Contacts of the strand formed by residues 237 - 250 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ALA* 2.7 20.7 - - - +
80B VAL* 3.1 20.9 + - + +
123B CYS* 5.4 1.3 - - + -
124B PRO* 6.1 1.1 - - + -
127B THR* 4.1 23.8 - - + +
232B SER* 6.1 2.2 - - - -
233B SER* 4.5 15.3 - - - +
235B THR* 3.2 15.3 + - + +
236B ALA* 1.3 72.0 - - - +
238B ASN* 1.3 70.5 + - - +
239B THR* 3.3 2.6 + - + +
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLU* 6.2 1.4 - - - +
78B LEU* 3.6 9.5 + - - +
79B ALA* 3.5 16.6 - - - +
122B SER 5.4 0.7 - - - +
123B CYS* 4.0 8.5 - - - +
236B ALA* 4.1 2.8 + - - +
237B VAL* 1.3 80.4 - - - +
239B THR* 1.3 59.2 - - - +
240B GLY 5.8 0.7 - - - +
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 3.0 9.4 + - - -
80B VAL* 3.2 36.3 - - + +
119B TYR* 2.8 18.1 + - - -
122B SER* 2.9 27.2 + - - -
123B CYS* 3.2 19.9 + - - -
127B THR* 3.8 13.2 - - + -
161B VAL* 3.6 24.9 - - + +
228B MET* 3.8 9.7 - - - +
237B VAL 3.3 6.3 + - - +
238B ASN* 1.3 73.9 - - - +
240B GLY* 1.3 69.5 + - - +
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.9 0.7 - - - +
78B LEU* 3.1 30.3 + - - +
119B TYR* 3.4 12.3 - - - -
120B LEU 3.5 9.2 - - - -
122B SER* 4.3 5.8 - - - -
238B ASN* 5.8 1.0 - - - +
239B THR* 1.3 89.8 + - - +
241B ARG* 1.4 73.3 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 3.7 28.0 - - + +
76B THR 3.6 3.6 - - - +
77B GLU* 2.8 45.6 + - + -
78B LEU* 3.8 4.7 - - - +
119B TYR* 3.2 5.9 - - - -
120B LEU 2.8 33.6 + - - +
122B SER* 3.9 25.6 + - - -
240B GLY* 1.4 83.0 + - - +
242B LEU* 1.3 60.1 + - - +
243B TYR* 3.7 28.6 + - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.6 1.9 - - - +
75B SER* 2.8 23.0 + - - -
76B THR* 2.8 40.1 + - + +
78B LEU* 4.4 12.0 - - + +
117B TYR* 3.3 40.6 - - + -
118B THR 2.8 22.9 - - - +
119B TYR* 4.3 6.5 - - + +
131B ILE* 5.4 0.7 - - + -
133B MET* 4.0 24.0 - - - -
224B LEU* 4.2 9.4 - - + -
226B THR* 5.0 9.9 - - + -
241B ARG* 1.3 72.2 - - - +
243B TYR* 1.3 61.1 + - - +
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B CYS* 4.4 2.5 - - - -
73B GLU* 3.0 18.8 - - - +
74B LEU* 3.7 17.9 - - + -
75B SER* 4.4 1.1 - - - -
116B ARG 3.6 0.9 - - - +
117B TYR* 3.4 3.1 - - - -
118B THR* 2.7 41.4 + - - +
120B LEU* 3.8 35.5 - - + +
171B VAL* 3.9 29.8 - - + -
241B ARG* 3.7 43.1 + - + -
242B LEU* 1.3 78.8 - - - +
244B ALA* 1.3 60.0 + - - +
245B SER* 4.9 1.1 - - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B CYS* 3.0 9.4 - - - -
73B GLU* 2.8 34.3 + - + +
75B SER* 4.1 14.7 - - - +
96B VAL* 3.9 28.9 - - + +
115B ILE* 4.9 4.0 - - + -
116B ARG 3.3 7.2 - - - +
117B TYR* 4.7 7.4 - - + +
243B TYR* 1.3 70.6 - - - +
245B SER* 1.3 63.3 + - - +
246B TYR* 4.1 10.2 - - + -
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B HIS 3.2 8.5 - - - -
72B CYS* 3.4 14.6 - - - -
114B ALA* 3.8 1.9 - - - +
115B ILE* 3.5 3.3 - - - -
116B ARG* 3.0 48.3 + - - +
118B THR* 4.5 6.8 + - - -
170B PHE* 3.5 18.0 + - - -
171B VAL* 4.8 0.3 - - - +
243B TYR* 4.8 0.5 + - - +
244B ALA* 1.3 76.5 + - - +
246B TYR* 1.3 60.1 + - - +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.0 9.0 - - + -
70B SER* 3.0 5.0 - - - -
71B HIS* 2.9 73.6 + - + +
72B CYS* 4.3 0.9 - - - -
73B GLU* 2.7 27.7 + - - -
96B VAL* 4.5 6.5 - - + -
99B TRP* 3.7 2.3 - - - -
100B LEU* 3.1 38.7 - - + +
112B TRP* 3.4 23.6 - + + -
114B ALA 3.0 6.7 - - - +
115B ILE* 3.7 5.2 - - + -
244B ALA* 4.1 18.4 - - + -
245B SER* 1.3 82.7 - - - +
247B THR* 1.3 69.3 + - - +
248B ILE* 4.1 15.5 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.7 24.5 - - + -
69B LEU 3.2 2.2 - - - +
70B SER* 2.9 27.0 + - - +
113B VAL* 2.7 48.3 + - + +
114B ALA* 2.6 25.9 + - - +
246B TYR* 1.3 75.0 + - - +
248B ILE* 1.3 56.7 - - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 3.7 7.8 - - - +
69B LEU* 2.7 47.8 + - + +
93B PRO* 5.1 3.1 - - + -
100B LEU* 4.6 11.2 - - + -
110B TYR* 3.4 28.5 - - + -
111B ALA 3.7 8.1 - - - +
112B TRP* 3.9 22.9 - - + -
113B VAL* 4.4 1.7 - - - +
246B TYR* 3.7 10.9 - - + +
247B THR* 1.3 77.6 - - - +
249B ARG* 1.3 79.1 + - - +
250B LEU* 3.2 54.5 + - + -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 2.9 35.4 + - - -
66B VAL* 3.7 37.2 - - + +
67B THR 3.8 2.7 - - - +
68B ILE* 4.9 9.0 - - + +
110B TYR* 3.4 5.0 - - - -
111B ALA* 2.6 43.9 + - + +
113B VAL* 4.0 15.5 - - + -
196B ARG* 3.3 26.1 - - - +
248B ILE* 1.3 77.0 - - - +
250B LEU* 1.3 61.2 - - - +
251B ILE* 3.8 8.4 - - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP 4.7 0.2 - - - +
66B VAL* 3.8 4.2 - - - +
67B THR* 2.9 44.0 + - + +
69B LEU* 3.6 23.1 - - + -
100B LEU* 5.5 0.4 - - + -
103B VAL* 5.2 1.8 - - + -
104B ALA* 4.4 16.2 - - + +
107B TRP* 3.6 50.0 - - + -
109B LYS 4.7 0.2 - - - -
110B TYR* 4.2 8.1 - - + -
248B ILE* 3.2 50.7 - - + -
249B ARG* 1.3 72.6 - - - +
251B ILE* 1.4 67.2 - - - +
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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
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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