Contacts of the strand formed by residues 237 - 250 (chain C) in PDB entry 4SBV
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 VAL 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C ALA* 3.0 2.1 - - - -
80C VAL* 2.6 46.5 + - + +
127C THR* 4.1 23.6 - - + -
231C GLY 5.0 3.8 - - - +
232C SER* 6.2 0.7 - - - -
233C SER* 3.8 32.1 - - - +
235C THR 3.8 0.7 - - - +
236C ALA* 1.3 75.1 - - - +
238C ASN* 1.3 72.6 - - - +
239C THR* 3.5 3.3 + - - +
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Residues in contact with ASN 238 (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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78C LEU 4.2 3.3 - - - +
79C ALA* 3.4 16.7 - - + +
122C SER* 5.6 1.3 - - - -
123C CYS* 4.4 9.9 + - - +
236C ALA* 5.1 5.6 + - - +
237C VAL* 1.3 83.3 - - - +
239C THR* 1.3 62.2 - - - +
240C GLY 6.0 0.2 - - - +
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.0 18.3 + - + -
79C ALA* 4.6 1.6 - - - -
80C VAL* 4.3 6.5 - - - +
119C TYR* 2.3 34.5 - - + +
122C SER* 2.8 34.3 + - - -
123C CYS* 3.4 10.2 + - - -
127C THR* 4.8 4.0 - - - +
161C VAL* 2.8 51.9 - - + +
228C MET* 5.5 1.1 - - - -
237C VAL* 3.5 7.7 + - - +
238C ASN* 1.3 74.3 + - - +
240C GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 4.1 3.6 - - - +
78C LEU* 3.2 22.4 + - - +
119C TYR* 3.2 14.1 - - - -
120C LEU 2.9 18.4 - - - -
121C PRO 4.3 0.2 - - - -
122C SER* 4.1 4.7 - - - -
238C ASN* 6.0 0.2 - - - +
239C THR* 1.3 83.8 + - - +
241C ARG* 1.3 66.2 + - - +
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Residues in contact with ARG 241 (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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51C THR* 5.1 8.9 + - - -
53C VAL* 4.5 13.5 - - - +
74C LEU* 4.3 12.4 - - + +
76C THR 3.5 14.6 - - - +
77C GLU* 4.1 18.4 - - + +
78C LEU* 4.3 3.8 - - - +
119C TYR* 3.6 3.9 - - - -
120C LEU* 2.9 45.2 + - - +
121C PRO 4.2 4.6 + - - -
122C SER* 3.6 23.0 + - - -
240C GLY* 1.3 75.6 - - - +
242C LEU* 1.3 65.6 - - - +
243C TYR* 3.2 37.9 + - + +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 3.4 2.9 - - - +
75C SER* 2.8 42.6 + - - +
76C THR* 3.0 39.7 + - + +
78C LEU* 4.5 13.4 - - + +
117C TYR* 4.3 22.0 - - + -
118C THR 3.2 13.9 - - - +
119C TYR* 3.8 9.6 - - + -
131C ILE* 5.1 0.9 - - + -
133C MET* 3.4 40.6 - - + -
224C LEU* 5.1 5.2 - - + -
226C THR* 5.5 2.5 - - - +
241C ARG* 1.3 78.2 - - - +
243C TYR* 1.3 59.3 + - - +
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Residues in contact with TYR 243 (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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53C VAL* 4.0 20.3 - - + +
55C LEU* 4.9 7.6 - - + -
72C CYS* 4.3 7.4 - - - -
73C GLU 3.5 8.1 - - - +
74C LEU* 3.5 36.4 - - + +
75C SER* 4.1 2.9 - - - +
116C ARG 3.1 4.2 - - - +
117C TYR* 3.3 4.0 - - - -
118C THR* 2.7 34.0 + - - +
120C LEU* 3.8 30.3 - - + -
171C VAL* 3.6 35.2 - - + -
241C ARG* 3.2 46.0 + - + -
242C LEU* 1.3 79.9 - - - +
244C ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C CYS* 3.0 8.3 - - - +
73C GLU* 2.9 35.7 + - + +
75C SER* 4.5 5.0 - - - -
96C VAL* 3.6 35.7 - - + +
115C ILE* 4.9 2.2 - - + -
