Contacts of the strand formed by residues 51 - 63 (chain C) in PDB entry 2BG9
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 THR 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.3 22.5 - - + +
44C SER 4.2 0.3 - - - +
45C LEU 4.1 0.5 - - - -
46C LYS* 3.2 29.1 + - + +
49C ASP* 3.0 24.3 + - - +
50C GLU* 1.3 74.4 + - - +
52C LEU* 1.3 73.5 + - - +
53C THR* 5.4 0.9 - - - +
127C ARG* 3.5 36.3 - - + +
128C SER 2.8 13.7 + - - +
129C SER* 4.7 1.0 - - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 5.4 7.6 - - + -
44C SER 3.5 9.0 - - - +
45C LEU* 3.8 25.6 - - + -
46C LYS 4.6 0.2 - - - +
51C THR* 1.3 98.0 - - - +
53C THR* 1.3 62.6 + - - +
54C THR* 3.8 11.7 + - + +
126C PHE 3.5 0.9 - - - +
127C ARG* 3.1 3.6 - - - -
128C SER* 2.6 73.4 + - - +
130C CYS* 3.2 33.9 - - + +
132C ILE* 4.0 13.7 - - + -
136C TYR* 4.9 4.3 - - - +
144C CYS* 4.9 4.3 - - - -
146C LEU* 5.8 0.2 - - + -
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.1 36.5 + - + +
44C SER* 3.1 27.9 + - - +
51C THR* 5.4 0.7 - - - +
52C LEU* 1.3 70.4 - - - +
54C THR* 1.3 63.8 + - - +
125C ILE* 4.8 14.4 - - + -
126C PHE 2.9 15.5 - - - +
127C ARG* 4.1 22.5 + - + +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.2 10.8 - - + -
41C ASN 3.4 4.5 - - - +
42C LEU* 2.8 54.1 - - + -
43C ILE* 4.0 4.7 - - - -
52C LEU* 3.8 10.6 + - + +
53C THR* 1.3 73.4 - - - +
55C ASN* 1.3 54.5 + - - +
125C ILE* 4.7 0.4 - - - -
126C PHE* 2.6 75.8 + - - -
128C SER* 4.1 2.6 + - - -
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.3 3.3 - - - +
40C SER* 2.8 30.8 + - - -
41C ASN* 2.5 33.7 + - + +
43C ILE* 4.2 7.5 - - + +
54C THR* 1.3 72.9 - - - +
56C VAL* 1.3 68.8 + - - +
123C PRO* 3.8 11.4 - - - +
124C ALA 2.7 46.3 + - - +
125C ILE* 3.3 17.7 - - - +
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 5.1 5.4 - - + -
38C THR 3.4 8.7 - - - +
39C LEU* 3.9 25.4 - - + -
40C SER* 4.2 1.1 - - - +
55C ASN* 1.3 79.5 - - - +
57C TRP* 1.3 66.5 + - - +
58C MET* 3.4 7.7 + - + +
94C LEU* 5.4 3.1 - - + -
123C PRO* 3.3 2.8 - - - +
124C ALA* 2.6 57.2 + - + +
126C PHE* 3.0 35.7 - - + -
148C PHE* 4.4 23.1 - - + -
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Residues in contact with TRP 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER 3.2 11.4 - - - +
37C LEU* 4.2 1.0 - - - -
38C THR* 2.5 67.1 + - + +
39C LEU 4.1 5.6 - - - -
40C SER* 3.5 32.2 + - - -
55C ASN* 6.3 0.2 - - - -
56C VAL* 1.3 74.0 - - - +
58C MET* 1.3 57.5 + - - +
59C ASP* 2.9 25.0 + - - +
121C LEU* 4.9 9.6 - - + +
122C PRO 4.1 3.4 - - - -
123C PRO* 4.7 15.4 - - + +
182C GLU* 4.8 4.9 - - - -
183C ALA* 5.5 2.7 - - + -
149D TRP* 5.3 11.8 - + - -
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Residues in contact with MET 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 5.4 2.5 - - + -
36C SER 3.9 2.9 - - - -
37C LEU* 5.3 5.6 - - + -
56C VAL* 3.4 8.3 + - + +
57C TRP* 1.3 66.9 - - - +
59C ASP* 1.3 64.3 + - - +
60C HIS* 3.0 6.4 + - + -
92C ILE* 2.6 46.0 - - + +
94C LEU* 6.5 0.9 - - - -
102C TYR* 5.7 3.1 - - - -
105C ALA* 2.6 40.2 - - + +
120C TRP* 3.0 32.1 - - + +
121C LEU* 3.5 6.6 - - - -
122C PRO* 3.0 39.2 + - + +
124C ALA* 5.1 3.8 - - + -
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA 4.0 0.3 - - - +
35C LEU* 3.4 2.4 - - - -
36C SER* 2.5 61.8 + - - +
38C THR* 6.0 2.7 - - - +
57C TRP* 2.9 20.0 + - - +
58C MET* 1.3 69.0 - - - +
60C HIS* 1.3 59.3 + - - +
121C LEU* 2.6 46.2 - - - +
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 3.9 3.8 - - + +
34C ALA 3.6 5.8 + - - -
35C LEU* 2.9 26.8 - - + +
58C MET* 3.7 8.3 - - + +
59C ASP* 1.3 71.2 - - - +
61C ALA* 1.3 59.4 + - - +
62C TRP* 3.2 15.8 - - + -
90C PRO* 2.9 23.2 - - + +
92C ILE* 2.7 46.6 - - + +
119C THR* 3.4 8.3 - - - +
120C TRP* 2.8 44.5 + - + +
121C LEU* 4.2 0.9 - - - +
160C MET* 3.0 37.7 - - + -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ASN 4.0 0.8 - - - +
33C ILE* 3.3 3.3 - - - +
34C ALA* 2.8 48.7 + - + +
60C HIS* 1.3 77.0 - - - +
62C TRP* 1.3 67.8 + - - +
113C ARG* 4.0 22.9 - - - +
117C TYR* 5.2 4.5 - - + -
118C VAL 3.5 4.3 - - - +
119C THR* 5.1 1.3 - - + -
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Residues in contact with TRP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 4.1 2.9 - - + -
32C ASN 3.9 8.3 - - - -
33C ILE* 3.2 27.4 - - + -
60C HIS* 3.2 34.3 - - + -
61C ALA* 1.3 99.5 - - - +
63C TYR* 1.3 66.0 + - - +
64C ASP* 3.6 6.2 + - + -
87C ILE* 4.0 11.7 - - + -
88C TRP* 2.4 62.5 + + + +
89C ILE* 3.9 0.7 - - - -
90C PRO* 3.1 30.7 - - + -
117C TYR* 4.2 7.6 - - - -
118C VAL* 2.8 38.7 + - + +
119C THR 4.8 0.2 - - - -
120C TRP* 3.3 28.5 - + + -
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Residues in contact with TYR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PRO* 4.6 0.5 - - - +
31C VAL* 4.2 10.7 - - - +
32C ASN 4.5 3.8 + - - -
62C TRP* 1.3 74.0 - - - +
64C ASP* 1.3 80.8 + - - +
65C HIS* 2.6 53.3 + + + +
68C THR* 2.7 19.5 + - - -
88C TRP* 5.4 1.2 - - - -
115C ASN* 2.6 30.4 + - + +
116C GLY* 3.0 19.3 - - - -
117C TYR* 3.4 44.8 - + + +
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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
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Atomic class I II III IV V VI VII VIII
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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