LEU 3.2 15.4 + - - +
50X HIS* 3.1 29.2 - - + +
52X ASN* 1.3 79.0 - - - +
54X ARG* 1.3 51.0 + - - +
56X LEU* 3.9 2.6 - - - +
57X SER* 2.7 42.0 + - - +
82X TYR* 4.6 10.1 - - + +
85X ASP* 6.3 0.2 - - + -
86X SER* 3.8 13.2 - - - -
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Residues in contact with ARG 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X HIS 2.9 17.5 + - - +
51X SER* 3.4 11.0 + - - +
52X ASN 3.2 0.2 - - - -
53X VAL* 1.3 78.1 - - - +
55X LEU* 1.3 65.4 + - + +
57X SER* 2.9 7.0 + - - -
58X SER* 2.8 36.0 + - - -
83X HIS* 4.3 8.5 - - + -
86X SER* 3.7 16.6 - - - +
87X LEU* 3.5 27.4 - - - +
90X ASP* 2.5 30.5 + - - +
92X GLU* 3.9 25.9 + - - -
306Y LYS* 3.2 32.2 - - - +
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Residues in contact with LEU 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X SER* 3.3 11.5 + - - +
52X ASN 4.2 1.1 - - - +
54X ARG* 1.3 88.8 - - + +
56X LEU* 1.3 63.3 + - - +
58X SER* 3.7 5.2 - - - -
59X LEU* 3.2 30.0 + - + +
203Y LEU* 3.9 13.2 - - + -
204Y ASP* 3.4 31.2 - - - +
207Y LEU* 3.8 24.0 - - + -
239Y TRP* 4.5 20.0 - - + -
243Y TYR* 6.2 1.1 - - + -
272Y ASP* 3.7 30.5 - - - +
306Y LYS* 4.7 12.6 - - - +
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Residues in contact with LEU 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL* 5.7 1.3 - - + -
40X HIS* 6.3 0.4 - - + -
41X VAL* 3.7 22.9 - - + -
44X MET* 3.7 22.9 - - - -
52X ASN 3.3 14.5 + - - +
53X VAL* 3.9 3.4 - - - +
54X ARG 3.2 0.2 - - - -
55X LEU* 1.3 80.8 - - - +
57X SER* 1.3 57.2 + - - +
59X LEU* 3.5 1.2 + - - +
60X LEU* 2.9 42.7 + - + +
201Y LEU* 4.4 17.9 - - + +
203Y LEU* 3.6 26.9 - - + +
233Y LEU* 4.0 31.0 - - + -
235Y TRP* 4.1 9.0 - - + -
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Residues in contact with SER 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41X VAL* 5.1 8.9 - - - +
53X VAL* 2.7 27.2 + - - -
54X ARG* 2.9 8.8 + - - -
56X LEU* 1.3 71.9 - - - +
58X SER* 1.3 52.6 + - - +
60X LEU* 3.2 4.2 + - - -
61X LEU* 2.7 38.1 + - - +
79X LEU* 3.5 25.6 - - - +
82X TYR 5.2 0.7 - - - -
83X HIS* 2.8 41.0 + - - +
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Residues in contact with SER 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X ARG* 2.8 24.2 + - - -
55X LEU* 3.7 7.0 - - - -
57X SER* 1.3 71.4 + - - +
59X LEU* 1.3 67.8 + - - +
61X LEU* 3.1 7.9 + - - +
62X THR* 2.9 27.7 + - - +
83X HIS* 4.0 18.6 - - - -
270Y ASN* 5.6 0.2 - - - +
271Y VAL* 4.6 12.0 + - - +
272Y ASP* 4.5 21.3 + - - +
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Residues in contact with LEU 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 3.2 18.4 + - + +
56X LEU* 3.7 5.4 - - - +
58X SER* 1.3 79.0 - - - +
60X LEU* 1.3 62.0 + - - +
62X THR* 2.6 21.1 + - - -
63X MET* 2.9 17.5 + - - +
203Y LEU* 4.2 4.7 - - + -
235Y TRP* 4.1 27.4 - - + -
239Y TRP* 3.6 35.9 - - + +
267Y LEU* 4.3 14.8 - - + -
270Y ASN* 3.1 32.8 - - + +
272Y ASP* 4.8 14.6 - - + -
273Y LEU* 5.0 2.9 - - + -
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Residues in contact with LEU 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL* 3.8 22.4 - - + -
38X ILE* 4.6 9.4 - - + -
41X VAL* 3.7 29.8 - - + -
56X LEU* 2.9 30.8 + - + +
57X SER* 3.2 7.4 + - - +
59X LEU* 1.3 76.0 - - + +
