Contacts of the helix formed by residues 49 - 67 (chain Y) in PDB entry 5A31
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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169X PRO* 4.3 7.2 - - + -
170X LYS* 3.9 31.0 - - + +
173X MET* 3.8 38.4 - - + -
195X VAL* 5.5 3.4 - - + -
199X CYS* 6.4 0.2 - - + -
202X ALA* 5.3 3.1 - - + -
44Y MET* 3.6 51.7 + - + +
45Y ALA* 5.1 0.4 - - - +
47Y ALA* 3.8 16.6 - - + +
48Y GLY* 1.3 73.4 - - - +
50Y HIS* 1.3 65.3 + - - +
51Y SER 3.5 1.8 - - - -
52Y ASN* 3.6 10.9 + - - +
53Y VAL* 3.2 26.7 + - - +
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Residues in contact with HIS 50 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173X MET* 5.5 1.2 - - - +
48Y GLY* 3.3 28.1 + - - -
49Y LEU* 1.3 69.4 - - - +
51Y SER* 1.3 68.1 + - - +
53Y VAL* 3.2 10.3 - - + +
54Y ARG* 2.9 25.5 + - - +
85Y ASP* 3.3 40.9 + - + +
86Y SER* 3.4 14.7 + - - +
88Y PHE* 6.0 2.2 - + - -
89Y HIS* 3.2 52.9 + + + +
90Y ASP* 4.4 2.0 - - - +
141Y LYS* 6.2 0.7 - - - -
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Residues in contact with SER 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173X MET* 5.2 8.0 - - - +
177X ASN* 6.3 0.7 - - - -
204X ASP* 2.8 27.4 + - - +
49Y LEU 3.5 0.2 - - - -
50Y HIS* 1.3 80.4 - - - +
52Y ASN* 1.3 66.0 + - - +
54Y ARG* 3.3 7.5 + - - +
55Y LEU* 3.3 21.1 + - - +
89Y HIS* 5.3 1.4 - - - -
90Y ASP* 4.5 8.6 + - - -
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Residues in contact with ASN 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173X MET* 3.0 40.9 - - - +
195X VAL* 5.6 1.0 - - - +
202X ALA* 3.6 23.2 - - - +
203X LEU 5.0 2.8 + - - -
204X ASP* 3.2 35.2 - - + +
205X ALA* 4.3 3.8 - - - +
44Y MET* 3.3 21.0 - - + +
49Y LEU* 3.6 16.1 + - + +
50Y HIS 3.2 0.4 - - - -
51Y SER* 1.3 76.7 - - - +
53Y VAL* 1.3 65.6 + - - +
55Y LEU* 3.5 0.7 + - - +
56Y LEU* 3.3 23.6 + - - +
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Residues in contact with VAL 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Y VAL* 4.1 16.5 - - + +
44Y MET* 3.4 37.2 - - + +
45Y ALA* 3.8 20.4 - - + +
49Y LEU 3.2 14.5 + - - +
50Y HIS* 3.2 22.9 - - - +
52Y ASN* 1.3 78.6 - - - +
54Y ARG* 1.3 50.7 + - - +
56Y LEU* 3.8 3.2 - - - +
57Y SER* 2.7 43.8 + - - +
82Y TYR* 4.3 11.2 - - + +
85Y ASP* 6.0 0.9 - - + -
86Y SER* 3.7 12.8 - - - -
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Residues in contact with ARG 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271X VAL* 5.5 8.9 - - - +
272X ASP* 5.3 5.0 + - - -
304X LEU* 5.6 4.6 - - - +
306X LYS* 5.6 14.3 - - - +
50Y HIS 2.9 18.7 + - - +
51Y SER* 3.4 7.6 - - - +
53Y VAL* 1.3 74.2 - - - +
55Y LEU* 1.3 82.0 + - - +
57Y SER* 3.1 6.1 + - - -
58Y SER* 2.9 43.7 + - - -
83Y HIS* 3.5 24.3 + - + -
86Y SER* 3.7 17.5 - - - +