116C ARG 3.1 7.2 - - - +
117C TYR* 4.0 16.8 - - + -
243C TYR* 1.3 73.8 - - - +
245C SER* 1.3 63.5 - - - +
246C TYR* 4.2 3.8 - - + -
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Residues in contact with SER 245 (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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71C HIS 3.4 6.3 - - - -
72C CYS* 3.9 13.9 - - - -
114C ALA* 3.7 2.5 - - - +
115C ILE* 3.1 4.0 + - - -
116C ARG* 2.6 58.9 + - - +
118C THR* 3.8 12.1 - - - +
170C PHE 4.3 14.3 + - - -
171C VAL* 5.5 0.2 - - - +
244C ALA* 1.3 79.3 - - - +
246C TYR* 1.3 59.6 - - - +
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Residues in contact with TYR 246 (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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69C LEU* 4.2 9.2 - - + -
70C SER* 3.2 2.3 + - - -
71C HIS* 3.1 64.4 + - + +
72C CYS* 4.1 4.9 - - - -
73C GLU* 2.5 38.2 + - + -
96C VAL* 4.6 14.4 - - + -
99C TRP* 4.4 2.4 - - - -
100C LEU* 3.5 44.2 + - + +
112C TRP* 3.5 20.0 - + + -
114C ALA* 2.8 14.8 - - - +
115C ILE* 4.2 4.3 - - + -
244C ALA 4.4 1.3 - - - -
245C SER* 1.3 79.7 - - - +
247C THR* 1.3 68.7 + - - +
248C ILE* 4.3 13.9 - - + -
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 3.6 25.4 - - + -
69C LEU 3.2 3.4 - - - +
70C SER* 2.4 28.1 + - - +
112C TRP* 3.6 0.7 - - - -
113C VAL* 2.6 58.4 + - + +
114C ALA* 2.8 20.2 + - - +
246C TYR* 1.3 74.3 + - - +
248C ILE* 1.3 57.8 - - - +
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Residues in contact with ILE 248 (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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68C ILE* 3.6 4.3 - - - +
69C LEU* 2.9 51.5 + - + +
93C PRO* 4.2 13.2 - - + -
100C LEU* 4.1 26.7 - - + -
104C ALA* 4.6 1.8 - - + -
110C TYR* 3.9 15.7 - - + -
111C ALA 3.5 10.1 - - - +
112C TRP* 4.0 21.3 - - + -
113C VAL* 4.1 4.0 - - - +
246C TYR* 4.3 5.8 - - + -
247C THR* 1.3 77.8 - - - +
249C ARG* 1.3 62.3 + - - +
250C LEU* 3.6 23.8 - - + -
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Residues in contact with ARG 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 2.6 35.4 + - - -
66C VAL* 3.3 28.6 - - + +
67C THR 3.7 1.8 - - - -
68C ILE* 3.5 21.8 - - + -
110C TYR* 3.1 26.6 - - - +
111C ALA* 2.7 29.0 + - + +
113C VAL* 4.0 10.1 - - + +
196C ARG* 2.8 19.8 - - - +
248C ILE* 1.3 70.4 - - - +
250C LEU* 1.3 63.1 + - - +
251C ILE* 3.0 22.7 - - + +
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Residues in contact with LEU 250 (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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66C VAL* 3.6 0.3 - - - -
67C THR* 2.6 45.4 + - + +
69C LEU* 4.7 9.4 - - + -
103C VAL* 4.5 7.6 - - + -
104C ALA* 4.0 18.4 - - + +
107C TRP* 3.3 57.9 - - + -
109C LYS 4.4 1.1 - - - -
110C TYR* 4.0 6.1 - - + -
248C ILE* 3.6 36.8 - - + +
249C ARG* 1.3 80.2 - - - +
251C ILE* 1.4 75.1 - - - +
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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
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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