61X LEU* 1.3 58.5 + - - +
63X MET* 3.1 19.0 + - - +
64X SER* 2.8 28.8 + - - -
71X PHE* 3.7 25.2 - - + -
79X LEU* 3.7 17.5 - - + -
232Y ASN 4.5 2.5 - - - +
233Y LEU* 4.2 13.7 - - + -
235Y TRP* 5.2 0.4 - - + +
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Residues in contact with LEU 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X SER 2.7 17.6 + - - +
58X SER* 3.4 7.4 - - - +
60X LEU* 1.3 72.5 - - - +
62X THR* 1.3 53.5 + - + +
64X SER* 3.0 6.8 + - - -
65X ASN* 2.8 49.5 + - - +
76X LYS* 5.2 1.8 - - + +
79X LEU* 3.8 23.8 - - + -
80X LEU* 4.1 26.9 - - + -
83X HIS* 3.6 45.5 - - + +
99X LYS* 4.1 15.5 - - - +
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Residues in contact with THR 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X SER* 2.9 15.7 + - - +
59X LEU* 2.6 26.2 + - - -
61X LEU* 1.3 76.2 - - + +
63X MET* 1.3 56.2 + - - +
65X ASN* 3.3 8.1 + - - +
66X ASN* 2.9 35.3 + - - +
266Y LEU 3.8 4.2 + - - -
267Y LEU* 4.5 2.1 - - - +
269Y ASP 2.9 28.7 - - - +
270Y ASN* 2.9 31.0 + - + -
271Y VAL* 4.3 14.1 - - + +
300Y LEU* 5.6 0.4 - - + -
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Residues in contact with MET 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X LEU 2.9 19.1 + - - +
60X LEU* 3.1 19.5 + - + +
62X THR* 1.3 75.3 - - - +
64X SER* 1.3 61.9 + - - +
66X ASN 4.0 0.2 - - - -
67X ASN 3.1 19.1 + - - -
70X LEU* 3.6 27.8 - - + +
71X PHE* 4.6 1.3 - - + -
232Y ASN* 3.4 23.6 - - + +
234Y ASP* 5.6 1.1 - - + +
235Y TRP* 3.1 36.1 - - + -
266Y LEU* 3.6 50.6 - - + +
267Y LEU* 4.1 11.0 - - + -
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Residues in contact with SER 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LEU 2.8 14.9 + - - -
61X LEU* 3.4 13.7 - - - -
63X MET* 1.3 74.7 - - - +
65X ASN* 1.3 67.4 + - - +
67X ASN 2.9 25.1 + - - +
68X PRO* 3.6 5.7 - - - +
70X LEU* 4.6 0.2 - - - -
71X PHE* 3.6 26.8 + - - +
76X LYS* 3.8 27.9 + - - +
79X LEU* 4.8 5.2 - - - -
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Residues in contact with ASN 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F HIS* 3.3 29.5 + - + +
61X LEU* 2.8 34.2 + - - +
62X THR* 3.6 9.6 - - - +
64X SER* 1.3 77.4 + - - +
66X ASN* 1.3 67.3 + - - +
68X PRO* 4.0 7.1 - - - +
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Residues in contact with ASN 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL 3.6 17.3 - - - +
36F HIS* 3.5 33.9 - - - +
37F SER* 5.6 0.2 - - - -
62X THR* 2.9 18.6 + - - +
63X MET 4.1 0.2 - - - +
65X ASN* 1.3 81.5 - - - +
67X ASN* 1.3 65.2 + - - +
68X PRO* 3.9 0.2 - - - -
265Y SER 2.8 29.2 + - - +
266Y LEU* 3.2 17.6 + - - +
268Y ARG* 3.3 24.4 - - - +
269Y ASP* 3.8 15.0 - - - +
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Residues in contact with ASN 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X MET 3.1 7.7 + - - +
64X SER* 2.9 12.4 + - - +
66X ASN* 1.3 85.8 - - - +
68X PRO* 1.3 71.2 - - - +
70X LEU* 3.2 26.1 + - + +
265Y SER* 4.7 12.6 + - - -
266Y LEU* 3.6 29.7 + - + +
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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) + - + + + + + -
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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