87Y LEU* 3.7 14.0 - - + +
90Y ASP* 3.7 20.6 + - - +
92Y GLU* 4.5 18.1 + - - -
95Y ASN* 5.9 0.4 - - - +
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Residues in contact with LEU 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203X LEU* 3.2 33.7 - - + -
204X ASP* 3.4 26.7 - - - +
207X LEU* 3.7 23.1 - - + -
239X TRP* 4.7 5.2 - - + -
272X ASP* 4.3 23.1 - - + +
306X LYS* 5.0 10.3 - - - +
51Y SER* 3.3 8.9 + - - +
52Y ASN 4.2 0.4 - - - +
54Y ARG* 1.3 99.3 - - - +
56Y LEU* 1.3 63.5 + - - +
58Y SER* 3.7 4.1 - - - -
59Y LEU* 3.2 27.0 + - - +
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Residues in contact with LEU 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201X LEU* 3.7 42.6 - - + +
203X LEU* 4.9 14.3 - - + +
233X LEU* 4.9 18.6 - - + -
235X TRP* 4.9 12.8 - - + -
236X LEU* 6.3 1.3 - - + -
37Y VAL* 5.9 1.3 - - + -
41Y VAL* 3.7 22.9 - - + -
44Y MET* 3.9 9.4 - - - -
52Y ASN 3.3 15.3 + - - +
53Y VAL* 4.0 3.4 - - - +
55Y LEU* 1.3 81.0 - - - +
57Y SER* 1.3 56.9 + - - +
59Y LEU* 3.5 2.6 + - - +
60Y LEU* 2.9 49.8 + - + +
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Residues in contact with SER 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y VAL* 5.0 9.4 - - - +
53Y VAL* 2.7 28.1 + - - -
54Y ARG* 3.1 5.9 + - - -
56Y LEU* 1.3 70.0 - - - +
58Y SER* 1.3 55.6 + - - +
60Y LEU* 3.2 5.3 + - - -
61Y LEU* 2.6 38.3 + - - +
79Y LEU* 3.5 25.4 - - - +
82Y TYR 5.1 0.4 - - - -
83Y HIS* 2.9 40.0 + - - +
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Residues in contact with SER 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271X VAL* 4.7 18.4 + - - +
272X ASP* 5.2 8.8 + - - +
54Y ARG* 2.9 31.6 + - - -
55Y LEU* 3.7 5.8 - - - -
57Y SER* 1.3 76.5 + - - +
59Y LEU* 1.3 58.8 + - - +
61Y LEU* 3.3 7.2 + - - +
62Y THR* 3.0 33.0 + - - +
83Y HIS* 3.9 19.5 - - - -
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Residues in contact with LEU 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203X LEU* 4.4 12.8 - - + -
235X TRP* 3.2 48.9 - - + -
239X TRP* 3.8 24.0 - - + +
267X LEU* 3.1 33.7 - - + -
270X ASN* 4.9 7.6 - - - +
55Y LEU 3.2 14.0 + - - +
56Y LEU* 3.6 6.7 - - + +
58Y SER* 1.3 80.3 - - - +
60Y LEU* 1.3 55.6 + - - +
62Y THR* 2.6 23.0 + - - -
63Y LEU* 3.0 21.6 + - + +
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Residues in contact with LEU 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232X ASN* 5.9 1.1 - - + +
233X LEU* 4.1 13.0 - - + -
235X TRP* 5.1 0.7 - - + -
37Y VAL* 3.7 30.7 - - + -
38Y ILE* 4.9 7.2 - - + -
41Y VAL* 3.8 22.0 - - + -
56Y LEU* 2.9 33.7 + - + +
57Y SER* 3.6 6.5 - - - +
59Y LEU* 1.3 77.5 - - + +
61Y LEU* 1.3 56.1 + - - +
63Y LEU* 3.1 19.8 + - + +
64Y SER* 2.8 28.6 + - - -
71Y PHE* 3.7 25.9 - - + -
79Y LEU* 3.7 16.8 - - + -
