Contacts of the strand formed by residues 237 - 250 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA* 2.6 31.8 - - - +
80A VAL* 3.0 37.5 + - + +
127A THR* 4.5 15.9 - - + -
232A SER* 5.9 5.6 - - - +
233A SER* 4.8 11.0 - - - +
235A THR* 3.9 13.7 - - - +
236A ALA* 1.3 73.4 - - - +
238A ASN* 1.3 71.5 + - - +
239A THR 3.2 1.2 + - - -
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU* 5.5 6.2 - - - +
78A LEU 3.6 7.6 - - - +
79A ALA* 3.7 12.1 - - - +
122A SER* 4.8 3.4 + - - -
123A CYS* 4.9 5.4 + - - +
127A THR* 5.2 1.0 - - - +
236A ALA* 3.8 11.3 + - - +
237A VAL* 1.3 85.5 - - - +
239A THR* 1.3 59.7 + - - +
240A GLY 3.8 0.2 - - - -
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 2.8 14.0 + - - +
79A ALA* 4.2 1.3 - - - +
80A VAL* 4.3 6.7 - - - +
119A TYR* 3.1 17.8 + - + +
122A SER* 3.0 24.7 + - - -
123A CYS* 3.0 24.2 - - - -
127A THR* 4.4 2.0 - - - +
161A VAL* 2.8 33.0 - - + +
228A MET* 3.3 34.5 - - + -
237A VAL 3.2 6.3 + - - -
238A ASN* 1.3 73.3 - - - +
240A GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.8 1.4 - - - +
78A LEU 2.9 25.0 + - - +
119A TYR* 3.9 10.1 - - - -
120A LEU 3.2 13.5 - - - -
122A SER* 3.2 13.5 + - - -
239A THR* 1.3 83.3 - - - +
241A ARG* 1.3 71.1 + - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.6 23.7 - - + +
76A THR 3.5 5.2 - - - +
77A GLU* 2.9 34.3 + - + +
78A LEU* 4.0 7.0 - - - -
119A TYR* 3.1 4.8 - - - -
120A LEU 2.8 33.7 + - - +
122A SER* 5.1 14.3 - - - -
240A GLY* 1.3 84.4 - - - +
242A LEU* 1.3 62.5 + - - +
243A TYR* 3.6 29.9 + - + -
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.7 4.5 - - - +
75A SER* 2.8 30.8 + - - -
76A THR* 2.7 39.5 + - + +
78A LEU* 4.1 7.8 - - + +
89A GLU* 6.1 2.0 - - + -
117A TYR* 3.8 31.4 - - + -
118A THR 3.2 17.0 - - - +
119A TYR* 3.8 9.0 - - + -
131A ILE* 4.5 5.4 - - + -
133A MET* 3.2 33.0 - - + -
224A LEU* 3.9 15.5 - - + -
226A THR* 4.9 6.5 - - + -
241A ARG* 1.3 74.8 - - - +
243A TYR* 1.3 56.8 - - - +
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A CYS* 5.0 2.7 - - - -
73A GLU* 3.1 21.3 - - - +
74A LEU* 3.8 20.4 - - + -
116A ARG 3.2 1.9 - - - +
117A TYR* 3.2 6.7 - - - -
118A THR* 2.5 43.1 + - - +
120A LEU* 3.7 41.2 - - + +
171A VAL* 4.5 31.2 - - + -
241A ARG* 3.6 44.1 + - + -
242A LEU* 1.3 73.4 - - - +
244A ALA* 1.3 60.3 - - - +
245A SER* 5.2 0.7 - - - -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A CYS* 3.2 5.0 - - - -
73A GLU* 2.7 42.4 + - + +
75A SER* 4.2 7.1 - - - +
96A VAL* 3.5 32.5 - - + +
115A ILE* 4.9 2.9 - - + -
116A ARG 3.2 5.4 - - - +
117A TYR* 3.8 18.6 - - + -
243A TYR* 1.3 73.0 - - - +
245A SER* 1.3 62.4 + - - +
246A TYR* 3.9 9.6 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS 3.5 3.6 + - - -
72A CYS* 2.7 31.3 - - - +
114A ALA* 4.2 1.0 - - - +
115A ILE* 3.1 3.8 + - - -
116A ARG* 2.8 47.1 + - - +
118A THR* 5.4 1.3 - - - -
170A PHE* 3.1 22.3 + - - -
243A TYR 5.2 0.9 - - - -
244A ALA* 1.3 71.5 - - - +
246A TYR* 1.3 61.1 - - - +
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.5 6.3 - - + -
70A SER* 3.3 1.0 - - - -
71A HIS* 2.9 75.4 + - + +
73A GLU* 2.7 33.4 + - + -
96A VAL* 4.6 7.6 - - + -
99A TRP* 3.3 1.6 - + - -
100A LEU* 3.3 33.5 - - + +
112A TRP* 3.7 22.0 - + + -
114A ALA* 3.0 13.7 - - - +
115A ILE* 4.0 7.2 - - + -
244A ALA* 3.9 24.9 - - + -
245A SER* 1.3 78.4 - - - +
247A THR* 1.3 68.6 + - - +
248A ILE* 4.6 8.7 - - + -
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.1 18.2 - - + -
69A LEU 3.5 6.1 - - - +
70A SER* 2.4 34.2 + - - +
112A TRP 3.8 0.2 - - - -
113A VAL* 2.7 54.9 + - + +
114A ALA* 2.5 25.1 + - - +
246A TYR* 1.3 71.7 + - - +
248A ILE* 1.3 56.7 - - - +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR 4.0 0.9 - - - +
68A ILE* 3.6 3.8 - - - +
69A LEU* 2.9 52.4 + - + +
93A PRO* 3.9 16.2 - - + -
100A LEU* 4.3 15.7 - - + -
104A ALA* 5.2 1.1 - - + -
110A TYR* 3.2 33.0 - - + -
111A ALA 3.6 11.9 - - - +
112A TRP* 3.7 26.5 - - + -
113A VAL 4.4 0.4 - - - +
246A TYR* 4.0 4.6 - - + -
247A THR* 1.3 78.8 - - - +
249A ARG* 1.3 62.9 - - - +
250A LEU* 3.1 26.4 - - + +
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.1 43.1 - - + +
67A THR 3.5 3.6 - - - -
68A ILE* 4.3 12.6 - - + -
110A TYR* 3.1 23.4 - - - -
111A ALA* 3.1 20.8 + - - +
113A VAL* 4.2 16.8 - - + +
196A ARG* 3.6 14.0 - - - +
247A THR 4.3 0.2 + - - -
248A ILE* 1.3 75.4 - - - +
250A LEU* 1.3 60.6 + - - +
251A ILE* 3.1 17.8 - - - +
191C GLU* 2.5 30.8 + - - -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.9 0.9 - - - +
67A THR* 2.9 34.4 + - + +
69A LEU* 3.3 31.0 - - + -
100A LEU* 5.5 0.9 - - + -
103A VAL* 4.5 4.3 - - + -
104A ALA* 4.6 10.1 - - + -
107A TRP* 3.4 53.1 - - + -
109A LYS 4.1 4.0 - - - -
110A TYR* 4.2 4.0 - - + -
248A ILE* 3.1 46.2 - - + -
249A ARG* 1.3 67.9 - - - +
251A ILE* 1.4 72.0 + - - +
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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