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Residues in contact with LEU 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Y SER 2.6 19.0 + - - +
58Y SER* 3.5 5.6 - - - +
60Y LEU* 1.3 71.0 - - - +
62Y THR* 1.3 59.7 + - + +
64Y SER* 3.0 7.7 + - - -
65Y ASN* 2.8 44.8 + - - +
76Y LYS* 5.2 2.9 - - + +
79Y LEU* 4.0 20.8 - - + +
80Y LEU* 4.1 26.9 - - + -
83Y HIS* 3.6 46.9 - - + +
99Y LYS* 4.1 14.6 - - - +
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Residues in contact with THR 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266X LEU 3.6 5.8 + - - +
267X LEU* 4.7 1.6 - - - +
269X ASP 3.2 28.9 - - - +
270X ASN* 3.5 22.7 + - + -
271X VAL* 4.6 14.6 - - + +
58Y SER* 3.0 17.6 + - - +
59Y LEU* 2.6 26.5 + - - -
61Y LEU* 1.3 76.3 - - + +
63Y LEU* 1.3 56.5 + - - +
65Y ASN* 3.7 9.4 - - - +
66Y ASN* 3.0 33.6 + - - +
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Residues in contact with LEU 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X ASN 4.5 7.0 - - - +
235X TRP* 3.4 33.0 - - + +
266X LEU* 3.6 47.7 - - + +
267X LEU* 3.8 23.3 - - + +
59Y LEU* 3.0 18.6 + - + +
60Y LEU* 3.1 28.2 + - + +
62Y THR* 1.3 76.2 + - - +
64Y SER* 1.3 57.4 + - - +
66Y ASN* 3.9 0.5 - - - +
67Y ASN* 3.0 30.8 + - - +
70Y LEU* 4.6 6.8 - - + +
71Y PHE* 4.5 11.0 - - + -
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Residues in contact with SER 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Y LEU 2.8 17.0 + - - -
61Y LEU* 3.0 15.2 + - - -
63Y LEU* 1.3 70.5 - - - +
65Y ASN* 1.3 67.7 + - - +
67Y ASN 3.0 26.0 + - - +
68Y PRO* 3.7 5.4 - - - +
70Y LEU* 4.9 0.2 - - - -
71Y PHE* 3.6 22.1 + - - -
76Y LYS* 3.7 34.1 + - - +
79Y LEU* 4.9 4.9 - - - -
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Residues in contact with ASN 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Y LEU* 2.8 35.0 + - - +
62Y THR* 3.7 9.3 - - - +
64Y SER* 1.3 75.9 + - - +
66Y ASN* 1.3 68.8 + - - +
68Y PRO* 4.0 11.6 - - - +
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Residues in contact with ASN 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265X SER* 2.8 29.1 + - - +
266X LEU* 3.7 10.2 + - - +
268X ARG* 3.4 21.4 - - - +
269X ASP* 3.8 24.7 + - - +
62Y THR 3.0 19.9 + - - +
63Y LEU 4.2 0.2 - - - +
65Y ASN* 1.3 84.4 - - - +
67Y ASN* 1.3 64.5 + - - +
68Y PRO* 3.6 7.0 - - - +
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Residues in contact with ASN 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265X SER* 4.3 12.3 + - - -
266X LEU* 3.3 31.9 - - + +
63Y LEU 3.0 9.6 + - - +
64Y SER* 3.0 11.9 + - - +
66Y ASN* 1.3 84.6 - - - +
68Y PRO* 1.4 70.6 + - - +
70Y LEU* 3.1 31.7 + - + +
71Y PHE 4.8 0.2 + - - -
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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